Contacts of the helix formed by residues 959 - 970 (chain A) in PDB entry 3SQD
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 SER 959 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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953A GLU* 3.6 10.2 + - - -
958A PHE* 1.3 82.7 - - - +
960A LEU* 1.3 64.6 + - - +
961A GLU* 3.4 13.5 + - - +
962A GLU* 3.1 29.2 + - - +
963A SER* 3.0 17.7 + - - -
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Residues in contact with LEU 960 (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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908A VAL* 4.2 10.3 - - + -
914A PHE* 4.4 8.3 - - + -
918A ILE* 3.7 29.6 - - + -
924A ILE* 4.0 25.6 - - + -
946A ILE* 6.1 1.1 - - + -
947A LEU* 3.8 47.6 - - + +
949A ASP 6.0 0.4 - - - +
953A GLU* 2.8 19.3 + - + +
958A PHE* 3.6 23.0 - - + -
959A SER* 1.3 71.4 - - - +
961A GLU* 1.3 62.9 + - - +
963A SER* 3.0 13.8 + - - -
964A LEU* 3.0 17.9 + - + +
1057A LEU* 4.9 0.2 - - + -
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Residues in contact with GLU 961 (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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946A ILE* 5.8 13.2 - - + +
948A ARG* 5.8 3.1 + - - -
953A GLU* 4.5 1.2 + - - +
959A SER* 3.4 10.3 + - - +
960A LEU* 1.3 79.5 - - - +
962A GLU* 1.3 62.9 + - - +
964A LEU* 3.3 11.3 + - - +
965A LYS* 3.0 56.4 + - + +
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Residues in contact with GLU 962 (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 SER* 3.1 26.1 + - - +
961A GLU* 1.3 80.8 - - - +
963A SER* 1.3 58.0 + - - +
965A LYS* 3.4 17.4 + - - +
966A ARG* 2.9 81.5 + - - +
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Residues in contact with SER 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ILE* 3.9 11.4 - - - -
958A PHE* 3.4 14.6 - - - -
959A SER 3.0 3.9 + - - -
960A LEU* 3.0 12.6 + - - -
962A GLU* 1.3 74.0 - - - +
964A LEU* 1.3 59.7 + - - +
966A ARG* 3.3 1.1 + - - -
967A ALA* 2.9 27.0 + - - +
1057A LEU 2.7 27.8 + - - -
1058A THR* 3.5 11.5 + - - -
1059A GLN* 3.4 24.7 - - - +
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Residues in contact with LEU 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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918A ILE* 3.8 22.2 - - + +
921A VAL* 4.0 23.8 - - + +
922A LYS 4.7 7.0 - - - +
923A HIS* 4.9 0.4 - - - -
924A ILE* 3.9 47.3 - - + +
946A ILE* 6.0 5.8 - - + -
960A LEU* 3.0 23.0 + - + +
961A GLU* 3.8 10.3 - - - +
963A SER* 1.3 76.3 - - - +
965A LYS* 1.3 62.5 + - + +
967A ALA* 3.2 3.4 + - - +
968A HIS* 3.0 39.7 + - + +
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Residues in contact with LYS 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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961A GLU* 3.0 47.2 + - + +
962A GLU* 3.6 21.5 - - - +
964A LEU* 1.3 76.1 - - + +
966A ARG* 1.3 63.0 + - + +
968A HIS* 3.2 10.8 + - - +
969A VAL* 3.2 27.2 + - + +
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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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958A PHE* 6.2 1.0 - - - +
962A GLU* 2.9 62.3 + - - +
963A SER 3.8 2.9 - - - +
965A LYS* 1.3 74.7 - - + +
967A ALA* 1.3 64.8 + - - +
969A VAL* 3.1 9.8 + - - +
970A SER* 3.1 24.3 + - - +
1058A THR* 3.0 12.1 + - - -
1059A GLN* 3.1 25.6 + - + +
1060A THR* 2.9 35.3 - - - +
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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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918A ILE 3.7 22.4 - - - +
919A SER* 4.0 19.2 - - - +
963A SER 2.9 18.0 + - - +
964A LEU* 3.2 6.9 + - - +
966A ARG* 1.3 75.1 - - - +
968A HIS* 1.3 68.0 + - + +
970A SER 3.3 17.9 + - - +
971A PRO* 4.3 3.7 - - - +
1059A GLN* 3.6 20.3 + - - +
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Residues in contact with HIS 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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919A SER 5.8 0.4 - - - -
920A VAL 5.2 4.9 - - - -
921A VAL 3.0 25.9 + - - -
922A LYS* 3.9 22.3 - - + +
964A LEU* 3.0 29.6 + - + +
965A LYS* 3.7 10.0 - - - +
966A ARG 3.2 0.4 - - - -
967A ALA* 1.3 78.7 - - + +
969A VAL* 1.3 68.0 + - + +
970A SER 3.4 0.3 + - - -
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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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965A LYS* 3.2 14.9 + - + +
966A ARG* 3.1 12.2 + - - +
968A HIS* 1.3 80.5 - - + +
970A SER* 1.3 69.8 + - - +
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Residues in contact with SER 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 ARG 3.1 15.8 + - - +
967A ALA* 3.3 11.2 + - - +
968A HIS 3.3 3.0 + - - -
969A VAL* 1.3 91.6 - - - +
971A PRO* 1.3 79.3 + - - +
972A LEU* 3.3 4.0 + - - -
974A LYS* 3.8 18.2 + - - +
1059A GLN* 4.5 0.7 - - - +
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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