Contacts of the helix formed by residues 963 - 970 (chain A) in PDB entry 5Y36
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 VAL 963 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762A GLU* 4.1 11.7 - - - +
958A LEU* 4.9 6.1 - - + -
959A LYS 4.6 1.8 - - - +
960A SER* 2.9 28.5 + - - +
962A LEU* 1.3 78.5 - - + +
964A SER* 1.4 64.9 + - - +
966A PHE* 2.8 27.4 + - + +
967A ARG* 3.0 42.3 + - + +
989A LEU* 4.8 11.2 - - + -
990A ASN* 4.3 11.4 - - - +
993A VAL* 5.5 6.1 - - + -
32D T 6.3 0.2 - - - -
33D C 6.2 0.7 - - - -
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Residues in contact with SER 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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960A SER 4.1 1.7 + - - -
961A LYS* 4.3 12.4 + - - -
962A LEU 3.5 0.6 - - - -
963A VAL* 1.4 75.5 - - - +
965A ASP* 1.4 66.1 + - - +
967A ARG* 3.2 14.8 + - - +
968A LYS* 3.2 12.3 + - - +
1038A PHE* 4.7 15.0 - - - -
31D T 5.4 5.1 - - - +
32D T 2.9 52.6 + - - +
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Residues in contact with ASP 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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962A LEU 4.4 3.4 + - - +
963A VAL 3.3 0.6 - - - -
964A SER* 1.4 78.6 - - - +
966A PHE* 1.3 59.5 + - + +
968A LYS* 3.5 14.5 + - + +
969A ASP* 3.1 35.0 + - - +
1038A PHE* 5.8 1.1 - - - -
1039A TYR* 3.9 17.8 - - - +
1042A ILE* 3.4 45.4 - - + +
1043A MET* 3.8 15.7 - - + +
1049A GLU* 5.5 5.4 - - - +
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Residues in contact with PHE 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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962A LEU* 3.3 27.6 - - + -
963A VAL* 2.8 21.5 + - + +
965A ASP* 1.3 74.1 - - + +
967A ARG* 1.4 60.8 + - - -
969A ASP* 4.4 11.2 - - - -
970A PHE* 3.2 53.1 + + + +
972A PHE* 4.4 1.9 - - - -
989A LEU* 5.0 12.1 - - + -
992A VAL* 5.1 10.8 - - + -
993A VAL* 3.7 35.2 - - + -
996A ALA* 6.2 1.3 - - + -
1042A ILE* 5.3 6.3 - - + -
1046A PHE* 4.5 27.4 - + - -
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Residues in contact with ARG 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* 3.0 33.7 + - + +
964A SER 3.2 8.5 + - - +
966A PHE* 1.4 76.2 - - - +
968A LYS* 1.3 59.9 + - - +
971A GLN* 3.1 3.6 + - - -
972A PHE* 2.8 61.4 + - - +
974A LYS* 3.7 19.7 - - - +
982A HIS* 3.9 0.8 - - - -
985A HIS* 5.0 1.0 - - - +
986A ASP* 2.7 37.2 + - - +
989A LEU* 3.6 22.1 - - - +
32D T 3.8 30.7 + - - +
33D C 3.2 40.9 + - - -
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Residues in contact with LYS 968 (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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964A SER 3.2 9.7 + - - +
965A ASP* 3.5 15.7 - - - +
967A ARG* 1.3 75.2 - - - +
969A ASP* 1.4 66.6 + - - +
971A GLN* 3.0 32.1 + - - +
1049A GLU* 2.8 38.5 + - - +
1051A THR* 4.9 4.9 - - - +
1057A ILE* 5.7 9.3 - - - +
1059A LYS* 4.9 6.6 + - - +
1251A ASP* 5.2 10.5 - - - +
32D T 5.2 8.1 + - - +
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Residues in contact with ASP 969 (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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965A ASP* 3.1 24.9 + - - +
966A PHE* 4.0 14.8 - - - +
968A LYS* 1.4 76.0 - - - +
970A PHE* 1.3 68.6 + - + +
971A GLN* 3.6 5.5 + - - +
1048A THR* 3.6 21.9 + - - +
1049A GLU* 3.5 13.3 - - - +
1059A LYS* 2.8 31.3 + - - +
1080A PHE* 3.4 29.1 - - + -
1084A ARG* 4.8 0.9 + - - -
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Residues in contact with PHE 970 (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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966A PHE* 3.2 47.4 + + - +
969A ASP* 1.3 80.0 - - + +
971A GLN* 1.4 71.0 + - - +
972A PHE* 3.3 38.6 - + + -
989A LEU* 4.1 11.4 - - + -
992A VAL* 5.9 4.9 - - + -
1080A PHE* 3.4 38.8 - + - -
1083A VAL* 3.6 42.6 - - + -
1084A ARG* 3.7 22.1 + - + +
1087A LEU* 5.1 1.6 - - - +
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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