Contacts of the helix formed by residues 616 - 634 (chain A) in PDB entry 2VWJ
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 SER 616 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 1.3 84.3 - - - +
617A GLU* 1.3 66.7 + - - +
618A ILE* 3.6 17.4 - - - +
619A ALA* 2.9 17.8 + - - +
620A LYS 3.0 10.4 + - - -
659A LYS 3.9 12.1 - - - -
660A LEU* 4.4 10.5 - - - -
661A VAL 4.1 11.7 - - - -
662A ILE* 4.5 2.5 - - - -
732A TYR* 4.4 2.9 - - - -
736A GLN* 2.5 29.7 + - - +
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Residues in contact with GLU 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 3.9 16.6 - - + -
616A SER* 1.3 70.3 - - - +
618A ILE* 1.3 54.6 + - - +
620A LYS* 3.0 2.8 + - - -
621A GLU* 2.5 47.1 + - + +
658A GLU 5.4 0.2 - - - +
659A LYS* 3.6 35.7 + - + +
661A VAL 4.6 3.6 + - - +
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Residues in contact with ILE 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A SER* 3.1 13.0 - - - +
617A GLU* 1.3 73.7 - - - +
619A ALA* 1.3 65.1 + - - +
621A GLU* 3.8 21.1 - - - +
622A THR* 2.7 39.0 + - - +
646A VAL* 4.2 24.2 - - + -
650A LEU* 4.5 5.2 - - + -
655A VAL* 4.0 26.7 - - + -
659A LYS* 3.0 26.6 + - + +
660A LEU* 3.5 24.7 - - + -
732A TYR* 4.3 5.8 - - + -
736A GLN* 5.4 0.2 - - + -
737A VAL* 3.8 15.9 - - + -
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Residues in contact with ALA 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ILE* 3.6 21.7 - - + +
612A ARG* 6.2 1.1 - - - +
615A TRP* 5.7 0.4 - - + -
616A SER* 2.9 21.5 + - - +
618A ILE* 1.3 83.8 - - - +
620A LYS* 1.3 61.8 + - - +
622A THR* 4.0 2.1 - - - -
623A GLN* 3.3 17.5 + - - +
736A GLN* 3.7 31.4 - - - +
737A VAL* 4.2 12.1 - - - +
740A ALA* 4.3 3.7 - - + +
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Residues in contact with LYS 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ILE* 3.7 28.7 - - + +
615A TRP* 3.4 46.0 - - + -
616A SER 3.0 6.4 + - - +
617A GLU* 3.0 7.4 + - + +
619A ALA* 1.3 76.8 - - - +
621A GLU* 1.3 63.6 + - - +
622A THR 3.2 0.2 + - - -
623A GLN* 3.4 3.5 + - - +
624A ALA* 3.1 24.8 + - - +
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Residues in contact with GLU 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A GLU* 2.5 31.0 + - + +
618A ILE* 3.8 18.5 - - - +
620A LYS* 1.3 73.2 - - - +
622A THR* 1.3 59.2 + - - +
624A ALA* 3.5 6.0 - - - +
625A ARG* 2.8 53.8 + - + +
646A VAL* 5.3 3.5 - - - +
659A LYS* 2.9 35.6 + - - -
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Residues in contact with THR 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ILE* 2.7 25.1 + - - +
619A ALA 4.0 2.7 - - - -
620A LYS 3.2 0.2 - - - -
621A GLU* 1.3 76.8 + - - +
623A GLN* 1.3 61.2 + - - +
625A ARG* 3.1 8.4 + - - +
626A VAL* 2.9 33.4 + - + +
642A ILE* 4.4 7.2 - - + -
643A VAL* 4.3 21.5 - - + -
646A VAL* 3.7 35.9 - - + +
737A VAL* 4.2 21.5 - - + +
741A VAL* 5.4 2.9 - - + -
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Residues in contact with GLN 623 (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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608A LEU 2.8 29.9 + - - -
609A GLU* 4.1 15.6 - - - +
610A ILE* 3.6 23.8 + - + +
619A ALA 3.3 14.1 + - - +
620A LYS* 3.9 4.1 - - - +
622A THR* 1.3 77.8 - - - +
624A ALA* 1.3 64.6 + - - +
626A VAL* 3.1 9.7 + - - +
627A LEU* 3.0 38.9 + - + +
740A ALA* 3.2 30.9 + - + +
741A VAL* 4.8 5.1 - - - +
744A ILE* 4.1 16.0 - - + +
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Residues in contact with ALA 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 5.8 0.7 - - - +
620A LYS 3.1 15.9 + - - +
621A GLU* 3.5 7.9 - - - +
623A GLN* 1.3 80.5 + - - +
625A ARG* 1.3 63.0 + - + +
627A LEU* 3.5 9.5 + - - +
628A GLU* 3.2 24.8 + - - +
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Residues in contact with ARG 625 (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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621A GLU* 2.8 47.3 + - + +
622A THR* 3.1 6.9 + - - +
624A ALA* 1.3 77.0 - - + +
626A VAL* 1.3 58.4 + - - +
628A GLU* 3.5 14.1 + - - +
