Contacts of the helix formed by residues 612 - 618 (chain N) in PDB entry 4G7H
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 GLY 612 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605N ASP 4.3 1.6 - - - -
606N ILE 3.2 13.0 - - - -
607N LEU 3.8 3.8 - - - -
608N SER 3.6 13.9 + - - -
609N GLY 2.8 16.9 + - - -
610N LYS 3.2 0.2 - - - -
611N GLN* 1.3 79.3 - - - +
613N ARG* 1.3 60.9 + - - -
614N PHE 3.3 2.9 - - - -
615N ARG 3.5 0.7 + - - -
616N GLN* 2.9 31.8 + - - +
617N ASN* 4.7 0.4 - - - -
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Residues in contact with ARG 613 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016M ILE* 3.7 21.4 - - - +
1017M THR* 3.3 19.9 - - - +
1084M SER* 4.5 5.8 - - - +
1087M VAL* 3.5 13.5 - - - +
1088M LEU* 4.5 11.4 - - + -
1091M GLU* 2.6 43.0 + - - +
601N ARG* 6.1 0.8 - - - +
606N ILE* 2.7 31.3 + - - +
607N LEU* 3.4 17.7 + - + -
612N GLY* 1.3 71.0 - - - -
614N PHE* 1.3 60.0 + - - +
617N ASN* 2.9 56.5 + - - -
618N LEU* 3.3 23.1 + - + +
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Residues in contact with PHE 614 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088M LEU* 3.6 39.7 - - + -
1092M LEU* 5.2 5.2 - - + -
607N LEU* 3.7 23.6 + - + +
608N SER* 5.7 0.2 - - - -
609N GLY 6.0 0.2 - - - +
612N GLY 3.3 0.8 - - - -
613N ARG* 1.3 79.9 - - - +
615N ARG* 1.3 62.2 + - + +
618N LEU* 3.2 17.3 + - + +
619N LEU* 2.8 32.3 + - - +
1434N TRP* 5.3 3.4 - + - -
1435N LEU* 4.2 20.0 - - + -
1438N ALA* 4.0 25.8 - - + -
1439N SER* 3.7 27.8 - - - -
1443N THR* 4.0 20.6 - - + -
1447N LEU* 4.9 6.3 - - + -
1467N ILE* 4.2 10.5 - - + -
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Residues in contact with ARG 615 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031M ARG* 3.1 17.0 + - - -
1034M GLU* 3.1 29.5 + - - +
609N GLY* 3.7 19.0 + - - +
610N LYS* 3.6 52.2 - - + +
612N GLY 3.5 2.0 + - - -
613N ARG 3.5 0.2 - - - -
614N PHE* 1.3 82.6 - - + +
616N GLN* 1.3 59.3 + - - +
619N LEU* 4.5 6.3 - - + -
620N GLY 4.1 7.8 + - - -
1096N ARG* 3.2 51.7 - - - +
1439N SER 4.0 11.4 - - - +
1440N PHE 4.6 5.9 + - - -
13Q A 3.1 25.7 + - - -
14Q G 5.0 3.4 + - - -
15Q T 3.9 8.9 + - - -
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Residues in contact with GLN 616 (chain N).
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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1019M GLN* 4.2 1.0 - - - +
1031M ARG* 3.0 46.5 + - - +
610N LYS 2.9 19.8 + - - +
611N GLN* 3.7 29.7 + - - +
612N GLY 2.9 20.3 + - - +
615N ARG* 1.3 79.7 - - - +
617N ASN* 1.3 73.4 + - - +
620N GLY 2.8 15.0 - - - +
326P ASP 5.7 1.2 + - - -
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Residues in contact with ASN 617 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017M THR* 3.4 21.1 + - - +
1019M GLN* 2.7 46.9 + - - +
1031M ARG* 5.8 0.2 - - - +
1084M SER* 3.9 9.2 - - - +
611N GLN 5.2 0.7 - - - +
612N GLY 4.7 0.3 - - - -
613N ARG* 2.9 48.3 + - - +
616N GLN* 1.3 89.5 + - - +
618N LEU* 1.3 66.1 + - - +
620N GLY 3.3 7.4 - - - -
621N LYS* 3.5 9.2 + - - +
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Residues in contact with LEU 618 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053M LEU* 4.3 1.2 - - - +
1082M PRO* 5.8 0.2 - - + -
1084M SER* 3.7 30.5 - - - +
1085M PHE* 3.9 4.0 - - + +
1088M LEU* 3.8 29.8 - - + -
613N ARG* 3.6 15.7 - - + +
614N PHE* 3.2 35.2 + - + +
617N ASN* 1.3 88.1 - - + +
619N LEU* 1.3 62.5 + - - +
620N GLY 3.2 6.0 + - - -
621N LYS* 3.7 17.2 + - - +
1466N VAL* 3.7 19.4 - - - +
1467N ILE* 3.9 31.5 - - + +
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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