Contacts of the helix formed by residues 5245 - 5257 (chain d) 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 SER5245 (chain d).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5459c ILE* 2.8 30.5 - - - +
5464c GLU* 3.1 23.1 - - - -
5221d THR* 3.0 11.4 + - - +
5223d PHE* 3.3 20.4 - - - -
5242d GLU* 3.4 3.1 - - - -
5244d TYR* 1.3 74.8 - - - +
5246d MET* 1.3 66.8 + - - +
5247d VAL* 3.0 3.1 - - - +
5248d THR* 3.0 14.9 + - - -
5249d ALA* 3.0 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET5246 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5237a TYR* 3.4 22.7 - - - +
5239a PHE* 4.2 14.1 - - + -
5242d GLU* 2.8 20.0 + - - +
5244d TYR* 3.8 12.3 + - + -
5245d SER* 1.3 72.8 - - - +
5247d VAL* 1.3 57.5 + - + +
5249d ALA* 3.5 2.1 + - - +
5250d ASN* 3.0 28.8 + - - +
5261d PHE* 4.9 2.7 - - + -
5262d SER* 3.9 6.5 - - - +
5263d ASN* 3.2 17.7 - - - +
5264d LYS* 2.9 55.0 - - + +
5267d LEU* 5.3 1.6 - - + -
5356d PQ9 3.9 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5247 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5239a PHE* 3.8 19.7 - - + -
5240a GLY* 3.3 36.6 - - - +
5464c GLU* 4.5 11.7 - - - +
5466c VAL* 4.0 14.1 - - + +
5467c LEU* 4.6 21.1 - - + -
5242d GLU* 5.2 2.5 - - - +
5245d SER* 3.0 2.4 - - - -
5246d MET* 1.3 76.4 - - + +
5248d THR* 1.3 63.7 + - - +
5250d ASN* 3.9 4.7 + - - +
5251d ARG* 3.4 19.1 + - - +
5029t ILE* 5.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR5248 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5137a LEU* 4.4 4.1 - - + +
5139a MET* 3.9 26.9 - - + -
5459c ILE* 3.6 17.2 - - + +
5464c GLU* 2.5 26.0 + - - +
5466c VAL* 3.3 30.9 - - + +
5221d THR* 4.0 3.6 - - + -
5245d SER* 3.0 16.8 + - - -
5247d VAL* 1.3 76.2 - - - +
5249d ALA* 1.3 67.5 + - - +
5251d ARG* 3.1 5.9 + - - +
5252d PHE* 3.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5249 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5139a MET* 5.5 0.7 - - - -
5217d THR* 3.8 24.0 - - + -
5221d THR* 4.0 10.9 - - + +
5244d TYR* 5.3 1.1 - - + -
5245d SER 3.0 12.1 + - - +
5246d MET* 3.6 9.4 - - - +
5248d THR* 1.3 72.3 - - - +
5250d ASN* 1.3 69.2 + - - +
5251d ARG 2.7 3.5 + - - -
5252d PHE* 2.7 25.1 + - - +
5253d TRP* 3.3 8.9 + - - -
5356d PQ9 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN5250 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5239a PHE* 3.3 26.8 - - + -
5472c LEU* 5.6 3.1 - - - +
5246d MET 3.0 15.6 + - - +
5247d VAL 3.9 2.1 - - - +
5249d ALA* 1.3 77.1 - - - +
5251d ARG* 1.3 62.6 + - - +
5254d SER* 2.8 25.5 + - - -
5260d ALA* 3.3 13.0 + - - +
5261d PHE 3.0 28.5 + - - +
5262d SER* 3.1 17.1 + - - -
5356d PQ9 3.7 7.8 - - + +
5024t ARG* 5.5 2.0 + - - +
5027t PRO* 3.6 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG5251 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5024a THR 2.5 27.1 + - - -
5025a ASP* 3.0 25.5 - - - +
5137a LEU* 3.8 16.3 - - + +
5466c VAL* 4.0 20.5 + - + +
5469c MET* 4.1 21.0 + - - +
5470c PRO 3.4 22.8 + - - -
5471c SER* 4.0 4.8 - - - +
5472c LEU* 3.8 23.0 - - - +
