Contacts of the helix formed by residues 5094 - 5104 (chain v) 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 ASN5094 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5037v PRO* 3.3 19.5 - - + +
5038v LEU 3.6 1.9 - - - +
5039v ASN 3.6 18.4 - - - +
5040v SER* 3.7 28.3 - - - +
5091v PRO* 4.3 11.7 + - - +
5092v ARG 2.8 4.7 + - - +
5093v ASP* 1.3 90.6 + - - +
5095v ILE* 1.3 65.1 + - - +
5096v GLU* 3.2 10.0 + - - +
5097v GLY* 2.8 25.4 + - - -
5098v LEU* 3.1 10.3 + - - +
5146v LEU* 3.9 9.1 - - - +
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Residues in contact with ILE5095 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5036v VAL* 3.7 17.5 - - + -
5037v PRO 3.1 13.3 + - - +
5038v LEU* 3.4 23.8 + - + +
5045v ILE* 4.3 11.0 - - + -
5047v LEU* 5.1 5.2 - - + -
5094v ASN* 1.3 73.0 - - - +
5096v GLU* 1.3 71.0 + - - +
5097v GLY 3.0 0.5 + - - -
5098v LEU* 3.1 1.6 + - - +
5099v VAL* 2.8 41.2 + - + +
5139v VAL* 4.3 22.2 - - + +
5142v ALA* 4.6 6.7 - - + -
5143v GLY* 3.9 20.6 - - - +
5146v LEU* 3.6 20.2 - - + -
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Residues in contact with GLU5096 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5038v LEU* 3.1 32.7 + - + +
5039v ASN* 4.0 15.7 - - + -
5040v SER 5.6 0.7 - - - +
5094v ASN* 3.2 6.5 + - - +
5095v ILE* 1.3 82.6 - - - +
5097v GLY* 1.3 56.8 + - - +
5099v VAL* 3.3 9.7 + - - +
5100v ASP* 2.8 30.0 + - - +
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Residues in contact with GLY5097 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5090v PRO* 6.2 0.9 - - - -
5091v PRO 3.8 19.3 - - - -
5092v ARG* 3.0 31.3 + - - -
5094v ASN* 2.8 20.3 + - - -
5096v GLU* 1.3 69.4 - - - +
5098v LEU* 1.3 66.5 + - - +
5100v ASP* 3.2 5.9 + - - -
5101v TYR 3.1 5.0 + - - -
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Residues in contact with LEU5098 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5085v LEU* 4.1 14.1 - - + -
5092v ARG* 3.3 20.7 + - + +
5094v ASN 3.1 8.0 + - - +
5095v ILE 3.8 2.2 - - - +
5097v GLY* 1.3 72.8 - - - +
5099v VAL* 1.3 64.5 + - - +
5101v TYR* 3.0 22.4 + - - +
5102v MET* 3.1 16.8 + - + +
5142v ALA* 3.6 43.7 - - + +
5145v ILE* 4.0 14.8 - - + -
5146v LEU* 3.7 30.3 - - + -
5552v HEM 3.8 27.8 - - + -
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Residues in contact with VAL5099 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5095v ILE* 2.8 46.8 + - + +
5096v GLU* 3.3 11.2 - - - +
5098v LEU* 1.3 76.2 - - - +
5100v ASP* 1.3 64.9 + - - +
5101v TYR 3.2 0.3 + - - -
5102v MET* 3.2 18.8 + - - +
5103v LYS* 3.2 25.7 + - + +
5135v GLU* 3.6 24.0 - - - +
5138v LEU* 4.3 27.6 - - + +
5139v VAL* 4.7 5.4 - - + -
5142v ALA* 4.3 1.6 - - + -
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Residues in contact with ASP5100 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5090v PRO* 4.4 6.2 - - - +
5092v ARG* 2.7 28.2 + - - +
5096v GLU 2.8 16.7 + - - +
5097v GLY* 3.4 10.8 - - - +
5099v VAL* 1.3 74.3 - - - +
5101v TYR* 1.3 50.2 + - - +
5103v LYS* 2.9 13.7 + - - +
5104v ASN* 2.7 44.8 + - - +
5106v THR* 5.7 0.7 - - - +
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Residues in contact with TYR5101 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5092v ARG* 3.4 37.2 - - - +
5097v GLY 3.1 3.2 + - - +
5098v LEU* 3.0 18.3 + - - +
5100v ASP* 1.3 75.1 - - - +
5102v MET* 1.3 58.8 + - + +
5103v LYS 2.9 8.2 + - - -
5104v ASN 4.2 4.3 - - - -
5105v PRO* 2.9 49.3 - - + +
5106v THR 3.4 27.6 + - - -
5107v THR 5.5 1.1 - - - -
5108v TYR* 6.5 0.2 - - - -
5114v ILE* 4.8 1.4 - - - +
5118v HIS* 3.7 27.3 - + - -
5119v PRO 5.0 0.2 - - - +
5120v SER* 4.5 0.2 - - - -
5552v HEM 3.4 72.6 + + + +
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Residues in contact with MET5102 (chain v).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5098v LEU* 3.1 35.0 + - + +
5099v VAL* 3.2 7.6 + - - +
5101v TYR* 1.3 83.6 - - + +
5103v LYS* 1.3 58.8 + - - +
5118v HIS* 6.1 1.1 - - + -
5119v PRO 4.9 4.3 - - - +
5120v SER* 3.3 9.5 - - - +
5121v LEU* 3.0 27.3 + - - +
5130v MET* 4.0 9.4 - - + +
5138v LEU* 3.7 38.8 - - + +
5141v ILE* 4.0 13.2 - - - -
5142v ALA* 3.6 28.7 - - + -
5145v ILE* 4.7 2.9 - - + -
5552v HEM 3.9 34.5 - - + -
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Residues in contact with LYS5103 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5099v VAL* 3.3 24.4 - - + +
5100v ASP* 2.9 12.3 + - - +
5101v TYR 2.9 0.4 - - - -
5102v MET* 1.3 81.5 - - - +
5104v ASN* 1.3 61.1 + - + +
5105v PRO* 4.1 1.3 - - - -
5120v SER* 3.7 1.0 - - - -
5121v LEU* 4.0 15.7 - - + +
5122v ARG* 2.8 35.4 + - - +
5135v GLU* 3.0 44.2 + - - -
5138v LEU* 3.9 14.4 - - + -
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Residues in contact with ASN5104 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5092v ARG* 5.1 0.3 + - - -
5100v ASP* 2.7 28.8 + - - +
5101v TYR* 3.0 4.7 + - - -
5103v LYS* 1.3 78.2 - - + +
5105v PRO* 1.3 73.6 - - - +
5106v THR* 3.8 9.2 + - - +
5113v GLU* 2.5 39.8 + - - +
5115v ALA* 3.6 7.8 - - - +
5122v ARG* 3.2 34.6 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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