Contacts of the strand formed by residues 964 - 972 (chain A) in PDB entry 6M0X
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 PRO 964 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962A VAL 3.9 4.3 - - - +
963A SER* 1.3 88.3 - - - +
965A TRP* 1.3 63.9 + - - +
966A ARG 5.0 1.8 - - - +
983A LEU 3.8 8.1 - - - +
984A LYS* 3.9 16.6 - - + +
985A TYR* 3.2 21.6 + - - -
1045A LEU 5.4 0.4 - - - +
1046A SER* 3.4 35.2 - - - +
1047A ARG* 4.6 8.1 - - + +
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Residues in contact with TRP 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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815A ASP 5.0 2.4 - - - +
816A SER 2.9 24.3 + - - -
817A LYS 3.6 18.2 + - - -
818A PHE* 3.7 26.3 - + + +
964A PRO* 1.3 76.5 - - - +
966A ARG* 1.3 89.0 + - + +
983A LEU* 2.7 30.3 + - + +
984A LYS* 3.6 2.3 - - - +
985A TYR* 3.8 28.2 + + + +
988A LEU* 3.7 40.4 - - + -
999A ILE* 5.4 0.4 - - + -
1024A TYR* 3.6 34.2 - + - -
1025A LYS* 4.7 6.9 + - - +
1044A PHE* 6.0 0.2 - - - -
1045A LEU 5.7 0.9 - - - +
1119A LEU* 5.7 0.7 - - + -
1121A PHE* 4.3 14.8 - + - -
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Residues in contact with ARG 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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964A PRO* 5.0 1.8 - - - +
965A TRP* 1.3 111.3 - - + +
967A ALA* 1.3 57.7 + - - +
968A ASP* 2.9 36.0 + - - +
982A GLY* 3.7 1.6 - - - -
983A LEU* 2.7 45.4 + - + +
1022A THR* 3.6 11.1 + - + +
1023A LEU 3.6 8.3 - - - +
1024A TYR* 2.9 47.8 + - + -
1044A PHE* 5.0 4.3 - - - -
1046A SER* 6.3 0.4 - - - -
1047A ARG* 5.3 2.1 - - - +
1117A PRO* 3.8 9.1 - - - +
1118A LYS* 3.0 33.3 + - - +
1119A LEU* 3.3 17.1 - - - +
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Residues in contact with ALA 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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966A ARG* 1.3 74.8 - - - +
968A ASP* 1.3 64.2 + - - +
969A VAL* 3.9 1.4 + - - +
980A ILE* 3.7 17.5 - - + -
981A LEU 3.0 11.4 - - - +
1022A THR* 3.4 3.3 - - - +
1023A LEU* 2.9 35.0 + - + +
1044A PHE* 3.4 30.5 - - + -
1047A ARG* 4.2 10.3 - - + -
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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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966A ARG* 2.9 30.7 + - - -
967A ALA* 1.3 72.0 - - - +
969A VAL* 1.3 62.8 + - - +
970A TYR* 3.5 15.1 - - + -
980A ILE* 3.5 2.2 - - - -
981A LEU* 2.7 45.4 + - + +
983A LEU* 4.3 1.0 - - - +
1004A TYR* 2.4 45.8 + - - +
1019A PHE* 4.1 4.3 - - + -
1021A PHE 3.9 2.9 - - - -
1022A THR* 2.7 23.5 + - - +
1117A PRO* 3.8 3.3 - - - +
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Residues in contact with VAL 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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967A ALA 4.5 1.8 - - - +
968A ASP* 1.3 74.6 - - - +
970A TYR* 1.3 72.7 + - - +
978A TYR* 4.1 15.9 - - + -
979A GLU 4.0 2.0 - - - -
980A ILE* 4.4 25.8 - - + +
1019A PHE* 3.5 6.4 - - - -
1020A LYS* 2.9 27.5 + - + -
1021A PHE* 2.7 45.9 + - + +
1023A LEU* 3.6 30.7 - - + -
1096A ILE* 5.8 3.6 - - + -
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Residues in contact with TYR 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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968A ASP* 3.5 28.7 - - + -
969A VAL* 1.3 77.9 - - - +
971A PHE* 1.3 62.7 + - - +
978A TYR* 3.3 22.9 - - - -
979A GLU* 2.9 29.5 + - + +
981A LEU* 4.1 10.5 - - + -
1004A TYR* 2.6 34.1 + - - -
1008A LYS* 3.7 26.5 + - - -
1013A VAL* 3.7 24.7 - - + -
1017A SER* 3.7 25.1 - - - -
1018A GLU 3.2 7.6 - - - +
1019A PHE* 3.8 26.5 - + + -
1020A LYS* 3.8 2.9 - - - -
1117A PRO* 3.4 10.3 - - + +
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Residues in contact with PHE 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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970A TYR* 1.3 77.7 - - - +
972A ASN* 1.3 71.2 + - - +
973A LYS* 4.0 13.1 + - + +
976A GLY* 3.4 38.8 - - - -
977A LYS 3.6 10.5 - - - -
978A TYR* 3.6 37.2 - + - +
979A GLU* 4.6 1.1 - - - +
1017A SER* 3.3 5.6 - - - -
1018A GLU* 2.9 60.4 + - + +
1020A LYS* 4.0 11.9 - - + -
1094A ILE 5.4 0.4 - - - -
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Residues in contact with ASN 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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971A PHE* 1.3 74.7 - - - +
973A LYS* 1.3 62.2 + - - +
974A THR* 3.4 17.7 + - - -
975A THR* 3.4 25.8 + - - +
976A GLY* 2.8 29.3 + - - -
977A LYS 3.0 10.4 + - - +
979A GLU* 3.1 29.9 + - - -
1014A ASP* 3.5 22.1 + - - +
1016A ASP 4.3 6.1 - - - +
1017A SER* 3.3 13.5 + - - +
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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