Contacts of the helix formed by residues 873 - 884 (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 LEU 873 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648B LEU* 3.3 25.6 - - + -
649B PHE* 5.2 0.7 - - - -
802B GLU* 3.6 15.7 - - + +
803B THR* 3.8 10.5 - - + +
872B ASP* 1.3 86.5 + - - +
874B SER* 1.3 64.5 + - - +
875B HIS* 3.1 4.0 + - - -
876B SER* 3.2 7.3 + - - +
877B ILE* 3.0 33.5 + - + +
909B THR* 3.5 20.6 - - - +
910B ALA* 3.6 20.9 - - + -
914B PHE* 4.0 4.9 - - + -
5102B YSH 3.6 41.1 - - + +
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Residues in contact with SER 874 (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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840B HIS* 2.6 34.9 + - - -
867B ALA* 3.4 17.5 - - - +
871B ARG* 2.9 13.1 + - - -
872B ASP 3.4 0.2 - - - -
873B LEU* 1.3 76.0 - - - +
875B HIS* 1.3 61.8 + - - +
877B ILE* 3.3 4.4 + - - +
878B MET 3.0 18.5 + - - -
900B LEU* 3.6 23.5 - - - +
5302B CA 2.8 20.6 - - - -
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Residues in contact with HIS 875 (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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649B PHE* 5.4 13.9 - - + -
708B TYR 5.2 3.3 + - - -
709B GLY* 6.2 1.3 - - - -
710B SER 4.9 8.3 - - - -
712B LEU* 3.4 38.0 - - + +
871B ARG* 4.7 3.6 + - + +
872B ASP 4.9 1.0 + - - -
873B LEU 3.3 1.6 - - - -
874B SER* 1.3 76.9 - - - +
876B SER* 1.3 64.8 + - - +
878B MET* 3.2 5.1 + - - +
879B GLU* 2.8 50.4 + - - +
900B LEU* 3.7 23.2 - - + +
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Residues in contact with SER 876 (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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649B PHE* 5.9 2.4 - - - -
873B LEU* 3.2 6.5 + - - -
875B HIS* 1.3 78.7 - - - +
877B ILE* 1.3 57.2 + - - +
879B GLU* 3.2 16.6 + - - +
880B ARG* 3.0 24.6 + - - +
914B PHE* 3.4 28.5 - - - -
1010B THR* 3.5 17.0 + - - +
1011B VAL* 4.3 4.3 - - - +
5102B YSH 3.2 26.0 - - - -
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Residues in contact with ILE 877 (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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840B HIS* 3.4 35.4 - - + +
842B PHE* 4.7 8.5 - - + -
865B SER* 6.1 0.4 - - - -
873B LEU* 3.0 25.4 + - + +
874B SER* 3.5 8.1 - - - +
875B HIS 3.1 0.2 - - - -
876B SER* 1.3 78.3 - - - +
878B MET* 1.3 58.0 + - - +
880B ARG 3.4 1.0 + - - -
881B ALA* 3.0 24.4 + - - +
909B THR 3.5 11.7 - - - +
910B ALA 3.9 1.1 - - - +
914B PHE* 3.4 33.0 - - + +
915B GLY* 3.6 21.8 - - - +
5202B ACY 3.5 25.8 - - + +
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Residues in contact with MET 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B LEU* 3.5 21.1 - - + -
842B PHE* 3.8 17.7 - - + -
863B HIS* 3.8 17.0 - - - +
865B SER* 3.6 29.2 - - - +
874B SER 3.0 5.9 + - - -
875B HIS 3.6 8.1 - - - +
877B ILE* 1.3 73.9 - - - +
879B GLU* 1.3 65.5 + - - +
881B ALA* 3.1 7.9 + - - +
882B LEU* 2.9 25.3 + - + +
898B GLY* 3.7 24.0 - - - -
899B ARG 3.4 28.7 - - - +
900B LEU* 3.7 17.0 - - + -
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Residues in contact with GLU 879 (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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712B LEU* 4.0 12.0 - - + +
