Contacts of the helix formed by residues 736 - 747 (chain A) in PDB entry 2VWK
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 GLN 736 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A ARG* 3.7 14.6 + - - +
614A ASP* 3.1 20.2 + - - +
615A TRP* 4.0 3.4 - - - +
616A SER* 2.6 44.0 + - - +
619A ALA* 3.7 22.5 - - + +
662A ILE* 3.6 22.6 - - + +
731A TYR* 3.4 4.7 + - + +
732A TYR* 3.3 31.7 + - + +
734A GLU 3.7 0.2 - - - -
735A ASN* 1.3 96.1 - - - +
737A VAL* 1.3 69.3 + - + +
738A LEU 3.7 1.1 - - - -
739A PRO* 3.7 5.8 - - - +
740A ALA* 3.7 8.0 + - - +
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Residues in contact with VAL 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ILE* 3.8 39.3 - - + +
619A ALA* 4.5 4.9 - - - +
622A THR* 3.8 29.8 - - + +
643A VAL* 5.0 6.1 - - + -
646A VAL* 4.2 9.2 - - + -
647A THR* 4.7 11.7 - - + -
650A LEU* 3.8 14.8 - - + -
732A TYR 2.8 23.2 + - - +
733A ILE* 4.2 4.9 - - - +
736A GLN* 1.3 70.8 - - - +
738A LEU* 1.3 67.8 + - - +
740A ALA* 3.1 18.2 + - - +
741A VAL* 3.5 7.7 + - + +
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Residues in contact with LEU 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A VAL* 3.9 17.3 - - + -
647A THR* 4.0 12.3 - - + -
733A ILE* 2.9 35.3 + - + +
734A GLU* 3.4 35.9 - - - +
737A VAL* 1.3 72.9 - - - +
739A PRO* 1.3 59.3 - - + +
741A VAL* 2.9 8.6 + - + +
742A GLU* 2.8 32.7 + - + +
752A LYS* 4.8 17.0 - - + +
755A LEU* 3.8 32.9 - - + +
756A ARG* 4.4 8.5 - - + -
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Residues in contact with PRO 739 (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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612A ARG* 4.6 3.4 - - - +
734A GLU 3.2 28.0 - - - +
735A ASN 3.3 15.5 - - - +
736A GLN 3.7 10.5 - - - +
737A VAL 3.6 3.4 - - - -
738A LEU* 1.3 91.0 - - + +
740A ALA* 1.3 58.0 - - - +
741A VAL 3.5 0.5 + - - -
742A GLU* 4.0 13.8 + - + +
743A ARG* 4.7 4.9 + - - +
770A LYS* 4.8 4.0 - - + -
771A PRO* 3.7 23.6 - - + -
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Residues in contact with ALA 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ILE* 3.8 32.5 - - + -
612A ARG* 5.8 0.2 - - - +
619A ALA* 4.0 13.5 - - + +
622A THR* 6.4 0.2 - - - -
623A GLN* 3.1 33.4 + - + +
736A GLN 3.7 10.4 + - - +
737A VAL 3.1 12.3 + - - +
738A LEU 3.1 0.2 + - - -
739A PRO* 1.3 78.0 - - - +
741A VAL* 1.3 59.2 + - + +
743A ARG* 5.4 0.8 - - - +
744A ILE* 4.2 5.2 + - - +
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Residues in contact with VAL 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A THR* 4.3 5.4 - - + +
623A GLN* 3.8 29.8 - - + +
626A VAL* 3.8 18.6 - - + -
643A VAL* 3.9 30.5 - - + -
737A VAL* 3.7 13.0 - - + +
738A LEU* 2.9 16.7 + - + +
740A ALA* 1.3 85.0 - - + +
742A GLU* 1.3 61.7 + - - +
743A ARG 3.4 2.7 - - - -
744A ILE* 3.6 8.3 + - + +
745A LEU* 3.0 38.2 + - + +
755A LEU* 4.8 2.9 - - + -
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Residues in contact with GLU 742 (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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738A LEU* 2.8 20.6 + - + +
739A PRO* 4.0 8.9 + - + +
740A ALA 3.8 0.6 - - - -
741A VAL* 1.3 76.7 - - - +
743A ARG* 1.3 67.5 + - - +
745A LEU* 3.8 0.3 - - - +
746A ARG* 2.8 51.5 + - - +
750A TYR 5.0 2.4 - - - +
751A ARG* 6.0 0.3 - - - -
752A LYS* 4.3 33.0 + - + +
755A LEU* 4.6 12.3 - - + +
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Residues in contact with ARG 743 (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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589A VAL* 3.3 34.3 + - + +
590A THR* 4.1 22.0 - - - +
593A LYS* 4.4 20.1 - - + +
608A LEU* 4.9 8.1 - - + -
739A PRO 4.7 5.7 + - - +
740A ALA 5.4 0.8 - - - +
741A VAL 3.4 0.4 - - - -
742A GLU* 1.3 89.7 + - - +
744A ILE* 1.3 68.5 + - - +
745A LEU 3.3 0.2 + - - -
746A ARG* 3.3 25.2 + - - +
747A ALA* 3.3 16.4 + - - +
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Residues in contact with ILE 744 (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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587A PHE* 4.1 11.7 - - + -
589A VAL* 4.8 7.2 - - - -
608A LEU* 3.8 29.6 - - + +
623A GLN* 4.0 29.4 - - + +
626A VAL* 4.0 13.7 - - + -
627A LEU* 3.4 26.5 - - + -
630A ILE* 3.8 28.3 - - + -
740A ALA 4.2 8.3 + - - +
741A VAL* 3.6 8.1 + - - +
742A GLU 3.5 0.2 - - - -
743A ARG* 1.3 79.6 - - + +
745A LEU* 1.3 63.6 + - + +
747A ALA* 3.4 16.3 - - - +
748A PHE* 3.5 9.2 - - - -
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Residues in contact with LEU 745 (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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626A VAL* 4.1 19.3 - - + -
630A ILE* 4.2 14.6 - - + -
636A VAL* 4.8 6.1 - - + +
639A ALA* 4.2 8.3 - - + +
640A VAL* 4.1 19.3 - - + -
643A VAL* 4.0 21.1 - - + -
741A VAL* 3.0 26.1 + - + +
742A GLU 4.5 0.7 - - - +
744A ILE* 1.3 76.9 - - + +
746A ARG* 1.3 64.7 + - - +
747A ALA 3.1 1.6 - - - -
748A PHE* 3.1 17.2 + - + +
749A GLY 3.3 0.5 + - - -
750A TYR* 3.1 33.6 + - + +
755A LEU* 3.7 29.4 - - + -
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Residues in contact with ARG 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A GLU* 2.8 36.3 + - - +
743A ARG* 3.3 17.9 + - - +
745A LEU* 1.3 76.3 - - - +
747A ALA* 1.3 57.5 + - - +
748A PHE 3.0 0.2 - - - -
749A GLY* 2.9 21.7 + - - -
750A TYR 3.2 17.6 + - - +
751A ARG* 5.4 9.9 - - - +
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Residues in contact with ALA 747 (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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394A ARG* 4.4 24.6 - - + +
395A GLY 4.8 4.5 + - - +
587A PHE* 5.4 1.3 - - + -
588A PHE 5.3 2.0 - - - +
589A VAL* 3.8 39.5 - - + -
743A ARG* 3.3 6.4 + - - +
744A ILE 3.4 13.2 - - - +
745A LEU 3.1 0.4 - - - -
746A ARG* 1.3 78.2 - - - +
748A PHE* 1.3 66.2 + - + +
749A GLY 3.4 0.4 + - - -
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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