Contacts of the helix formed by residues 5027 - 5050 (chain h) 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 THR5027 (chain h).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5215b PHE* 3.9 12.1 - - + -
5219b VAL* 3.6 23.4 - - + +
5220b ARG 4.3 0.7 + - - -
5222b PRO* 3.0 9.1 - - - +
5519b CLA 3.4 34.0 + - + +
5026h GLY* 1.3 70.1 - - - -
5028h THR* 1.3 53.7 + - - +
5029h PRO* 3.2 4.5 - - - -
5030h LEU* 2.7 44.2 + - + +
5031h MET 3.0 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR5028 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5222b PRO* 3.3 10.1 - - - +
5224b ARG* 5.3 0.7 - - - +
5225b LEU* 3.3 35.3 - - + +
5519b CLA 3.6 8.0 + - - -
5025h TRP* 3.1 46.8 + - + -
5027h THR* 1.3 75.9 - - - +
5029h PRO* 1.3 61.1 - - + +
5031h MET* 3.2 12.1 + - + +
5032h ALA* 2.9 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO5029 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5025h TRP* 3.4 18.2 - - + +
5026h GLY 3.6 5.6 - - - +
5027h THR 3.4 5.2 - - - -
5028h THR* 1.3 95.0 - - + +
5030h LEU* 1.3 61.4 + - - +
5032h ALA* 3.4 9.2 + - + +
5033h VAL* 2.9 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5030 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5215b PHE* 4.8 7.6 - - + -
5519b CLA 3.9 20.2 - - + -
5027h THR* 2.7 28.1 + - + +
5029h PRO* 1.3 77.4 - - - +
5031h MET* 1.3 61.8 + - - +
5033h VAL* 3.2 13.2 + - + +
5034h PHE* 3.1 46.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET5031 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5225b LEU* 3.8 19.5 - - + -
5519b CLA 3.3 104.2 - - + +
5027h THR 3.0 3.4 + - - -
5028h THR* 3.2 18.8 - - + +
5030h LEU* 1.3 76.3 - - - +
5032h ALA* 1.3 67.3 + - + +
5034h PHE* 3.3 4.4 + - - +
5035h MET* 2.9 43.8 + - - +
5107h BCR 4.4 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5032 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5028h THR* 2.9 18.0 + - + +
5029h PRO* 3.7 10.5 - - + +
5030h LEU 3.3 0.2 - - - -
5031h MET* 1.3 78.3 - - + +
5033h VAL* 1.3 60.7 + - + +
5035h MET* 3.8 10.0 - - - +
5036h GLY* 3.3 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5033 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5029h PRO 2.9 19.3 + - - +
5030h LEU* 3.5 15.3 - - + +
5031h MET 3.1 0.6 - - - -
5032h ALA* 1.3 77.8 - - + +
5034h PHE* 1.3 71.9 + - + +
5036h GLY* 3.4 2.1 + - - -
5037h LEU* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5034 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5519b CLA 3.5 44.9 - + + -
5030h LEU* 3.1 48.9 + - + +
5031h MET* 3.3 4.2 + - - +
5033h VAL* 1.3 81.7 - - + +
5035h MET* 1.3 53.8 + - - +
5037h LEU* 2.9 21.9 + - + +
5038h PHE* 2.7 37.2 + - - +
5107h BCR 4.4 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET5035 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5513b CLA 3.9 14.8 - - + +
5519b CLA 3.7 49.1 - - + +
5482c UNK 4.8 17.5 - - + -
5031h MET* 2.9 45.6 + - - +
5032h ALA* 3.8 8.5 - - - +
5034h PHE* 1.3 74.0 - - - +
5036h GLY* 1.3 66.2 - - - +
5038h PHE* 2.8 10.5 + - - +
