Contacts of the helix formed by residues 873 - 884 (chain A) 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 LEU 873 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648A LEU* 3.4 24.7 - - + -
649A PHE* 5.3 0.2 - - - -
802A GLU* 3.6 14.6 - - + +
803A THR* 3.9 10.5 - - + +
872A ASP* 1.3 86.1 + - - +
874A SER* 1.3 63.5 + - - +
875A HIS 3.1 4.0 + - - -
876A SER* 3.2 7.4 + - - +
877A ILE* 3.1 34.5 + - + +
909A THR* 3.4 21.8 - - - +
910A ALA* 3.5 22.0 - - + -
914A PHE* 4.0 5.2 - - + -
5101A YSH 3.5 41.5 - - + -
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Residues in contact with SER 874 (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 HIS* 2.6 36.0 + - - -
865A SER* 5.2 0.5 + - - -
867A ALA* 3.3 13.2 - - - +
871A ARG* 2.9 12.2 + - - -
872A ASP 3.4 0.2 - - - -
873A LEU* 1.3 77.0 - - - +
875A HIS* 1.3 60.8 + - - +
877A ILE* 3.4 4.0 + - - +
878A MET 3.1 17.0 + - - -
900A LEU* 3.5 27.9 - - - +
5301A CA 2.7 20.6 - - - -
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Residues in contact with HIS 875 (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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649A PHE* 5.6 11.7 - - + -
708A TYR 5.4 3.2 + - - -
709A GLY* 6.2 1.7 - - - -
710A SER 4.8 9.9 - - - -
712A LEU* 3.5 38.4 - - + +
871A ARG* 4.7 2.9 + - + +
872A ASP 5.0 1.4 + - - -
873A LEU 3.1 1.4 + - - -
874A SER* 1.3 76.8 - - - +
876A SER* 1.3 65.8 + - - +
878A MET* 3.1 5.9 + - - +
879A GLU* 2.9 49.8 + - - +
900A LEU* 3.5 22.2 - - + +
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Residues in contact with SER 876 (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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649A PHE* 6.0 1.6 - - - -
873A LEU* 3.2 5.8 + - - -
875A HIS* 1.3 77.8 - - - +
877A ILE* 1.3 57.0 + - - +
879A GLU* 3.1 17.2 + - - +
880A ARG* 2.9 26.5 + - - +
914A PHE* 3.5 24.1 - - - -
1010A THR* 3.3 21.7 + - - +
1011A VAL* 4.4 4.0 - - - +
5101A YSH 3.2 24.4 - - - -
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Residues in contact with ILE 877 (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 HIS* 3.4 34.5 - - + +
842A PHE* 4.7 8.5 - - + -
865A SER* 6.2 0.2 - - - -
873A LEU* 3.1 24.7 + - + +
874A SER* 3.6 5.6 - - - +
875A HIS 3.1 0.2 - - - -
876A SER* 1.3 77.6 - - - +
878A MET* 1.3 57.9 - - - +
880A ARG 3.3 0.9 + - - -
881A ALA* 3.0 25.3 + - - +
909A THR 3.5 11.4 - - - +
910A ALA 3.9 1.1 - - - +
914A PHE* 3.5 33.5 - - + +
915A GLY* 3.6 22.2 - - - +
5201A ACY 3.5 25.6 - - + +
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Residues in contact with MET 878 (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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712A LEU* 3.7 19.3 - - + -
842A PHE* 3.8 17.7 - - + -
863A HIS* 3.8 18.2 - - + -
865A SER* 3.7 27.4 - - - +
874A SER 3.1 4.6 + - - -
875A HIS 3.1 9.2 + - - +
877A ILE* 1.3 75.8 - - - +
879A GLU* 1.3 66.7 + - - +
881A ALA* 3.2 6.5 + - - +
882A LEU* 2.9 26.9 + - + +
898A GLY* 3.7 22.7 - - - -
899A ARG 3.5 29.4 - - - +
900A LEU* 3.6 19.3 - - + -
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Residues in contact with GLU 879 (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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712A LEU* 4.0 13.5 - - + +
