Contacts of the helix formed by residues 962 - 976 (chain A) in PDB entry 4AY6
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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936A MET* 3.7 13.7 - - - -
960A ALA* 3.3 2.7 + - - +
961A LYS* 1.3 89.2 + - - +
963A ARG* 1.3 69.6 + - - +
964A GLN* 2.9 15.2 + - + +
965A GLU* 2.8 37.8 + - - +
966A TYR* 2.9 21.0 + - - +
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Residues in contact with ARG 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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846A SER* 3.5 34.1 + - - -
850A MET* 4.0 32.0 - - + +
936A MET* 3.5 30.1 - - - +
962A ASN* 1.3 74.2 - - - +
964A GLN* 1.3 66.5 + - - +
966A TYR* 3.1 12.7 + - - +
967A GLU* 3.1 23.5 + - - +
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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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857A ARG* 4.4 4.9 - - - +
962A ASN* 3.0 12.6 + - + +
963A ARG* 1.3 82.5 - - - +
965A GLU* 1.3 63.8 + - - +
967A GLU* 3.2 19.1 + - - +
968A ASP* 3.0 44.1 + - - +
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Residues in contact with GLU 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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959A ILE 4.3 7.2 - - - +
960A ALA* 3.9 7.9 - - + -
961A LYS* 3.1 45.0 + - - +
962A ASN* 2.8 23.3 + - - +
964A GLN* 1.3 73.9 - - - +
966A TYR* 1.3 63.3 + - - +
968A ASP* 3.1 12.5 + - + +
969A ILE* 2.9 42.8 + - + +
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Residues in contact with TYR 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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850A MET* 3.7 22.0 - - - -
851A TRP* 3.2 24.1 + + - -
854A ILE* 3.8 22.7 - - + -
912A LEU* 3.4 9.8 - - + +
913A ASP 3.0 35.0 + - - -
915A PRO* 4.8 4.7 - - + -
934A VAL* 3.6 36.2 - - + +
935A THR 4.0 1.3 - - - -
936A MET* 3.7 29.2 - - + -
960A ALA* 3.4 12.4 - - + +
962A ASN 2.9 11.9 + - - +
963A ARG* 3.2 13.0 - - - +
965A GLU* 1.3 78.9 - - - +
967A GLU* 1.3 66.3 + - - +
969A ILE* 3.2 3.2 + - - +
970A ALA* 3.1 21.0 + - - +
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Residues in contact with GLU 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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850A MET* 3.5 27.9 - - + +
853A ASN* 2.9 35.5 + - + +
854A ILE* 3.7 29.1 - - + +
857A ARG* 4.0 14.2 + - - +
963A ARG* 3.1 17.0 + - - +
964A GLN* 3.6 22.4 + - - +
966A TYR* 1.3 79.2 - - + +
968A ASP* 1.3 58.2 + - - +
970A ALA* 3.3 2.9 + - - +
971A VAL* 2.9 34.4 + - - +
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Residues in contact with ASP 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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857A ARG* 3.0 31.8 + - - +
964A GLN* 3.0 33.7 + - - +
965A GLU* 3.1 11.9 + - + +
967A GLU* 1.3 76.0 - - - +
969A ILE* 1.3 54.8 + - + +
971A VAL* 3.1 3.3 + - - +
972A LYS* 2.8 37.1 + - - +
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Residues in contact with ILE 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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934A VAL* 4.3 16.4 - - + -
957A GLU 3.3 28.3 - - - +
958A LEU* 4.2 13.5 - - + +
959A ILE 4.1 5.4 - - - +
960A ALA* 3.8 33.0 - - + +
965A GLU* 2.9 34.4 + - + +
966A TYR* 3.7 4.9 - - - +
968A ASP* 1.3 74.2 - - + +
970A ALA* 1.3 62.9 + - - +
972A LYS* 3.6 6.9 + - - +
973A LEU* 3.2 31.9 + - + +
979A TYR* 5.7 4.9 - - + +
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Residues in contact with ALA 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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834A TYR* 3.1 12.1 + - + -
854A ILE* 3.8 30.1 - - + -
912A LEU* 4.0 18.4 - - + -
934A VAL* 4.4 11.2 - - + +
966A TYR 3.1 10.2 + - - +
967A GLU 3.4 8.5 - - - +
969A ILE* 1.3 79.5 - - - +
971A VAL* 1.3 56.7 - - - +
973A LEU* 3.1 8.7 + - - +
974A GLY 2.9 23.4 + - - -
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Residues in contact with VAL 971 (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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834A TYR* 4.3 0.2 - - - -
854A ILE* 4.2 13.7 - - + -
857A ARG* 3.8 55.0 - - + +
858A VAL* 3.8 22.9 - - + -
967A GLU 2.9 21.7 + - - +
968A ASP 3.1 3.1 + - - +
970A ALA* 1.3 75.3 - - - +
972A LYS* 1.3 64.1 + - - +
974A GLY* 3.0 1.7 + - - -
975A THR* 2.9 37.0 + - + +
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Residues in contact with LYS 972 (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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968A ASP 2.8 20.9 + - - +
969A ILE* 3.7 8.1 - - - +
971A VAL* 1.3 73.7 - - - +
973A LEU* 1.3 56.2 + - - +
975A THR* 3.9 5.8 - - - -
976A ASP* 2.9 51.4 + - + +
979A TYR* 3.6 46.8 + - + -
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Residues in contact with LEU 973 (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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910A VAL* 3.7 30.1 - - + -
932A PRO* 5.4 1.6 - - + -
934A VAL* 3.9 23.1 - - + -
958A LEU* 3.9 15.9 - - + -
969A ILE* 3.2 19.4 + - + +
970A ALA* 3.1 8.4 + - - +
972A LYS* 1.3 76.5 - - - +
974A GLY* 1.3 61.1 + - - +
975A THR 3.5 0.7 + - - -
976A ASP 4.0 2.8 + - - +
977A LEU* 4.8 0.3 + - - +
979A TYR* 3.8 28.3 - - + -
980A LEU* 3.4 47.9 - - + +
983A VAL* 4.0 21.5 - - + -
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Residues in contact with GLY 974 (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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832A ILE* 3.5 34.1 - - - +
834A TYR* 3.2 20.9 - - - -
858A VAL* 3.6 11.2 - - - +
910A VAL* 6.1 0.2 - - - -
970A ALA 2.9 10.1 + - - -
971A VAL 3.0 3.5 + - - -
973A LEU* 1.3 78.3 - - - +
975A THR* 1.3 59.4 + - - +
977A LEU* 4.2 4.9 - - - +
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Residues in contact with THR 975 (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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857A ARG 4.6 5.6 - - - +
858A VAL* 3.9 18.6 - - + -
859A PRO* 5.4 4.3 - - + -
971A VAL* 2.9 26.4 + - + +
972A LYS* 3.6 6.9 + - - -
974A GLY* 1.3 83.9 - - - +
976A ASP* 1.3 66.8 + - - +
977A LEU* 3.0 19.3 + - - +
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Residues in contact with ASP 976 (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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972A LYS* 2.9 32.7 + - + +
973A LEU 4.3 2.2 - - - -
975A THR* 1.3 76.4 + - - +
977A LEU* 1.3 50.9 + - - +
978A GLU* 3.5 11.4 + - - +
979A TYR* 2.9 28.9 + - + +
980A LEU* 2.8 33.8 + - - +
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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