Contacts of the helix formed by residues 1477 - 1481 (chain A) in PDB entry 2H7C
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 GLY1477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1156A ALA* 3.6 6.6 - - - +
1473A PHE 3.4 0.4 + - - -
1474A SER 3.1 8.1 + - - -
1475A VAL 3.3 1.4 + - - -
1476A PHE* 1.3 79.2 - - - +
1478A ALA* 1.3 65.0 + - - +
1479A PRO 3.2 3.1 - - - -
1480A PHE* 3.0 24.6 + - - +
1481A LEU* 3.6 5.9 + - - +
1493A SER* 3.2 20.9 - - - -
1497A MET* 3.8 12.4 - - - -
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Residues in contact with ALA1478 (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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1103A ASN* 3.8 33.0 - - + +
1455A PHE* 3.7 20.9 - - + -
1473A PHE* 2.8 26.8 + - + +
1476A PHE 3.4 2.4 + - - -
1477A GLY* 1.3 72.0 - - - +
1479A PRO* 1.3 65.5 - - + +
1480A PHE 2.9 1.7 + - - -
1481A LEU 3.0 0.5 + - - -
1482A LYS* 2.8 34.2 + - + +
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Residues in contact with PRO1479 (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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1455A PHE* 3.9 15.3 - - + -
1473A PHE 3.3 13.2 - - - +
1474A SER* 5.5 0.7 - - - +
1477A GLY* 3.2 7.0 - - - -
1478A ALA* 1.3 91.9 - - + +
1480A PHE* 1.3 61.9 + - + +
1482A LYS 3.9 9.6 - - - +
1485A ALA* 3.8 25.4 + - + +
1489A GLU* 3.7 24.2 - - + +
1490A ILE* 3.9 30.7 - - + +
1493A SER* 3.9 9.6 - - - +
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Residues in contact with PHE1480 (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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1040A LEU* 4.0 14.1 - - + +
1156A ALA* 4.2 7.6 - - + -
1160A HIS* 3.7 31.4 - + - +
1477A GLY* 3.0 15.9 + - - +
1478A ALA 3.0 1.2 - - - -
1479A PRO* 1.3 81.6 - - + +
1481A LEU* 1.3 67.2 + - - +
1482A LYS 4.4 1.6 - - - -
1490A ILE* 3.6 27.8 - - + -
1493A SER* 3.6 17.3 - - - -
1494A LYS* 3.3 33.9 - - + -
1497A MET* 3.5 31.2 - - + -
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Residues in contact with LEU1481 (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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1040A LEU* 4.1 10.5 - - + -
1103A ASN* 3.2 44.6 - - - +
1104A ARG* 4.5 5.6 - - - -
1105A LYS* 4.0 14.6 + - - +
1153A ASP* 4.0 24.0 - - + +
1155A LEU* 4.0 25.8 - - + -
1156A ALA* 4.0 17.5 - - + +
1477A GLY 3.7 10.3 - - - +
1478A ALA 3.0 1.4 + - - +
1480A PHE* 1.3 88.2 - - - +
1482A LYS* 1.3 63.2 + - - +
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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