875A HIS* 2.9 40.4 + - - +
876A SER* 3.1 14.2 + - - +
878A MET* 1.3 76.5 - - - +
880A ARG* 1.3 62.7 + - - +
882A LEU* 3.1 5.0 + - - +
883A PHE* 2.9 32.3 + - + -
1010A THR* 3.7 25.8 + - + +
1011A VAL* 6.1 0.3 - - - +
1142A PHE* 3.4 39.5 - - + -
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Residues in contact with ARG 880 (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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876A SER 2.9 11.2 + - - +
877A ILE 3.8 1.3 - - - +
879A GLU* 1.3 76.2 - - - +
881A ALA* 1.3 61.9 + - - +
883A PHE* 3.1 14.8 + - - -
884A HIS* 2.7 49.3 + - + +
913A GLY 3.4 14.4 - - - -
914A PHE* 3.1 33.7 - - + +
916A GLY* 4.0 6.1 - - - +
1005A PHE* 3.4 20.6 - - - -
1006A GLY 2.9 26.0 + - - -
1008A SER 2.9 22.2 + - - +
1010A THR* 4.3 4.8 - - + +
1079A ALA* 5.0 1.8 + - - +
1150A PHE* 3.7 10.5 - - - -
5101A YSH 2.9 40.2 + - - -
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Residues in contact with ALA 881 (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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842A PHE* 4.0 23.1 - - + -
863A HIS* 5.1 3.6 - - + -
877A ILE 3.0 12.5 + - - +
878A MET* 3.2 14.3 + - - +
880A ARG* 1.3 77.1 - - - +
882A LEU* 1.3 58.3 + - - +
884A HIS 2.9 16.8 + - - -
885A MET* 3.2 3.2 + - - +
915A GLY 3.5 25.5 - - - +
916A GLY 4.5 0.2 - - - +
919A ALA* 2.9 26.3 - - + +
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Residues in contact with LEU 882 (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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712A LEU* 3.6 42.4 - - + +
713A LYS 4.1 1.8 - - - +
714A ILE* 3.7 18.5 - - + +
863A HIS* 3.8 24.7 - - + +
878A MET* 2.9 20.2 + - + +
879A GLU 3.6 6.7 - - - +
881A ALA* 1.3 76.8 - - - +
883A PHE* 1.3 59.0 + - - +
884A HIS 3.1 0.9 + - - -
885A MET* 3.4 15.5 - - - +
896A GLY* 3.7 31.6 - - - +
897A THR 3.9 3.8 - - - +
898A GLY 4.4 1.8 - - - +
954A HIS* 2.8 23.7 + - - -
1142A PHE* 4.0 14.4 - - + -
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Residues in contact with PHE 883 (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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714A ILE* 4.4 4.0 - - + -
879A GLU* 2.9 30.1 + - + -
880A ARG* 3.1 13.2 + - - +
882A LEU* 1.3 76.8 - - - +
884A HIS* 1.3 68.5 + - + +
885A MET 3.7 0.2 - - - -
886A ASP* 3.5 2.6 - - - +
954A HIS* 3.4 9.4 - - - -
955A PHE* 3.3 40.6 - + + -
1004A LYS* 4.3 2.4 + - - -
1010A THR* 4.3 15.0 - - + -
1140A TYR* 3.4 45.1 - + + -
1142A PHE* 3.6 21.1 - + - -
1149A ALA* 3.8 17.9 - - + -
1150A PHE* 3.7 25.8 - + + -
1153A PHE* 6.0 0.2 - - - -
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Residues in contact with HIS 884 (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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880A ARG* 2.7 54.7 + - + +
881A ALA 2.9 7.2 + - - +
883A PHE* 1.3 93.5 - - + +
885A MET* 1.3 56.3 + - - +
886A ASP* 2.9 16.2 + - - -
887A ASN 3.1 10.2 + - - -
916A GLY* 4.5 10.5 - - - +
919A ALA* 4.1 2.3 - - - -
920A LEU* 3.3 31.5 + - + +
1004A LYS* 3.4 30.7 - - + -
1005A PHE* 3.6 11.0 - + - -
1006A GLY 2.9 25.0 + - - -
1150A PHE* 3.9 6.5 - + - -
1153A PHE* 5.5 1.0 - - - -
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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