Contacts of the helix formed by residues 5001 - 5029 (chain z) in PDB entry 2AXT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET5001 (chain z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5002z THR* 1.3 65.5 + - - +
5003z ILE* 3.3 9.5 - - - +
5004z LEU* 3.1 36.9 - - - +
5005z PHE* 2.9 24.7 + - - +
5057z LEU* 3.9 8.7 - - + -
5060z PHE* 3.4 63.5 - - + +
5061z VAL* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR5002 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5014k ALA* 4.9 4.5 - - - +
5001z MET* 1.3 78.8 - - - +
5003z ILE* 1.3 82.7 + - + +
5005z PHE* 3.1 9.7 + - - -
5006z GLN* 2.6 53.2 + - - +
5061z VAL* 4.4 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5003 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5001z MET 4.9 5.8 - - - +
5002z THR* 1.3 94.2 - - + +
5004z LEU* 1.3 67.8 + - - +
5006z GLN* 3.7 9.0 - - - +
5007z LEU* 3.0 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5004 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5001z MET* 3.1 24.4 + - - +
5003z ILE* 1.3 81.8 - - - +
5005z PHE* 1.3 53.5 + - - +
5007z LEU* 3.4 5.2 + - - +
5008z ALA* 2.7 39.4 + - + +
5053z VAL* 6.0 2.2 - - + -
5057z LEU* 3.3 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5005 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5014k ALA* 3.4 31.0 - - + -
5015k TYR* 3.7 30.5 - + - -
5001z MET 2.9 12.0 + - - +
5002z THR* 3.5 10.8 - - - +
5004z LEU* 1.3 77.3 - - - +
5006z GLN* 1.3 69.5 + - + +
5008z ALA* 3.0 2.4 + - - +
5009z LEU* 2.7 45.3 + - + +
5054z VAL* 3.4 33.4 - - + -
5057z LEU* 3.2 37.2 - - + -
5058z ASN* 4.1 9.0 - - - -
5061z VAL* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN5006 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5014k ALA* 5.3 2.8 - - + +
5017k ILE* 2.8 37.8 - - + +
5018k PHE* 4.9 6.4 - - + -
5002z THR* 2.6 52.3 + - - +
5003z ILE* 3.7 6.4 - - - +
5005z PHE* 1.3 83.6 - - + +
5007z LEU* 1.3 57.6 + - + +
5009z LEU* 3.7 6.3 - - - +
5010z ALA* 2.7 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5007 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5003z ILE* 3.0 38.8 + - + +
5004z LEU* 3.8 4.5 - - - +
5006z GLN* 1.3 79.1 - - + +
5008z ALA* 1.3 57.2 + - - +
5010z ALA* 3.3 9.7 + - + +
5011z ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5008 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5004z LEU* 2.7 26.6 + - + +
5005z PHE 3.2 4.7 - - - +
5007z LEU* 1.3 70.7 - - - +
5009z LEU* 1.3 61.3 + - - +
5011z ALA* 2.9 28.5 + - - +
5012z LEU* 3.1 5.0 + - - +
5050z LEU* 3.7 12.9 - - + +
5053z VAL* 4.8 7.6 - - + -
5054z VAL* 4.1 8.3 - - + -
5057z LEU* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5009 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5504c BCR 3.8 32.5 - - + -
5015k TYR* 3.6 34.8 - - + -
5018k PHE* 3.5 29.4 - - + -
5005z PHE* 2.7 31.9 + - + +
5006z GLN* 3.8 4.0 - - - +
5008z ALA* 1.3 73.9 - - - +
5010z ALA* 1.3 61.1 + - - +
5012z LEU* 3.2 19.7 + - + +
5013z VAL* 3.3 9.9 + - - +
5054z VAL* 3.5 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5010 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5018k PHE* 4.6 9.0 - - + -
5006z GLN 2.7 23.5 + - - +
5007z LEU* 3.5 14.6 - - + +
5008z ALA 3.1 0.2 - - - -
5009z LEU* 1.3 69.6 - - - +
5011z ALA* 1.3 62.1 + - - +
5013z VAL* 3.5 11.1 + - - +
