Contacts of the helix formed by residues 5475 - 5479 (chain b) 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 PHE5475 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5471b ALA* 3.0 26.7 - - - +
5472b ARG* 4.2 2.9 - - - -
5473b THR 2.7 4.8 + - - -
5474b LEU* 1.3 90.3 - - + +
5476b ARG* 1.3 70.2 + - - +
5477b ASP* 3.2 11.9 + - - -
5478b VAL* 2.9 20.0 + - + +
5479b PHE* 3.1 9.6 + - - -
5481c UNK 6.2 1.3 - - + -
5130d PHE* 4.0 18.4 - + - -
5133d ALA* 3.9 10.8 - - + -
5134d ARG* 3.5 50.9 - - + -
5138d VAL 3.1 24.9 - - - -
5139d ARG* 4.7 0.4 - - - -
5140d PRO* 3.6 34.3 - - + -
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Residues in contact with ARG5476 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5230b ARG* 5.3 13.9 - - - +
5233b ASN* 5.1 13.1 + - - +
5472b ARG* 3.6 16.6 + - + +
5473b THR* 3.4 12.2 + - - +
5475b PHE* 1.3 76.9 - - - +
5477b ASP* 1.3 83.9 + - - +
5478b VAL 2.6 13.0 + - - -
5479b PHE* 2.8 25.5 + - + +
5480b SER* 4.6 0.7 + - - -
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Residues in contact with ASP5477 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5225a ARG* 3.6 20.6 + - - -
5475b PHE* 3.5 8.7 + - - -
5476b ARG* 1.3 99.5 + - - +
5478b VAL* 1.3 74.4 + - - +
5134d ARG* 2.8 35.8 + - - -
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Residues in contact with VAL5478 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5225a ARG* 4.6 3.1 - - - +
5475b PHE* 2.9 15.0 + - + +
5476b ARG 2.6 5.7 + - - -
5477b ASP* 1.3 102.8 - - - +
5479b PHE* 1.3 53.5 + - - +
5480b SER 2.9 3.8 - - - -
5481b GLY* 2.6 52.1 + - - +
5482b ILE* 3.7 11.2 - - - -
5483b ASP 4.8 0.7 - - - +
5134d ARG* 3.6 13.5 - - - +
5137d GLY* 4.1 16.2 - - - +
5139d ARG* 3.8 23.3 - - + +
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Residues in contact with PHE5479 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5229a GLU* 4.1 20.9 - - + -
5233a ALA* 5.5 0.3 - - - +
5007b ARG* 3.5 33.4 - - - -
5468b TRP* 4.9 4.7 - + - -
5472b ARG* 3.0 57.4 - - + -
5475b PHE 3.1 6.5 + - - +
5476b ARG* 2.8 24.2 + - + +
5478b VAL* 1.3 76.9 - - - +
5480b SER* 1.3 64.3 + - - +
5521b CLA 3.6 8.5 - - - -
5139d ARG* 2.9 32.2 + - - +
5141d TYR* 4.7 3.6 - + - -
5360d MGE 4.1 19.1 + - - -
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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