Contacts of the helix formed by residues 775 - 789 (chain B) in PDB entry 2VE8
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 GLY 775 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769B GLN* 3.5 4.0 - - - -
774B ILE* 1.3 79.0 - - - +
776B TYR* 1.3 68.8 - - - -
777B ASN 3.4 2.5 - - - -
778B ARG* 3.4 9.3 + - - +
779B ALA* 3.0 21.5 + - - +
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Residues in contact with TYR 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B ILE* 3.4 41.7 - - + +
766B SER 5.7 0.2 - - - -
769B GLN* 3.2 30.6 - - - +
775B GLY* 1.3 72.9 - - - -
777B ASN* 1.3 75.5 + - - +
779B ALA 3.3 0.7 + - - -
780B ALA* 2.8 34.8 + - + +
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Residues in contact with ASN 777 (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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775B GLY 3.4 0.2 - - - -
776B TYR* 1.3 97.0 - - - +
778B ARG* 1.3 63.7 + - - +
780B ALA* 3.7 5.9 - - - +
781B ARG* 2.9 38.3 + - + +
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Residues in contact with ARG 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B ASP* 2.8 42.9 + - - +
748B PRO* 3.9 2.2 - - - +
749B LEU* 3.6 17.9 - - - +
774B ILE* 4.0 29.2 - - + +
775B GLY* 3.4 12.2 + - - +
776B TYR 3.3 0.4 - - - -
777B ASN* 1.3 79.9 - - - +
779B ALA* 1.3 62.5 + - - +
781B ARG* 3.5 5.9 + - - +
782B MET* 3.3 22.7 + - + +
772C LEU 2.8 23.2 + - - -
773C LYS* 2.9 34.8 + - - +
774C ILE* 4.0 9.3 - - - +
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Residues in contact with ALA 779 (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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765B ILE* 3.9 9.6 - - + +
768B VAL* 3.8 23.4 - - + +
769B GLN* 3.8 20.0 - - + -
774B ILE* 3.9 11.8 - - + +
775B GLY 3.0 17.4 + - - +
776B TYR 3.7 2.7 - - - +
778B ARG* 1.3 76.7 - - - +
780B ALA* 1.4 64.3 + - - +
782B MET* 3.2 5.9 + - - +
783B ILE* 3.1 26.9 + - - +
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Residues in contact with ALA 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765B ILE* 3.9 30.9 - - + +
776B TYR* 2.8 28.2 + - + +
777B ASN* 3.7 9.2 - - - +
779B ALA* 1.4 74.5 - - - +
781B ARG* 1.3 64.1 + - + +
783B ILE* 3.2 3.9 + - - +
784B GLU* 3.0 37.3 + - - +
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Residues in contact with ARG 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B GLU* 4.5 41.1 + - + +
777B ASN* 2.9 28.1 + - + +
778B ARG* 4.0 5.8 - - - +
779B ALA 3.3 0.2 - - - -
780B ALA* 1.3 77.7 - - - +
782B MET* 1.3 63.8 + - + +
784B GLU* 2.9 34.7 + - - +
785B ALA* 3.0 21.3 + - - +
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Residues in contact with MET 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B GLU 5.8 0.4 - - - -
747B ASP* 3.6 32.3 - - + +
749B LEU* 3.6 35.9 - - + +
750B TYR* 3.6 14.6 - - + -
753B ALA* 3.8 6.5 - - + -
768B VAL* 4.6 2.7 - - + -
772B LEU* 4.1 13.9 - - + -
774B ILE* 3.5 31.6 - - + -
778B ARG* 3.3 11.9 + - + +
779B ALA* 3.2 9.2 + - - +
781B ARG* 1.3 78.0 - - - +
783B ILE* 1.3 58.6 + - + +
785B ALA* 3.2 9.8 + - + +
786B MET* 3.0 40.7 + - + +
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Residues in contact with ILE 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B VAL* 5.4 0.4 - - + -
763B ALA* 3.3 24.9 - - + +
764B SER 3.8 4.0 - - - +
765B ILE* 3.6 34.8 - - + +
768B VAL* 4.0 17.7 - - + -
779B ALA 3.1 15.2 + - - +
780B ALA* 3.2 5.4 + - - +
782B MET* 1.3 73.9 - - + +
784B GLU* 1.3 64.9 + - - +
786B MET* 3.1 18.9 + - + +
787B GLU* 2.9 21.1 + - - +
792B VAL* 4.0 5.1 - - + +
801B ARG* 3.3 39.3 - - - +
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Residues in contact with GLU 784 (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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780B ALA* 3.0 29.1 + - - +
781B ARG* 2.9 48.3 + - - +
783B ILE* 1.3 75.9 - - - +
785B ALA* 1.3 62.7 + - - +
787B GLU* 3.2 10.7 + - - +
788B MET* 3.0 27.9 + - + +
801B ARG* 4.7 13.0 - - - +
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Residues in contact with ALA 785 (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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745B GLU 4.6 6.7 - - - +
746B ASP* 4.6 15.5 - - - +
750B TYR* 3.7 20.5 + - + -
781B ARG 3.0 13.9 + - - +
782B MET* 3.2 12.1 + - + +
784B GLU* 1.3 77.0 - - - +
786B MET* 1.3 55.5 + - - +
788B MET* 3.2 12.1 + - - +
789B ALA* 3.0 27.9 + - - +
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Residues in contact with MET 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750B TYR* 3.7 20.4 - - + +
753B ALA* 3.5 44.6 - - + +
754B VAL* 3.8 15.7 - - + +
757B VAL* 4.0 31.0 - - + -
768B VAL* 5.2 0.4 - - + -
782B MET* 3.0 25.7 + - + +
783B ILE* 3.1 20.6 + - + +
785B ALA* 1.3 74.2 - - - +
787B GLU* 1.3 61.8 + - - +
789B ALA 3.3 0.9 + - - -
790B GLY 3.1 3.6 + - - -
791B VAL* 2.9 39.6 + - + +
792B VAL* 3.9 13.0 - - + -
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Residues in contact with GLU 787 (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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783B ILE 2.9 9.0 + - - +
784B GLU* 3.2 10.6 + - - +
786B MET* 1.3 77.2 - - - +
788B MET* 1.3 63.6 + - - +
790B GLY* 3.0 13.3 + - - -
792B VAL* 3.6 20.7 - - + +
793B THR 4.1 1.8 - - - +
794B PRO* 3.6 27.6 - - + +
795B MET 4.6 1.0 + - - -
801B ARG* 2.9 36.5 + - - +
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Residues in contact with MET 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B GLU* 3.0 16.1 + - + +
785B ALA* 3.2 12.3 + - - +
787B GLU* 1.3 78.7 - - + +
789B ALA* 1.3 59.9 + - - +
790B GLY 3.5 0.5 + - - -
771H LYS* 5.8 6.1 - - - +
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Residues in contact with ALA 789 (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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750B TYR* 3.5 26.0 - - + +
785B ALA 3.0 9.5 + - - +
786B MET 3.8 2.9 - - - +
787B GLU 3.1 0.6 - - - -
788B MET* 1.3 76.9 - - - +
790B GLY* 1.3 61.1 + - - +
791B VAL* 3.4 8.1 + - + +
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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
------------------------------------------------------------
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