Contacts of the strand formed by residues 628 - 634 (chain A) in PDB entry 2VWU
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 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A VAL* 4.1 36.3 - - + +
622A GLY 3.8 6.7 - - - +
623A ALA* 4.6 0.7 - - - +
627A GLY* 1.3 78.2 - - - -
629A VAL* 1.3 63.1 + - - +
630A CYS* 4.2 10.2 - - - -
646A ILE 4.4 0.2 - - - -
647A LYS* 3.5 5.4 - - - +
648A THR* 3.3 41.9 + - - +
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Residues in contact with VAL 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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620A VAL* 3.8 2.1 - - - +
621A ILE* 2.8 37.4 + - + +
622A GLY* 3.0 27.5 + - - +
623A ALA 4.1 2.0 - - - +
624A GLY* 3.9 21.8 - - - +
628A GLU* 1.3 79.6 - - - +
630A CYS* 1.3 62.2 + - - +
645A ALA* 4.6 0.7 - - + -
646A ILE 3.4 7.9 - - - +
647A LYS* 4.1 17.7 - - + -
1888A 7X1 4.0 48.9 - - + +
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Residues in contact with CYS 630 (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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617A ILE* 3.8 31.4 - - + -
619A GLU 3.3 10.1 - - - +
620A VAL* 4.1 23.3 - - - -
621A ILE* 4.2 5.6 - - - +
628A GLU* 4.3 17.0 - - - -
629A VAL* 1.3 80.1 - - - +
631A ARG* 1.3 61.4 + - - +
645A ALA* 3.3 7.8 - - - +
646A ILE* 2.7 47.6 + - + +
648A THR* 4.8 10.1 - - - -
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Residues in contact with ARG 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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617A ILE* 3.8 0.5 - - - -
618A GLU* 2.8 58.2 + - - +
619A GLU* 2.8 38.1 + - - +
621A ILE* 3.8 13.3 - - + +
630A CYS* 1.3 76.7 - - - +
632A GLY* 1.3 57.1 + - - +
633A ARG* 4.5 12.1 - - - +
643A CYS* 4.2 16.0 - - - -
644A VAL 3.5 6.3 - - - +
646A ILE* 4.5 1.6 - - - -
695A PHE* 3.7 43.1 - - + -
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Residues in contact with GLY 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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616A LYS 3.0 14.1 - - - -
618A GLU* 3.9 7.0 - - - -
631A ARG* 1.3 78.9 - - - +
633A ARG* 1.3 65.4 + - - +
643A CYS* 3.7 9.4 - - - -
644A VAL* 2.8 36.1 + - - -
646A ILE* 3.9 10.0 - - - +
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Residues in contact with ARG 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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614A TYR 3.4 3.8 - - - +
615A VAL* 3.5 3.1 - - - +
616A LYS* 2.8 45.3 + - + +
618A GLU* 3.9 26.6 + - - +
631A ARG* 4.5 11.1 - - - +
632A GLY* 1.3 79.0 - - - +
634A LEU* 1.3 58.2 + - - +
635A LYS* 5.5 0.4 - - - -
641A GLU* 3.7 37.4 + - + +
642A SER 3.5 5.2 - - - +
643A CYS* 5.2 5.6 - - + -
644A VAL* 4.0 3.3 - - - +
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Residues in contact with LEU 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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610A ILE* 4.0 31.0 - - + -
614A TYR* 3.4 24.9 - - + +
615A VAL* 4.9 0.2 - - - +
633A ARG* 1.3 73.6 - - - +
635A LYS* 1.3 66.3 + - - +
636A ALA* 4.2 7.2 - - + +
640A LYS 4.3 1.0 - - - +
641A GLU* 3.3 2.9 - - - -
642A SER* 2.8 44.2 + - - +
644A VAL* 3.8 21.9 - - + +
680A GLU* 3.8 36.8 - - + +
692A LEU* 4.3 7.6 - - + -
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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