Contacts of the helix formed by residues 937 - 946 (chain B) in PDB entry 1VDV
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 937 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935B GLY 4.7 0.7 - - - +
936B LEU* 1.3 91.7 - - + +
938B ALA* 1.3 66.0 + - - +
939B GLU* 3.3 25.4 - - - +
940B GLU* 2.9 42.6 + - + +
941B VAL* 3.2 6.2 + - - +
981B LYS* 4.3 10.8 - - - +
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Residues in contact with ALA 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928B SER* 5.9 1.6 - - - -
931B ALA* 3.7 22.8 - - + +
936B LEU 3.2 4.0 + - - -
937B PRO* 1.3 70.8 - - - +
939B GLU* 1.3 65.0 + - - +
941B VAL* 3.1 4.0 + - - +
942B ARG* 3.0 50.7 + - - +
977B TYR* 5.4 2.7 - - - +
999B CYS* 6.0 1.1 - - - -
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Residues in contact with GLU 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937B PRO* 3.5 17.8 - - - +
938B ALA* 1.3 77.6 + - - +
940B GLU* 1.3 62.5 + - + +
942B ARG* 4.6 1.8 - - - +
943B TRP* 3.1 30.1 + - - +
968B TRP* 3.6 28.2 + - + +
972B LEU* 5.0 2.5 - - + -
977B TYR* 2.9 31.4 + - + +
978B TYR* 3.4 30.2 - - - +
981B LYS* 2.9 25.7 + - - +
1000B ILE* 4.1 13.2 - - + +
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Residues in contact with GLU 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936B LEU* 3.9 21.1 - - - +
937B PRO* 2.9 36.1 + - + +
939B GLU* 1.3 83.9 - - + +
941B VAL* 1.3 63.6 + - + +
943B TRP* 3.6 6.6 + - + +
944B LYS* 3.3 47.1 + - - +
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Residues in contact with VAL 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854B GLY* 3.8 15.3 - - - +
927B MET* 3.8 16.8 - - + -
930B VAL* 3.8 13.0 - - + -
931B ALA* 3.8 26.7 - - + +
934B CYS* 5.4 0.2 - - + -
936B LEU* 3.9 25.1 - - + -
937B PRO 3.6 12.1 - - - +
938B ALA 3.1 5.8 + - - +
940B GLU* 1.3 77.2 - - - +
942B ARG* 1.3 61.5 - - + +
944B LYS* 3.0 16.0 - - + +
945B ASN* 2.8 37.2 + - - +
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Residues in contact with ARG 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889B TYR* 3.2 35.0 - - + +
924B GLU* 2.7 42.4 + - - +
927B MET* 3.8 17.4 - - + +
928B SER* 4.1 17.1 - - - +
931B ALA* 5.9 0.2 - - - +
938B ALA* 3.0 43.7 + - - +
939B GLU 4.0 3.8 - - - +
941B VAL* 1.3 77.7 - - + +
943B TRP* 1.3 61.8 + - - +
945B ASN 3.2 1.9 + - - -
946B MET* 3.1 21.4 + - + +
968B TRP* 4.1 15.5 - - + -
999B CYS* 4.1 14.5 - - - -
1000B ILE* 3.9 17.5 + - - +
1001B ILE* 3.2 22.7 - - - +
1002B PRO* 4.3 1.3 - - - -
1272B PHE* 4.8 3.4 - - - -
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Residues in contact with TRP 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939B GLU 3.1 19.0 + - - +
940B GLU* 3.9 7.6 - - + +
941B VAL 3.3 0.2 - - - -
942B ARG* 1.3 77.3 - - - +
944B LYS* 1.3 64.7 + - + +
946B MET* 3.1 48.1 + - - +
965B PRO* 4.1 27.4 - - + -
968B TRP* 3.5 37.2 - + - +
969B ASP* 4.5 12.1 - - - -
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Residues in contact with LYS 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853B THR* 2.7 40.3 + - - +
854B GLY 4.4 0.9 - - - -
855B THR* 4.3 20.3 + - - +
936B LEU* 4.3 3.8 - - - +
940B GLU* 3.3 39.7 + - - +
941B VAL* 3.0 22.0 - - - +
943B TRP* 1.3 85.2 - - + +
945B ASN* 1.3 63.3 + - - +
946B MET 3.3 3.5 + - - +
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Residues in contact with ASN 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854B GLY 2.9 23.2 + - - -
855B THR* 3.2 9.8 - - - +
856B ILE* 2.7 42.0 + - + +
889B TYR* 3.1 17.7 - - + -
890B LYS* 2.8 36.7 + - - +
927B MET* 3.9 7.3 - - + +
941B VAL* 2.8 31.0 + - - +
942B ARG 3.2 6.4 + - - +
944B LYS* 1.3 78.0 - - - +
946B MET* 1.3 60.2 + - - +
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Residues in contact with MET 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888B CYS* 3.2 14.4 - - + +
889B TYR* 4.1 2.9 - - + -
890B LYS* 4.5 2.9 - - - +
942B ARG 3.1 15.0 + - - +
943B TRP* 3.1 45.7 + - - +
944B LYS 4.6 2.8 - - - +
945B ASN* 1.3 80.1 - - - +
947B TYR* 1.3 77.1 + - - +
948B LYS* 4.9 1.7 - - - +
951B ASP* 4.9 0.3 - - - +
962B PHE* 4.2 8.1 - - + -
964B VAL* 3.6 30.7 - - + -
965B PRO* 4.5 7.9 - - - -
968B TRP* 3.9 31.6 - - + -
1002B PRO* 4.4 10.1 - - + -
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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