Contacts of the helix formed by residues 735 - 746 (chain B) in PDB entry 2VF8
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 GLU 735 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B SER* 3.7 5.4 + - - +
46B GLY 4.4 4.9 + - - -
101B ARG* 4.0 11.7 + - - -
719B LEU* 3.4 13.5 - - + +
721B TYR* 2.9 33.5 + - - +
722B LEU* 3.7 29.0 - - + +
730B GLU 4.3 0.5 - - - +
731B LEU* 3.7 10.6 - - + +
732B SER* 2.9 38.4 + - - +
734B GLY* 1.3 74.9 - - - +
736B ALA* 1.3 63.0 + - - +
737B GLN 3.3 1.1 - - - -
738B ARG* 3.7 11.9 - - - +
739B ILE* 2.9 33.4 + - - +
1843B ADP 4.4 7.9 + - - -
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Residues in contact with ALA 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B GLN 4.4 0.2 - - - +
592B LYS 4.2 5.8 - - - +
593B PRO* 4.1 24.2 - - + -
594B ILE* 4.1 17.5 - - + +
731B LEU* 5.0 9.0 - - + +
733B GLY* 3.1 22.2 + - - +
735B GLU* 1.3 79.9 - - - +
737B GLN* 1.3 64.1 + - - +
739B ILE* 2.9 17.2 + - - +
740B LYS* 3.0 19.9 + - + +
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Residues in contact with GLN 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B VAL* 3.5 26.7 + - + +
590B ASP 3.4 26.9 + - - +
591B GLN* 4.2 2.7 - - + +
733B GLY 2.6 21.0 + - - +
734B GLY* 4.3 7.2 - - - +
736B ALA* 1.3 73.6 - - - +
738B ARG* 1.3 70.2 + - - +
740B LYS* 3.3 6.6 - - - +
741B LEU* 3.2 24.4 + - - +
757B LEU* 4.9 2.3 - - - +
758B ASP 3.4 16.6 + - - -
759B GLU 3.6 3.0 + - - -
760B PRO* 3.2 45.6 - - - +
762B THR* 4.2 5.2 + - - +
772B LEU* 5.2 4.3 - - - +
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Residues in contact with ARG 738 (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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45B SER* 2.5 39.4 + - - -
717B VAL* 3.4 31.2 + - + +
718B GLY* 4.3 10.1 - - - -
719B LEU* 3.7 35.1 - - + +
721B TYR* 4.0 2.6 + - - -
732B SER* 5.2 0.2 + - - -
734B GLY 2.6 25.0 + - - +
735B GLU* 3.4 14.3 + - - +
736B ALA 3.2 0.6 - - - -
737B GLN* 1.3 87.9 - - - +
739B ILE* 1.3 63.2 + - - +
741B LEU* 3.2 9.9 + - + +
742B ALA 3.0 17.0 + - - -
763B GLY 4.7 0.6 + - - -
764B LEU* 3.6 26.3 - - + +
768B ASP* 4.6 11.2 + - - +
771B ARG* 6.0 0.6 - - - +
772B LEU* 4.4 23.8 - - + -
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Residues in contact with ILE 739 (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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594B ILE* 4.1 17.7 - - + -
602B MET* 3.6 34.3 - - + -
605B TYR* 3.6 29.2 - - + -
606B THR* 5.2 2.9 - - + -
714B LEU* 4.3 12.8 - - + -
719B LEU* 3.5 15.6 - - + +
722B LEU* 4.5 1.6 - - + -
731B LEU* 3.7 26.9 - - + -
735B GLU 2.9 18.1 + - - +
736B ALA* 2.9 9.1 + - - +
738B ARG* 1.3 72.7 - - - +
740B LYS* 1.3 65.6 + - - +
742B ALA* 2.7 19.6 + - - +
743B THR* 3.3 11.7 + - + +
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Residues in contact with LYS 740 (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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588B ARG 5.8 1.3 - - - +
589B VAL* 4.2 20.0 - - + -
590B ASP* 2.9 33.1 + - - +
592B LYS* 2.6 30.0 + - - +
593B PRO 4.4 10.3 - - - -
594B ILE* 4.4 3.8 - - + +
605B TYR* 3.5 36.3 - - + +
736B ALA 3.0 25.2 + - - +