5014z ILE* 3.3 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5011 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5007z LEU 2.9 12.4 + - - +
5008z ALA* 3.0 15.7 - - - +
5010z ALA* 1.3 74.7 - - - +
5012z LEU* 1.3 51.7 + - - +
5013z VAL 2.9 5.9 + - - -
5014z ILE* 3.2 5.8 + - - +
5015z LEU* 2.8 36.1 + - + +
5050z LEU* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5012 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5120c ILE* 6.4 0.9 - - + -
5504c BCR 4.0 24.3 - - + +
5008z ALA 3.1 7.1 + - - +
5009z LEU* 3.4 18.8 - - + +
5011z ALA* 1.3 77.8 - - - +
5013z VAL* 1.3 55.5 + - - +
5015z LEU* 4.6 0.7 - - - -
5016z SER* 2.7 32.7 + - - +
5047z TRP* 3.3 39.9 - - + +
5050z LEU* 3.6 20.5 - - + +
5051z VAL* 3.8 37.0 - - + +
5054z VAL* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5013 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5504c BCR 3.8 27.4 - - + -
5018k PHE* 3.8 15.5 - - + -
5021k LEU* 5.1 4.5 - - + -
5130x BCR 3.5 27.4 - - + +
5009z LEU 3.5 13.9 - - - +
5010z ALA* 3.5 11.4 - - - +
5011z ALA 2.9 2.4 - - - -
5012z LEU* 1.3 76.2 - - - +
5014z ILE* 1.3 67.4 + - + +
5016z SER* 2.9 8.3 + - - -
5017z PHE* 2.8 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5014 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5010z ALA* 3.3 19.3 - - + +
5011z ALA* 3.2 5.3 + - - +
5013z VAL* 1.3 78.7 - - + +
5015z LEU* 1.3 58.2 + - - +
5017z PHE* 3.2 10.0 + - + +
5018z VAL* 2.9 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5015 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5011z ALA 2.8 21.2 + - - +
5012z LEU 4.6 1.6 - - - +
5014z ILE* 1.3 71.8 - - - +
5016z SER* 1.3 52.5 + - - +
5018z VAL* 3.3 12.2 + - + +
5019z MET* 2.8 60.0 + - + +
5042z LEU* 6.2 0.2 - - + -
5043z GLY* 4.1 7.4 - - - +
5046z LEU* 3.4 39.7 - - + -
5047z TRP* 3.6 22.2 - - + +
5050z LEU* 3.4 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER5016 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5504c BCR 4.2 7.7 - - - +
5130x BCR 3.7 23.3 - - - +
5012z LEU* 2.7 20.6 + - - +
5013z VAL 2.9 5.2 + - - -
5015z LEU* 1.3 75.1 - - - +
5017z PHE* 1.3 67.5 + - - +
5019z MET* 3.3 10.0 + - - +
5020z VAL* 2.9 30.8 + - - +
5047z TRP* 2.5 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5017 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5130x BCR 4.0 34.9 - - + +
5013z VAL* 2.8 13.4 + - + +
5014z ILE* 3.3 15.9 - - + +
5016z SER* 1.3 75.9 - - - +
5018z VAL* 1.3 67.3 - - + +
5020z VAL* 3.2 23.3 - - - +
5021z ILE* 3.2 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5018 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5014z ILE* 2.9 35.3 + - + +
5015z LEU* 3.4 16.2 - - + +
5017z PHE* 1.3 79.4 - - + +
5019z MET* 1.3 60.3 + - - +
5021z ILE* 3.3 5.3 + - - +
5022z GLY* 2.8 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET5019 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5127c PHE* 4.7 3.1 - - + -
5501c CLA 3.8 16.2 - - + -
5015z LEU* 2.8 42.1 + - + +
5016z SER* 3.4 10.3 - - - +
5018z VAL* 1.3 73.0 - - - +
5020z VAL* 1.3 58.4 + - + +
5022z GLY* 2.9 4.0 + - - -
5023z VAL* 2.8 56.1 + - + +
5024z PRO* 3.6 1.4 - - - +
5040z ILE* 4.4 7.4 - - - +
5043z GLY* 3.3 26.9 - - - -
5044z SER* 3.7 28.7 - - - +
5047z TRP* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5020 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5501c CLA 3.5 49.7 - - + +
5504c BCR 4.3 19.3 - - + -
