Contacts of the helix formed by residues 1476 - 1484 (chain A) in PDB entry 5IYB
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 ASP1476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1474A LEU 4.3 0.2 + - - -
1475A LEU* 1.3 79.2 - - - +
1477A ALA* 1.3 64.5 + - - +
1478A GLU* 3.2 13.6 + - - +
1479A LYS* 2.5 41.6 + - + +
1480A CYS* 3.4 18.7 + - - +
103F PRO* 3.4 22.5 + - - +
105F ILE* 3.7 30.2 - - + +
22G LEU* 5.3 0.2 - - - +
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Residues in contact with ALA1477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475A LEU 4.1 1.8 + - - -
1476A ASP* 1.3 73.7 - - - +
1478A GLU* 1.3 69.9 + - + +
1480A CYS* 3.1 6.5 - - - +
1481A LYS* 3.1 21.9 + - - +
19G GLY 4.5 3.1 - - - +
22G LEU* 4.0 36.5 - - + +
23G LEU* 4.7 19.3 - - + -
68G TYR* 4.8 8.2 + - - +
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Residues in contact with GLU1478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476A ASP* 3.2 10.8 + - - +
1477A ALA* 1.3 78.1 - - + +
1479A LYS* 1.3 66.1 + - - +
1480A CYS 3.3 0.2 + - - -
1481A LYS* 3.3 27.2 + - - +
1482A TYR* 3.0 52.1 + - + -
23G LEU* 4.8 14.2 - - - +
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Residues in contact with LYS1479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476A ASP* 2.5 36.0 + - + +
1478A GLU* 1.3 72.5 - - - +
1480A CYS* 1.3 55.8 - - - +
1482A TYR* 4.0 3.9 - - - +
1483A GLY* 2.8 31.1 + - - -
80F MET* 4.5 2.4 - - - +
100F ARG 3.2 8.7 + - - -
101F LYS* 4.0 13.0 - - - +
102F ILE 2.6 29.5 + - - +
103F PRO* 3.7 18.8 - - + -
105F ILE* 6.5 0.9 - - + -
119F GLY* 6.5 0.7 - - - -
120F VAL* 3.2 8.3 - - - +
121F ASP* 2.4 42.7 + - - +
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Residues in contact with CYS1480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475A LEU* 6.4 1.1 - - + -
1476A ASP 3.4 12.4 + - - +
1477A ALA* 3.1 13.7 + - - +
1479A LYS* 1.3 76.6 - - - +
1481A LYS* 1.3 63.6 + - - +
1483A GLY 3.5 4.7 + - - -
1484A MET* 3.5 20.3 + - - +
78F PRO* 4.7 8.1 - - - -
80F MET* 3.8 23.9 - - + +
103F PRO* 4.5 6.2 - - + +
18G PHE* 4.2 11.7 - - - -
19G GLY* 3.7 35.2 - - - +
22G LEU* 5.0 3.1 - - + -
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Residues in contact with LYS1481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477A ALA 3.1 11.7 + - - +
1478A GLU* 3.3 35.7 + - - +
1480A CYS* 1.3 75.0 - - - +
1482A TYR* 1.3 71.2 + - + +
1484A MET* 2.8 29.2 - - - +
20G PRO* 3.0 49.5 - - + +
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Residues in contact with TYR1482 (chain A).
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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1478A GLU* 3.0 47.5 + - + +
1479A LYS* 4.1 4.3 - - - +
1481A LYS* 1.3 90.0 + - + +
1483A GLY* 1.3 66.6 + - - +
1484A MET 3.2 9.6 + - - +
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Residues in contact with GLY1483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479A LYS* 2.8 24.1 + - - -
1480A CYS 4.2 0.2 - - - -
1481A LYS 3.5 0.4 - - - -
1482A TYR* 1.3 71.4 - - - +
1484A MET* 1.3 66.6 + - - +
1485A GLU 3.4 6.4 + - - -
80F MET* 3.9 32.4 - - - +
101F LYS* 4.9 10.8 + - - +
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Residues in contact with MET1484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480A CYS* 3.5 12.7 + - - +
1481A LYS* 2.8 29.8 - - - +
1482A TYR 3.3 9.1 - - - +
1483A GLY* 1.3 77.9 - - - +
1485A GLU* 1.3 84.8 + - + +
78F PRO* 6.3 4.9 - - + -
79F VAL 5.1 2.9 - - - +
80F MET* 4.3 9.7 - - + +
19G GLY* 4.8 1.3 - - - -
20G PRO* 3.2 48.2 - - + -
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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