737B GLN* 3.3 9.3 - - - +
739B ILE* 1.3 72.5 - - - +
741B LEU* 1.3 65.0 + - - +
743B THR* 3.0 23.5 + - - -
744B GLU* 3.6 10.3 + - - +
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Residues in contact with LEU 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B VAL* 4.9 15.4 - - + +
717B VAL* 3.8 13.5 - - + -
737B GLN* 3.2 10.2 + - - +
738B ARG* 3.3 11.0 - - - +
739B ILE 3.2 0.4 - - - -
740B LYS* 1.3 79.5 - - - +
742B ALA* 1.3 62.2 + - - +
744B GLU* 3.1 18.9 + - + +
745B LEU* 3.3 36.8 + - + +
755B TYR* 5.8 2.9 - - + -
757B LEU* 5.3 7.9 - - + -
772B LEU* 3.5 32.3 - - + -
775B GLN* 5.1 3.4 - - + -
776B LEU* 4.0 22.7 - - + -
779B LEU* 4.6 13.5 - - + -
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Residues in contact with ALA 742 (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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713B THR* 3.0 57.6 + - - +
714B LEU* 3.7 22.9 - - + +
717B VAL* 4.0 4.5 - - + +
738B ARG 3.0 9.0 + - - +
739B ILE 2.7 16.4 + - - +
741B LEU* 1.3 72.9 - - - +
743B THR* 1.3 57.7 + - + +
744B GLU 3.1 4.4 + - - -
745B LEU* 3.7 2.8 - - - +
746B ARG* 3.3 12.0 + - - +
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Residues in contact with THR 743 (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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605B TYR* 4.2 27.4 - - + +
606B THR* 4.5 24.0 - - + -
739B ILE* 3.4 20.0 - - + +
740B LYS* 3.0 10.1 + - - +
742B ALA* 1.3 76.8 - - + +
744B GLU* 1.3 67.6 + - - +
746B ARG* 4.3 11.8 - - - +
747B ARG* 4.5 9.2 + - - +
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Residues in contact with GLU 744 (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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585B ARG* 2.7 32.5 + - - -
587B VAL* 3.8 20.2 - - + +
589B VAL* 5.4 3.8 - - + -
740B LYS 3.9 11.9 - - - +
741B LEU* 3.1 17.2 + - + +
743B THR* 1.3 87.6 + - - +
745B LEU* 1.3 68.3 + - + +
746B ARG 3.0 1.6 + - - -
747B ARG* 3.1 23.6 + - - +
748B SER* 3.3 8.6 - - - -
755B TYR* 3.5 32.1 + - + +
779B LEU* 5.4 1.1 - - + -
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Residues in contact with LEU 745 (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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713B THR* 4.4 14.1 - - + +
716B GLU* 3.3 25.6 - - + +
717B VAL* 5.4 3.1 - - + -
741B LEU* 3.3 38.5 + - + +
742B ALA* 3.7 8.3 - - - +
744B GLU* 1.3 76.7 - - - +
746B ARG* 1.3 64.0 + - - +
748B SER* 3.5 20.4 + - - +
775B GLN* 3.3 34.3 - - + +
778B LYS* 4.9 5.2 - - + +
779B LEU* 3.9 30.8 - - + +
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Residues in contact with ARG 746 (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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606B THR* 5.5 3.6 + - - -
607B GLY 5.8 1.0 - - - -
608B LEU* 5.4 7.1 - - - +
706B ALA* 3.7 17.1 + - - +
709B ARG* 4.2 23.2 - - + +
710B ALA* 3.7 37.3 - - + +
713B THR* 3.5 22.7 - - + +
742B ALA 3.3 14.4 + - - +
743B THR* 4.3 8.7 - - - -
744B GLU 3.0 1.0 - - - -
745B LEU* 1.3 82.9 - - - +
747B ARG* 1.3 111.5 + - + +
748B SER 3.4 3.5 + - - +
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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