5247d VAL 3.4 11.5 + - - +
5248d THR 3.1 9.6 + - - +
5249d ALA 2.7 5.1 + - - -
5250d ASN* 1.3 78.7 + - - +
5252d PHE* 1.3 71.3 + - - +
5254d SER* 3.0 14.8 + - - -
5255d GLN* 2.7 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5252 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5130a GLN* 3.9 18.8 - - + -
5133a LEU* 3.3 35.4 - - + +
5134a SER* 3.8 26.0 - - - -
5137a LEU* 3.9 3.6 - - - +
5139a MET* 3.8 26.9 - - + -
5143a ILE* 3.7 21.3 - - + -
5217d THR* 6.1 0.2 - - + -
5248d THR 3.0 11.1 + - - +
5249d ALA* 2.7 16.3 + - - +
5251d ARG* 1.3 78.7 - - - +
5253d TRP* 1.3 120.4 + + - +
5255d GLN 2.8 8.5 + - - -
5256d ILE* 3.2 21.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP5253 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5130a GLN* 3.4 22.7 - - - -
5143a ILE* 3.9 14.8 - - + +
5561a PHO 3.2 37.9 - - - -
5213d ILE* 3.8 13.7 - - + -
5216d ALA* 6.4 0.2 - - + -
5217d THR* 2.8 34.4 + - + +
5249d ALA 3.3 11.1 + - - +
5252d PHE* 1.3 106.5 - + - +
5254d SER* 1.3 65.7 + - - +
5256d ILE* 2.8 35.4 + - + -
5257d PHE* 2.8 23.9 + - + -
5258d GLY 3.5 1.7 + - - -
5259d ILE 3.8 8.5 - - - +
5260d ALA* 3.6 16.4 - - + -
5356d PQ9 3.3 37.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER5254 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5027a ARG* 3.0 23.1 + - - -
5028a LEU* 3.9 0.2 - - - +
5472c LEU* 4.1 10.2 - - - +
5250d ASN* 2.8 23.8 + - - -
5251d ARG* 3.0 13.3 + - - -
5252d PHE 3.1 0.4 + - - -
5253d TRP* 1.3 77.4 - - - +
5255d GLN* 1.3 61.1 + - - +
5258d GLY* 3.1 22.3 - - - -
5260d ALA* 3.3 13.3 - - - +
5024t ARG* 3.6 28.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN5255 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5024a THR 3.2 20.2 + - - +
5026a ASN 3.1 18.4 + - - +
5027a ARG 3.3 11.2 - - - +
5028a LEU* 3.4 6.6 - - - +
5029a TYR* 2.6 43.4 + - + +
5129a ARG* 3.6 5.0 + - - -
5133a LEU* 4.1 18.3 - - + +
5137a LEU* 4.3 1.6 - - - +
5472c LEU* 3.3 29.7 - - + +
5251d ARG* 2.7 44.4 + - - +
5252d PHE 2.8 9.9 + - - +
5254d SER* 1.3 74.4 - - - +
5256d ILE* 1.3 59.4 + - - +
5257d PHE 3.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5256 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5029a TYR* 5.6 0.7 - - + -
5126a TYR* 3.5 15.7 + - + -
5129a ARG* 2.9 38.0 + - + +
5130a GLN* 3.3 50.7 - - + +
5133a LEU* 4.1 10.5 - - + -
5252d PHE* 3.2 20.4 + - + +
5253d TRP* 2.8 42.8 + - + +
5255d GLN* 1.3 81.9 - - - +
5257d PHE* 1.3 58.3 + - - +
5361d MGE 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5257 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5028a LEU* 5.0 1.2 - - - +
5126a TYR* 3.2 21.5 - + - +
5129a ARG* 4.1 0.4 - - - +
5558a CLA 4.8 4.5 - - + -
5561a PHO 3.5 59.7 - + + -
5253d TRP* 2.8 18.1 + - + +
5255d GLN 3.6 0.6 - - - -
5256d ILE* 1.3 76.6 - - - +
5258d GLY* 1.3 54.7 + - - +
5259d ILE* 2.7 40.1 + - + +
5356d PQ9 4.3 14.6 - - + -
5361d MGE 4.2 73.3 - - + +
----------------------------------------------------------
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