Contacts of the strand formed by residues 631 - 640 (chain A) in PDB entry 2VKX
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 ILE 631 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A PRO* 4.6 8.5 - - + -
602A SER 5.8 0.4 - - - +
623A LYS* 6.0 1.1 - - + -
624A GLN 4.8 7.4 - - - +
625A ASP 5.5 0.2 - - - +
626A ASP* 3.5 31.2 - - + -
629A SER 4.6 0.4 - - - +
630A PRO* 1.3 71.4 - - - +
632A ARG* 1.3 59.8 + - - +
633A HIS 3.4 26.0 - - - +
634A TYR* 3.6 28.9 - - + +
653A SER* 2.9 26.6 + - - -
675A ALA* 4.1 17.3 - - + -
676A GLU 3.6 8.3 - - - +
677A ASN* 4.3 0.2 - - - -
507B GLN* 2.8 39.0 + - - +
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Residues in contact with ARG 632 (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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630A PRO 3.6 3.8 + - - +
631A ILE* 1.3 74.7 - - - +
633A HIS* 1.3 98.2 + - + +
650A ARG* 4.0 13.5 - - - +
652A PRO* 4.7 0.9 - - - +
653A SER* 3.9 10.8 + - - -
676A GLU* 2.7 37.8 + - - +
677A ASN* 4.3 10.5 - - - -
678A GLN* 5.0 12.3 - - - +
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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
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631A ILE* 3.4 11.0 - - - +
632A ARG* 1.3 138.5 + - + +
634A TYR* 1.3 63.3 + - - +
635A LEU* 4.1 10.5 - - + -
650A ARG* 3.4 50.2 + - + +
651A LEU 3.2 16.4 + - - +
652A PRO* 5.0 2.2 - - + +
653A SER 4.7 0.9 - - - +
675A ALA* 3.9 0.5 - - - -
676A GLU* 3.0 38.2 + - - +
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Residues in contact with TYR 634 (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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604A PRO* 4.2 17.3 - - + +
621A LEU* 4.2 23.6 - - + -
623A LYS* 3.6 28.8 - - + +
624A GLN 5.3 0.5 + - - -
631A ILE* 3.6 23.0 - - + +
633A HIS* 1.3 76.0 - - - +
635A LEU* 1.3 62.3 + - - +
636A VAL* 3.9 0.8 + - + -
649A ILE 3.5 2.8 - - - +
650A ARG* 3.6 1.9 - - - -
651A LEU* 2.8 48.2 + - + +
652A PRO 3.8 16.2 - - - -
653A SER* 3.4 26.1 + - - -
655A SER* 4.6 2.7 - - - -
673A VAL* 4.3 17.5 - - + -
674A VAL 3.2 15.3 - - - +
675A ALA* 3.9 20.4 - - + -
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Residues in contact with LEU 635 (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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633A HIS* 4.1 15.7 - - + -
634A TYR* 1.3 78.8 - - - +
636A VAL* 1.3 62.0 + - - +
637A ARG* 5.2 1.9 - - + +
648A GLU* 3.7 30.7 - - - +
649A ILE 3.4 2.2 - - - +
650A ARG* 4.3 18.8 - - + -
672A TYR 3.4 4.5 - - - +
673A VAL* 3.5 0.3 - - - -
674A VAL* 2.8 45.2 + - + +
676A GLU* 4.3 19.3 - - + +
681A LYS* 3.9 33.4 - - + +
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Residues in contact with VAL 636 (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 LEU* 6.2 0.4 - - + -
634A TYR 4.6 1.3 - - - +
635A LEU* 1.3 77.4 - - - +
637A ARG* 1.3 66.2 + - - +
638A TYR* 4.7 11.5 - - + -
647A PRO 4.8 0.5 - - - +
648A GLU* 3.6 5.6 - - - +
649A ILE* 2.8 53.1 + - + +
651A LEU* 3.6 31.2 - - + -
658A VAL* 4.4 19.5 - - + -
660A LEU* 5.0 2.2 - - + -
671A VAL* 4.0 24.0 - - + -
672A TYR 3.3 2.5 - - - +
673A VAL* 4.2 19.3 - - + -
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Residues in contact with ARG 637 (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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635A LEU* 5.2 2.0 - - + +
636A VAL* 1.3 79.3 - - - +
638A TYR* 1.3 63.7 + - - +
645A TRP* 3.7 41.4 - - + -
646A LYS 5.0 2.0 - - - -
647A PRO 5.8 0.7 - - - -
648A GLU* 3.7 43.7 + - + +
671A VAL* 3.3 1.2 - - - +
672A TYR* 2.6 50.7 + - + +
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Residues in contact with TYR 638 (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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636A VAL* 4.7 7.2 - - + -
637A ARG* 1.3 81.2 - - - +
639A ARG* 1.3 74.1 + - - +
645A TRP* 3.5 5.9 - - - -
646A LYS* 3.2 61.3 + - + +
647A PRO 5.0 3.6 - - - -
649A ILE* 4.1 17.9 - - + +
660A LEU* 3.4 37.9 - - + +
661A LYS 5.5 1.7 + - - -
663A LEU* 4.2 20.3 - - + +
669A TYR* 4.4 12.3 - + + -
670A GLU 3.1 13.0 - - - +
671A VAL* 3.8 17.0 - - + -
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Residues in contact with ARG 639 (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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638A TYR* 1.3 84.3 - - - +
640A ALA* 1.3 64.8 - - - +
641A LEU* 3.5 3.1 + - - +
642A SER* 5.6 4.4 - - - +
643A SER 3.2 24.3 + - - +
644A GLU* 3.5 17.5 - - - +
645A TRP* 2.9 48.4 - - + +
646A LYS* 5.0 3.1 - - - +
669A TYR* 3.0 14.4 - - - -
670A GLU* 2.6 62.3 + - + -
672A TYR* 5.3 1.0 + - - -
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Residues in contact with ALA 640 (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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639A ARG* 1.3 73.1 - - - +
641A LEU* 1.3 72.1 + - - +
643A SER* 2.9 33.3 + - - +
644A GLU 4.8 0.8 + - - -
646A LYS* 5.2 6.2 - - - +
664A ASP* 5.0 6.5 - - - +
667A ALA* 5.1 6.1 - - + -
668A GLU 3.2 11.9 - - - +
669A TYR* 3.4 26.6 - - + +
541C GLY* 6.4 0.7 - - - -
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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