5130x BCR 4.5 25.4 - - + -
5016z SER 2.9 22.4 - - - +
5017z PHE* 3.2 11.9 - - - +
5019z MET* 1.3 80.6 - - - +
5021z ILE* 1.3 64.9 + - + +
5024z PRO* 2.7 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5021 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5501c CLA 6.2 0.4 - - + -
5017z PHE* 3.2 39.4 + - + +
5018z VAL* 3.9 5.6 - - - +
5020z VAL* 1.3 87.2 - - + +
5022z GLY* 1.3 57.0 + - - +
5024z PRO* 3.8 1.1 - - - +
5025z VAL* 2.7 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5022 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5018z VAL* 2.8 15.7 + - - -
5019z MET* 2.9 4.1 + - - -
5021z ILE* 1.3 72.4 - - - +
5023z VAL* 1.3 52.7 + - - -
5024z PRO* 3.0 2.2 - - - -
5025z VAL* 2.6 14.8 + - - -
5026z ALA* 2.5 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5023 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5127c PHE* 3.5 32.3 - - + -
5130c VAL* 4.3 10.8 - - + -
5501c CLA 3.8 17.9 - - + -
5019z MET* 2.8 25.3 + - + +
5022z GLY* 1.3 68.5 - - - -
5024z PRO* 1.3 60.4 - - + +
5026z ALA* 3.2 9.2 - - - +
5027z TYR* 2.7 62.6 + - + -
5040z ILE* 4.1 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO5024 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5130c VAL* 4.4 9.9 - - + -
5134c ILE* 5.2 3.4 - - + +
5501c CLA 3.5 49.8 - - + -
5019z MET 3.6 0.7 - - - +
5020z VAL* 2.7 31.0 - - - +
5021z ILE 3.8 2.2 - - - +
5022z GLY 2.7 3.8 - - - -
5023z VAL* 1.3 95.4 - - + +
5025z VAL* 1.3 58.2 + - + +
5026z ALA 3.0 0.7 + - - -
5027z TYR* 3.6 2.1 - - + +
5028z ALA* 2.7 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5025 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5021z ILE* 2.7 36.3 - - + +
5022z GLY* 2.6 8.2 + - - +
5024z PRO* 1.3 77.6 - - + +
5026z ALA* 1.3 48.9 + - - +
5028z ALA* 3.5 6.4 - - - +
5029z SER* 2.4 54.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5026 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5022z GLY 2.5 17.7 + - - +
5023z VAL* 3.2 10.8 - - - +
5024z PRO 3.0 0.4 - - - -
5025z VAL* 1.3 75.8 - - - +
5027z TYR* 1.3 66.1 + - - +
5029z SER* 2.9 21.9 + - - +
5033z TRP* 5.3 5.9 - - - +
5036z SER* 4.0 20.2 - - - -
5040z ILE* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR5027 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5127c PHE* 3.6 22.9 - + - -
5130c VAL* 4.2 7.9 - - + -
5131c TYR* 3.4 47.3 - + + +
5134c ILE* 3.5 24.7 - - + +
5135c ARG* 3.0 29.8 + - + -
5503c CLA 5.5 1.7 - - - +
5023z VAL* 2.7 47.5 + - + +
5024z PRO 3.7 2.0 - - - +
5026z ALA* 1.3 75.2 - - - +
5028z ALA* 1.3 58.1 + - - +
5029z SER 3.6 0.7 + - - -
5030z PRO* 4.8 5.9 - - - +
5033z TRP* 6.2 0.4 - - - +
5040z ILE* 4.6 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5028 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5134c ILE* 4.1 10.7 - - + +
5501c CLA 5.3 16.8 - - + -
5024z PRO 2.7 25.6 + - - +
5025z VAL* 3.5 6.1 - - - +
5027z TYR* 1.3 73.7 - - - +
5029z SER* 1.3 56.0 + - - +
5030z PRO* 3.1 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER5029 (chain z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5025z VAL* 2.4 41.5 + - - +
5026z ALA* 2.9 14.9 + - - +
5027z TYR 4.9 0.4 - - - -
5028z ALA* 1.3 74.5 - - - +
5030z PRO* 1.4 58.9 - - - +
5031z GLN* 2.8 29.2 + - - +
5032z ASP 4.5 0.9 - - - -
5033z TRP* 4.3 6.6 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il