629A ALA* 3.0 28.1 + - - +
638A GLU* 5.2 0.4 + - - -
641A ARG* 5.0 5.9 - - - +
642A ILE* 3.5 52.2 - - + +
645A GLU* 4.8 8.7 + - - -
646A VAL* 4.8 11.1 - - - +
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Residues in contact with VAL 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A THR* 2.9 17.9 + - + +
623A GLN* 3.4 7.9 - - - +
625A ARG* 1.3 73.1 - - - +
627A LEU* 1.3 59.3 + - - +
629A ALA* 2.9 5.6 + - - +
630A ILE* 2.9 48.0 + - + +
639A ALA* 3.8 20.9 - - + +
642A ILE* 4.8 2.9 - - + -
643A VAL* 3.5 21.5 - - + -
741A VAL* 3.4 33.4 - - + -
744A ILE* 4.2 13.7 - - + -
745A LEU* 4.6 2.9 - - + -
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Residues in contact with LEU 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A PHE* 4.2 22.4 - - + -
595A ALA* 4.5 11.7 - - + -
603A ILE* 4.6 12.8 - - + -
605A THR* 4.2 22.4 - - + -
608A LEU* 4.8 4.9 - - + -
609A GLU* 5.5 1.3 - - - +
623A GLN* 3.0 38.5 + - + +
624A ALA* 4.0 6.5 - - - +
626A VAL* 1.3 75.1 - - - +
628A GLU* 1.3 53.7 + - - +
630A ILE* 4.5 3.6 - - - +
631A LEU* 2.7 46.7 + - + +
744A ILE* 3.7 28.5 - - + -
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Residues in contact with GLU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 4.3 12.4 - - + +
624A ALA 3.2 16.5 + - - +
625A ARG* 3.6 13.0 - - - +
627A LEU* 1.3 78.3 - - - +
629A ALA* 1.3 64.3 + - - +
632A LYS* 3.0 55.0 + - + +
633A HIS* 3.4 22.3 + - - +
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Residues in contact with ALA 629 (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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625A ARG 3.0 14.5 + - - +
626A VAL 2.9 11.0 + - - +
628A GLU* 1.3 78.8 - - - +
630A ILE* 1.3 59.1 + - - +
633A HIS* 3.5 14.6 + - - +
634A GLY 3.2 8.0 + - - -
635A ASP* 3.1 25.0 + - - +
638A GLU* 4.4 7.4 - - + -
639A ALA* 3.8 28.5 - - + +
642A ILE* 4.4 9.0 - - + -
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Residues in contact with ILE 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 4.0 13.0 - - + +
587A PHE* 3.7 29.6 - - + -
626A VAL* 2.9 26.7 + - + +
627A LEU* 3.8 3.6 - - - +
629A ALA* 1.3 76.5 - - - +
631A LEU* 1.3 62.7 + - + +
634A GLY* 2.9 26.7 - - - -
635A ASP 4.0 6.3 - - - +
636A VAL* 4.3 14.1 - - + -
639A ALA* 4.0 10.3 - - + -
744A ILE* 3.7 31.0 - - + -
745A LEU* 4.2 9.2 - - + -
748A PHE* 3.9 22.9 - - + -
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Residues in contact with LEU 631 (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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396A LEU* 4.1 4.5 - - + -
585A ARG* 3.0 28.7 + - - +
586A GLY* 3.9 15.5 - - - +
587A PHE* 3.7 27.1 - - + -
595A ALA* 3.7 38.1 - - + +
596A VAL* 4.2 4.0 - - - +
597A ILE* 3.4 27.7 - - + +
603A ILE* 3.7 27.8 - - + -
627A LEU* 2.7 28.9 + - + +
630A ILE* 1.3 78.9 - - + +
632A LYS* 1.3 57.2 + - - +
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Residues in contact with LYS 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ARG* 3.2 17.2 + - - +
597A ILE* 3.9 11.4 - - + -
601A ASP* 3.1 48.1 + - + +
603A ILE* 5.3 3.4 - - + -
628A GLU* 3.0 43.8 + - + +
631A LEU* 1.3 80.1 - - - +
633A HIS* 1.3 77.6 + - + +
634A GLY 3.5 0.2 - - - -
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Residues in contact with HIS 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ARG* 4.8 3.1 - - - -
628A GLU* 3.4 38.9 + - + -
629A ALA* 3.6 11.4 - - - +
632A LYS* 1.3 97.5 + - + +
634A GLY* 1.3 67.4 + - - +
635A ASP* 3.3 11.8 + - + +
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Residues in contact with GLY 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 3.9 20.9 - - - +
585A ARG* 4.0 10.7 - - - +
629A ALA 3.2 0.2 + - - -
630A ILE 2.9 21.2 + - - -
632A LYS 3.5 2.2 - - - -
633A HIS* 1.3 78.6 - - - +
635A ASP* 1.3 56.6 + - - +
636A VAL* 4.1 1.8 - - - -
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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
------------------------------------------------------------
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