5039h LEU* 2.7 23.6 + - - +
5107h BCR 3.8 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5036 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5482c UNK 4.7 11.8 - - - +
5032h ALA 3.3 12.1 + - - -
5033h VAL 3.9 2.2 - - - -
5035h MET* 1.3 78.6 - - - +
5037h LEU* 1.3 60.3 + - - +
5039h LEU* 3.6 10.4 - - - +
5040h VAL* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5037 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5033h VAL* 2.9 24.2 + - + +
5034h PHE* 2.9 31.8 + - + +
5035h MET 2.8 0.6 + - - -
5036h GLY* 1.3 77.2 - - - +
5038h PHE* 1.3 63.1 + - - +
5040h VAL* 3.3 4.8 + - + +
5041h PHE* 3.2 20.4 + - - +
5107h BCR 4.0 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5038 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5247b PHE* 5.6 0.2 - + - -
5512b CLA 3.7 37.0 - - + -
5513b CLA 3.4 48.9 - - + -
5034h PHE 2.7 11.7 + - - +
5035h MET* 2.8 9.0 + - - +
5037h LEU* 1.3 68.2 - - - +
5039h LEU* 1.3 66.6 + - - +
5041h PHE* 3.0 22.4 + + - +
5042h LEU* 3.1 30.1 + - + +
5107h BCR 3.3 86.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5039 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5513b CLA 3.4 32.8 - - + -
5518b CLA 5.0 17.3 - - + -
5519b CLA 3.9 28.0 - - + -
5482c UNK 3.6 28.9 - - + -
5355d CLA 5.0 15.7 - - + -
5035h MET 2.7 15.2 + - - +
5036h GLY* 3.6 11.7 - - - +
5038h PHE* 1.3 76.1 - - - +
5040h VAL* 1.3 68.1 + - + +
5042h LEU* 3.1 12.3 + - - +
5043h LEU* 3.2 9.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5040 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5355d CLA 4.9 22.9 - - + -
5036h GLY 3.2 16.8 + - - +
5037h LEU* 3.9 4.5 - - + +
5038h PHE 3.3 0.2 - - - -
5039h LEU* 1.3 81.0 - - + +
5041h PHE* 1.3 61.6 + - - +
5043h LEU* 3.3 15.0 + - + +
5044h ILE* 3.0 29.8 + - + +
5107h BCR 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5041 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5190b PHE* 3.3 17.0 - + - -
5511b CLA 3.3 33.4 - - + -
5512b CLA 3.7 41.5 - + + -
5037h LEU 3.2 5.5 + - - +
5038h PHE* 3.0 21.2 + + - +
5040h VAL* 1.3 79.1 - - - +
5042h LEU* 1.3 74.2 + - + +
5044h ILE* 2.9 18.2 + - + +
5045h ILE* 2.9 53.6 + - + +
5107h BCR 3.4 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5042 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5247b PHE* 4.7 13.2 - - + -
5512b CLA 4.3 24.3 - - + +
5513b CLA 3.8 22.0 - - + -
5519b CLA 4.4 14.8 - - + -
5038h PHE* 3.1 46.6 + - + +
5039h LEU 3.1 5.6 + - - +
5041h PHE* 1.3 104.5 - - + +
5043h LEU* 1.3 53.0 + - - +
5045h ILE* 3.1 12.2 + - + +
5046h LEU* 2.6 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5043 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5518b CLA 3.6 41.3 - - + -
5519b CLA 4.1 12.9 - - + +
5355d CLA 4.6 32.5 - - + +
5039h LEU* 3.2 11.3 + - + +
5040h VAL* 3.4 18.2 - - + +
5042h LEU* 1.3 76.7 - - - +
5044h ILE* 1.3 63.0 + - + +
5046h LEU* 4.2 2.7 - - + -
5047h GLU* 2.9 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5044 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5190b PHE* 5.8 2.5 - - + -
