Contacts of the helix formed by residues 962 - 967 (chain A) in PDB entry 3H0G
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 ASN 962 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641A LYS* 4.9 1.4 - - - +
885A GLU* 2.9 40.5 + - + +
886A TYR 5.5 2.3 + - - -
887A GLN* 3.1 16.1 + - - +
961A VAL* 1.3 70.4 - - - +
963A VAL* 1.3 58.7 + - - +
964A GLN* 3.1 25.0 + - - +
965A ARG* 3.2 40.7 + - + +
966A ILE* 3.3 25.6 + - - +
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Residues in contact with VAL 963 (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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887A GLN* 3.5 4.0 + - - +
961A VAL* 2.9 17.6 + - + +
962A ASN* 1.3 68.5 + - - +
964A GLN* 1.3 54.8 + - - +
965A ARG 2.5 18.4 + - - -
966A ILE* 2.8 44.7 + - + +
967A ILE* 3.5 7.8 + - + +
1021A PHE* 4.2 22.2 - - + -
1024A LEU* 4.6 9.0 - - + -
1025A LEU* 4.1 10.8 - - + -
1028A LYS* 4.1 22.0 - - + +
1029A PHE* 3.3 28.5 - - + -
1052A VAL* 5.1 0.7 - - + -
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Residues in contact with GLN 964 (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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595A ILE* 4.0 24.7 - - - +
887A GLN* 3.2 28.2 + - - +
888A VAL* 4.1 14.9 - - + +
962A ASN* 3.1 8.8 + - - +
963A VAL* 1.3 74.8 - - - +
965A ARG* 1.3 57.2 + - - +
967A ILE* 3.5 22.1 - - + +
968A GLN* 3.5 18.3 + - - +
1028A LYS* 4.5 16.2 - - + +
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Residues in contact with ARG 965 (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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592A ILE* 6.5 0.2 - - - +
593A ASN 4.7 10.7 + - - +
594A LEU* 5.0 4.8 - - - +
633A GLY* 5.7 4.8 + - - -
637A HIS* 5.7 1.4 - - - -
638A THR* 2.8 47.1 + - - +
641A LYS* 4.9 3.8 - - - +
642A GLU* 3.2 32.6 + - - -
885A GLU* 3.0 34.1 + - - -
962A ASN* 3.2 41.0 + - - +
963A VAL 2.5 7.1 + - - -
964A GLN* 1.3 73.6 - - - +
966A ILE* 1.3 55.6 + - - +
967A ILE 2.8 5.6 - - - -
968A GLN 2.6 48.2 + - - +
969A ASN* 3.0 10.0 + - - +
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Residues in contact with ILE 966 (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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642A GLU* 5.7 6.1 - - - +
961A VAL* 4.8 7.9 - - + -
962A ASN 3.3 13.2 + - - +
963A VAL* 2.8 46.0 + - + +
965A ARG* 1.3 76.8 - - + +
967A ILE* 1.3 56.7 + - + +
969A ASN* 3.1 6.8 - - - +
970A ALA* 2.9 19.2 - - - +
1029A PHE* 4.0 1.1 - - + -
1047A TRP* 3.9 12.6 - - + -
1048A ILE* 3.6 20.8 - - + +
1051A GLU* 4.6 20.9 - - + -
1052A VAL* 3.1 38.6 - - + +
1055A ARG* 5.5 7.4 - - + +
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Residues in contact with ILE 967 (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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963A VAL* 3.9 10.3 - - + +
964A GLN* 3.5 24.9 - - + +
965A ARG 2.8 1.2 - - - -
966A ILE* 1.3 79.3 - - + +
968A GLN* 1.3 65.5 + - + +
970A ALA* 3.0 9.3 - - - +
971A LEU* 2.9 38.0 + - + +
1028A LYS* 5.6 7.4 - - + +
1029A PHE* 4.0 31.4 - - + -
1038A TYR* 3.7 44.6 - - + +
1040A LEU* 5.9 0.2 - - + -
1048A ILE* 4.1 12.8 - - + -
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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