875B HIS* 2.8 42.9 + - - +
876B SER* 3.2 13.2 + - - +
878B MET* 1.3 77.0 - - - +
880B ARG* 1.3 62.8 + - - +
882B LEU* 3.2 6.0 + - - +
883B PHE* 2.9 34.7 + - + -
1010B THR* 3.9 23.2 + - + +
1011B VAL* 6.0 0.5 - - - +
1142B PHE* 3.5 38.6 - - + -
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Residues in contact with ARG 880 (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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876B SER 3.0 13.7 + - - +
879B GLU* 1.3 76.4 - - - +
881B ALA* 1.3 61.2 + - - +
883B PHE* 3.2 13.7 + - - -
884B HIS* 2.7 48.2 + - + +
913B GLY 3.4 14.8 - - - -
914B PHE* 3.1 32.5 - - + +
915B GLY 4.7 0.2 - - - -
916B GLY* 4.0 6.5 - - - +
1005B PHE* 3.5 19.1 - - - -
1006B GLY 2.9 23.6 + - - -
1008B SER 2.9 22.4 + - - +
1010B THR* 4.2 4.7 - - + +
1079B ALA* 5.1 1.8 + - - +
1150B PHE* 3.6 13.6 - - - -
5102B YSH 2.8 40.7 + - - -
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Residues in contact with ALA 881 (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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842B PHE* 4.1 20.4 - - + -
863B HIS* 5.0 4.0 - - + -
877B ILE 3.0 14.7 + - - +
878B MET* 3.2 17.9 - - - +
879B GLU 3.1 0.2 - - - -
880B ARG* 1.3 77.7 - - - +
882B LEU* 1.3 58.4 + - - +
884B HIS 2.9 17.5 + - - -
885B MET* 3.3 3.0 + - - -
915B GLY 3.6 22.4 + - - +
919B ALA* 2.9 24.8 - - + +
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Residues in contact with LEU 882 (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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712B LEU* 3.7 42.4 - - + +
713B LYS* 4.0 5.8 - - - +
714B ILE* 3.8 15.9 - - + -
863B HIS* 3.7 32.5 - - + +
878B MET* 2.9 19.0 + - + +
879B GLU* 3.6 6.5 - - - +
881B ALA* 1.3 76.4 - - - +
883B PHE* 1.3 51.6 + - - +
884B HIS 3.1 0.7 + - - -
885B MET* 3.4 13.1 - - - +
896B GLY* 3.9 17.9 - - - +
897B THR 3.8 10.1 - - - +
898B GLY* 4.3 2.7 - - - +
954B HIS* 2.7 30.8 + - - -
1142B PHE* 4.3 11.0 - - + -
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Residues in contact with PHE 883 (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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714B ILE* 4.0 7.6 - - + -
879B GLU* 2.9 28.9 + - + -
880B ARG* 3.5 12.1 - - - +
881B ALA 3.1 0.2 - - - -
882B LEU* 1.3 74.9 - - - +
884B HIS* 1.3 69.3 + - - +
885B MET 3.7 0.2 - - - -
886B ASP* 3.5 2.6 - - - +
954B HIS* 3.4 8.7 - - - -
955B PHE* 3.4 37.9 - + - -
1004B LYS* 4.2 2.6 + - - -
1010B THR* 4.4 17.7 - - + -
1140B TYR* 3.4 49.8 - + + -
1142B PHE* 3.8 15.3 - + - -
1149B ALA* 3.9 17.0 - - + -
1150B PHE* 3.5 25.7 - + + -
1153B PHE* 5.8 0.3 - - - -
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Residues in contact with HIS 884 (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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880B ARG* 2.7 54.8 + - + +
881B ALA 2.9 7.0 + - - +
883B PHE* 1.3 83.3 + - + +
885B MET* 1.3 57.4 + - - +
886B ASP* 3.0 14.7 + - - -
887B ASN 3.2 9.5 + - - +
916B GLY* 4.5 6.7 - - - -
919B ALA* 4.0 6.2 - - + -
920B LEU* 3.3 32.6 + - + +
1004B LYS* 3.5 29.6 - - - +
1005B PHE* 3.6 11.6 - + - -
1006B GLY 3.0 25.5 + - - -
1150B PHE* 3.9 18.1 - + - -
1153B PHE* 5.4 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