5511b CLA 5.7 9.4 - - + -
5040h VAL* 3.0 25.9 + - + +
5041h PHE* 2.9 14.6 + - + +
5043h LEU* 1.3 78.5 - - + +
5045h ILE* 1.3 69.0 + - + +
5047h GLU* 3.8 1.0 - - - -
5048h ILE* 3.0 39.9 + - + +
5053h LEU* 3.9 20.0 - - + +
5055h LEU* 6.0 1.6 - - + -
5107h BCR 3.7 52.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5045 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5190b PHE* 4.2 16.6 - - + +
5512b CLA 3.3 71.6 - - + +
5041h PHE* 2.9 52.2 + - + +
5042h LEU* 3.4 14.1 - - + +
5044h ILE* 1.3 74.1 - - + +
5046h LEU* 1.3 59.1 + - - +
5048h ILE* 2.5 36.1 + - + +
5049h TYR* 3.1 11.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5046 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5512b CLA 3.4 53.8 - - + +
5518b CLA 3.4 33.0 - - + -
5519b CLA 4.1 11.2 - - + -
5089d LEU* 4.9 3.1 - - + -
5042h LEU 2.6 20.6 + - - +
5043h LEU* 4.0 6.3 - - + +
5045h ILE* 1.3 72.0 - - - +
5047h GLU* 1.3 59.6 + - + +
5049h TYR* 3.7 1.6 + - - +
5050h ASN* 3.1 24.1 + - + +
5208h DGD 3.8 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU5047 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5518b CLA 5.3 0.5 - - - +
5089d LEU* 4.1 18.2 - - + +
5091d LEU* 3.5 30.5 - - - +
5093d TRP* 5.1 1.6 + - - -
5355d CLA 5.2 2.1 - - - +
5043h LEU* 2.9 54.0 + - + +
5044h ILE 3.8 3.4 - - - +
5045h ILE 2.7 3.8 + - - -
5046h LEU* 1.3 74.8 - - + +
5048h ILE* 1.3 57.4 + - - +
5050h ASN* 3.9 5.8 - - - -
5052h THR* 2.9 42.6 + - - +
5053h LEU* 3.0 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE5048 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5187b PRO 5.5 1.1 - - - +
5190b PHE* 4.1 35.7 - - + +
5192b PRO* 5.1 0.7 - - + -
5511b CLA 6.3 1.8 - - + -
5044h ILE* 3.0 31.6 + - + +
5045h ILE* 2.5 17.9 + - + +
5047h GLU* 1.3 72.7 - - - +
5049h TYR* 1.3 60.7 + - - +
5050h ASN 3.2 0.2 - - - -
5051h SER* 2.9 18.2 + - - -
5053h LEU* 3.8 26.2 - - + +
5055h LEU* 4.1 21.5 - - + -
5058h VAL* 4.3 15.5 - - + -
5060h VAL* 3.7 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR5049 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5192b PRO* 3.3 34.4 - - + +
5193b TYR* 4.6 12.1 - + - -
5255b THR* 3.9 17.1 - - + +
5258b TYR* 4.5 10.0 - - + +
5259b GLY 3.2 23.4 + - - -
5260b SER* 4.1 1.0 - - - -
5512b CLA 3.3 46.2 - - + -
5045h ILE* 3.1 7.9 + - + +
5046h LEU 3.8 9.0 - - - +
5048h ILE* 1.3 83.9 - - - +
5050h ASN* 1.3 60.2 + - - +
5051h SER* 3.2 4.9 + - - -
5060h VAL* 4.3 11.5 - - + +
5208h DGD 2.9 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN5050 (chain h).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5087d HIS 3.3 21.5 + - - +
5088d SER* 3.5 8.7 - - - +
5089d LEU* 2.9 42.0 + - + +
5069e ARG* 3.3 11.8 + - - +
5046h LEU* 3.1 20.9 + - + +
5047h GLU* 4.4 2.9 - - - -
5048h ILE 3.2 0.2 - - - -
5049h TYR* 1.3 75.3 - - - +
5051h SER* 1.3 69.2 + - - +
5052h THR* 3.1 12.0 + - - +
5208h DGD 3.9 32.9 + - - +
----------------------------------------------------------
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