Contacts of the strand formed by residues 911 - 920 (chain A) in PDB entry 2VZ9
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 911 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909A GLU* 3.1 15.0 - - - +
910A THR* 1.3 83.9 - - - +
912A VAL* 1.3 59.3 + - - +
961A GLN* 3.7 9.0 - - + +
962A TRP* 2.8 50.9 + - + +
965A PRO* 4.4 7.4 - - + -
1059A ILE 3.2 14.1 - - - +
1060A ASP* 3.4 30.1 - - + +
1061A PRO* 3.8 11.4 - - + -
1062A VAL* 5.3 4.0 - - + -
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Residues in contact with VAL 912 (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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896A TRP* 3.4 39.9 - - + +
899A LEU* 4.1 14.6 - - + -
910A THR 3.9 0.9 - - - +
911A PRO* 1.3 73.2 - - - +
913A VAL* 1.3 82.0 + - - +
914A PHE* 3.4 33.4 - - + -
959A VAL* 3.9 11.2 - - + -
960A TYR 3.5 11.4 - - - +
961A GLN* 4.8 0.2 - - - +
962A TRP* 4.2 2.4 - - - -
1058A ARG* 3.6 1.2 - - - -
1059A ILE* 2.9 40.1 + - + +
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Residues in contact with VAL 913 (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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912A VAL* 1.3 77.4 - - - +
914A PHE* 1.3 74.9 + - - +
915A GLU* 3.9 7.4 - - + +
958A LYS 3.5 1.0 - - - +
959A VAL* 3.1 24.9 - - - +
960A TYR* 3.0 46.0 + - + +
962A TRP* 3.4 41.7 - - + -
1056A SER* 5.3 1.6 - - - +
1057A ILE 3.5 4.3 - - - -
1058A ARG* 3.9 20.4 - - + -
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Residues in contact with PHE 914 (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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892A LEU* 3.6 54.7 - - + -
895A THR* 4.1 8.5 - - + -
896A TRP* 4.0 12.6 - - + -
912A VAL* 3.4 31.2 - - + -
913A VAL* 1.3 80.8 - - - +
915A GLU* 1.3 69.6 + - - +
917A VAL* 4.7 8.1 - - + -
944A PHE* 4.0 10.5 - + - -
958A LYS 3.2 4.9 - - - +
959A VAL* 3.2 22.7 - - + -
1056A SER* 3.4 17.0 - - - -
1057A ILE* 2.7 43.4 + - + +
1059A ILE* 5.0 9.0 - - + -
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Residues in contact with GLU 915 (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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913A VAL* 3.9 10.8 - - + +
914A PHE* 1.3 85.0 - - - +
916A ASP* 1.3 77.8 + - + +
917A VAL* 3.0 3.4 + - - +
958A LYS* 2.9 44.1 + - + +
960A TYR* 3.1 32.7 + - + +
1055A THR 3.6 9.6 - - - +
1056A SER* 5.1 4.1 + - - -
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Residues in contact with ASP 916 (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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915A GLU* 1.3 79.4 - - - +
917A VAL* 1.3 67.2 + - - +
918A THR* 3.4 10.0 + - - -
956A SER 3.6 4.9 - - - +
957A GLY* 4.0 3.9 - - - -
958A LYS* 5.3 9.2 + - + +
1053A ARG* 3.7 20.2 + - - +
1054A PHE 3.6 7.4 - - - -
1055A THR* 3.2 19.3 + - - +
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Residues in contact with VAL 917 (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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892A LEU* 4.0 13.7 - - + -
914A PHE* 4.7 11.7 - - + -
915A GLU 3.0 3.0 - - - +
916A ASP* 1.3 79.2 - - - +
918A THR* 1.3 63.2 + - - +
919A LEU* 3.9 22.7 - - + -
944A PHE* 4.0 25.6 - - + -
955A ALA* 5.2 0.7 - - + -
956A SER 3.3 7.0 - - - +
957A GLY* 4.0 3.4 - - - -
1053A ARG* 3.4 4.7 - - - +
1054A PHE* 3.0 67.3 + - + +
1056A SER 5.5 0.2 - - - +
1057A ILE* 4.3 9.4 - - + -
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Residues in contact with THR 918 (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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916A ASP 3.4 6.9 + - - -
917A VAL* 1.3 79.4 + - - +
919A LEU* 1.3 66.6 + - - +
920A HIS* 3.1 34.5 - - + +
955A ALA* 3.3 0.2 - - - -
956A SER* 2.8 36.8 + - - -
1052A THR* 3.4 13.0 - - + +
1053A ARG* 4.2 16.5 + - + +
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Residues in contact with LEU 919 (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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888A GLY* 4.0 24.9 - - - +
891A TYR* 4.0 18.4 - - + -
892A LEU* 5.3 3.4 - - + -
917A VAL* 3.9 17.5 - - + -
918A THR* 1.3 78.8 - - - +
920A HIS* 1.3 61.1 + - - +
921A GLN 5.1 2.9 - - - +
954A ILE 3.5 7.6 - - - +
955A ALA* 3.7 20.6 - - + -
1051A PRO* 3.9 37.9 - - + +
1052A THR* 3.0 29.4 + - - +
1054A PHE* 4.0 14.6 - - + -
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Residues in contact with HIS 920 (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 THR* 3.1 39.6 + - + +
919A LEU* 1.3 74.5 - - - +
921A GLN* 1.3 63.7 + - + +
953A LEU* 3.9 37.4 - - + +
954A ILE 2.9 18.2 + - - +
955A ALA* 4.0 4.9 - - - -
956A SER* 2.8 26.5 + - - -
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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