Contacts of the helix formed by residues 962 - 971 (chain A) in PDB entry 6S1M
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 LEU 962 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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839A LEU* 3.7 25.6 - - + -
840A VAL* 4.0 22.2 - - + +
843A LEU* 3.8 23.1 - - + -
867A VAL* 5.1 1.8 - - + -
868A ILE* 4.3 22.0 - - + -
871A LEU* 3.6 29.2 - - + -
957A TYR 3.2 15.7 + - - +
958A LEU* 3.8 12.5 + - + +
961A GLN* 1.3 78.3 - - + +
963A ALA* 1.3 67.5 + - - +
964A LYS 3.5 0.4 - - - -
965A PRO* 3.3 12.5 - - - +
966A LEU* 3.6 22.8 + - + +
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Residues in contact with ALA 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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958A LEU* 3.4 19.4 + - + +
959A GLU* 3.9 16.4 + - - +
961A GLN 3.7 1.2 - - - -
962A LEU* 1.3 78.3 - - - +
964A LYS* 1.3 59.5 + - - +
966A LEU* 3.3 12.1 + - - +
967A LEU* 3.0 37.5 + - + +
983A LEU* 5.9 6.3 - - + -
990A ARG* 6.4 0.4 - - - +
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Residues in contact with LYS 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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959A GLU 3.3 20.5 + - - +
960A GLN* 4.2 24.9 - - - +
963A ALA* 1.3 73.2 - - - +
965A PRO* 1.4 68.5 - - + +
967A LEU* 3.2 13.7 + - + +
968A ARG* 2.9 39.8 + - - +
7T C 3.5 35.0 - - - +
8T G 5.4 4.3 + - - +
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Residues in contact with PRO 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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830A GLU* 3.9 36.1 - - + +
840A VAL* 4.4 13.0 - - + -
844A VAL* 4.7 7.2 - - + -
961A GLN 3.5 18.8 - - - +
962A LEU 3.3 11.2 - - - +
964A LYS* 1.4 94.5 - - + +
966A LEU* 1.3 62.3 + - + +
968A ARG* 3.1 18.7 + - + +
969A ILE* 3.0 28.1 + - + +
7T C 4.7 5.8 - - - +
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Residues in contact with LEU 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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840A VAL* 6.6 0.2 - - + -
843A LEU* 4.4 33.4 - - + +
844A VAL* 5.2 10.5 - - + -
847A SER* 4.8 5.8 - - - +
864A ALA* 5.0 9.2 - - + -
868A ILE* 4.9 15.7 - - + -
962A LEU* 3.6 24.4 + - + +
963A ALA* 3.3 10.7 + - - +
964A LYS 3.3 0.4 - - - -
965A PRO* 1.3 77.3 - - + +
967A LEU* 1.3 60.8 + - + +
969A ILE* 3.2 5.1 + - + +
970A PHE* 2.9 60.6 + - + +
982A VAL* 5.1 13.5 - - + -
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Residues in contact with LEU 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 ALA* 3.0 30.1 + - + +
964A LYS* 3.2 12.1 + - + +
966A LEU* 1.3 75.2 - - + +
968A ARG* 1.3 66.0 + - - +
970A PHE* 4.4 1.3 - - + -
971A GLU* 3.3 39.3 - - + +
979A ALA* 4.3 32.1 - - + +
982A VAL* 5.4 11.0 - - + -
983A LEU* 5.1 18.6 - - + -
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Residues in contact with ARG 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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591A LYS* 6.1 0.2 - - - -
804A ILE* 4.5 28.1 - - + +
808A ARG* 4.7 4.3 - - - +
830A GLU* 3.8 21.0 + - - +
964A LYS* 2.9 29.9 + - - +
965A PRO* 3.1 22.3 + - + +
967A LEU* 1.3 80.5 - - - +
969A ILE* 1.3 66.5 + - + +
972A PRO* 3.4 18.7 - - - +
6T T 3.1 45.3 + - - +
7T C 3.2 32.4 + - - -
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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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802A LEU* 4.8 14.8 - - + +
804A ILE* 5.2 9.0 - - + -
829A LEU* 5.2 13.0 - - + -
830A GLU* 5.9 2.7 - - + -
844A VAL* 3.7 41.1 - - + -
847A SER* 5.5 3.8 - - - -
848A LEU* 3.8 23.6 - - + -
851A LEU* 4.5 15.9 - - + -
965A PRO* 3.0 18.1 + - + +
966A LEU* 4.1 7.6 - - + +
968A ARG* 1.3 80.0 - - + +
970A PHE* 1.3 73.2 + - + +
971A GLU 3.4 0.2 - - - -
972A PRO* 3.2 12.5 - - - +
973A ILE* 4.8 9.7 - - - +
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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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847A SER* 3.9 29.2 - - - -
851A LEU* 4.2 31.0 - - + -
860A ALA* 4.1 22.0 - - + -
861A VAL* 5.2 1.1 - - + -
864A ALA* 5.1 8.5 - - + -
966A LEU* 2.9 43.2 + - + +
967A LEU* 5.3 1.8 - - + -
969A ILE* 1.3 82.1 - - + +
971A GLU* 1.3 64.8 + - + +
972A PRO* 3.8 0.2 - - - -
973A ILE* 4.0 11.0 + - + +
974A LEU* 4.2 5.0 - - + +
978A ARG* 3.3 56.7 + - + +
982A VAL* 4.6 17.5 - - + -
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Residues in contact with GLU 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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967A LEU* 3.3 37.4 + - + +
968A ARG 4.7 0.4 - - - +
969A ILE 3.4 0.2 - - - -
970A PHE* 1.3 79.3 - - - +
972A PRO* 1.4 66.1 - - + +
974A LEU 2.8 30.3 + - - +
975A GLY 3.8 12.3 - - - +
976A GLU* 3.0 28.7 - - - +
978A ARG* 4.6 2.2 - - - -
979A ALA* 4.2 21.2 - - + +
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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