Contacts of the strand formed by residues 634 - 642 (chain A) in PDB entry 2V5I
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 ALA 634 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623A SER* 4.0 15.7 - - - +
624A HIS 3.2 17.0 - - - +
625A LEU* 4.3 2.5 - - - -
626A ASN* 3.3 8.7 - - - +
633A SER* 1.3 75.1 + - - +
635A TRP* 1.3 60.4 + - - +
636A THR* 5.6 0.9 - - - +
654A ASN* 3.0 25.9 + - - +
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Residues in contact with TRP 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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622A ARG 3.9 0.3 - - - +
623A SER* 3.3 3.9 - - - -
624A HIS* 2.9 83.3 + + + +
625A LEU 4.2 5.3 + - - -
626A ASN* 3.3 24.1 + - - -
634A ALA* 1.3 74.4 - - - +
636A THR* 1.3 66.4 + - - +
637A GLU* 3.6 28.7 - - + -
652A LYS* 3.8 39.5 - - + -
653A VAL 3.2 16.8 - - - +
655A ARG* 3.4 40.0 - - + +
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Residues in contact with THR 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A LEU* 3.9 23.6 - - + -
622A ARG 3.3 11.2 - - - +
623A SER* 4.6 8.5 + - - -
634A ALA* 5.6 0.7 - - - +
635A TRP* 1.3 76.4 + - - +
637A GLU* 1.3 65.1 + - - +
651A LEU* 3.9 0.3 - - - +
652A LYS* 3.4 1.7 - - - -
653A VAL* 2.8 45.5 + - + +
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Residues in contact with GLU 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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620A ALA 3.6 0.7 - - - +
621A LEU* 3.4 8.7 - - - +
622A ARG* 2.8 59.4 + - + +
624A HIS* 2.7 27.8 + - - +
635A TRP* 3.6 24.3 - - + -
636A THR* 1.3 77.2 - - - +
638A LEU* 1.3 59.6 + - - +
639A THR* 3.4 16.8 - - + +
647A ASN* 5.2 2.7 - - - +
650A SER* 2.5 29.8 + - - +
651A LEU* 3.1 15.0 - - - +
652A LYS* 4.5 1.2 - - - -
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Residues in contact with LEU 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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607A LEU* 6.5 0.4 - - + -
620A ALA 3.4 10.1 - - - +
621A LEU* 4.6 19.1 - - + -
637A GLU* 1.3 72.7 - - - +
639A THR* 1.3 61.9 + - - +
649A VAL 4.1 0.3 - - - +
650A SER* 3.5 0.9 - - - -
651A LEU* 2.9 51.2 + - + +
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Residues in contact with THR 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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607A LEU* 5.7 0.2 - - - +
619A GLY* 3.2 15.6 - - - -
620A ALA* 2.9 23.6 + - - +
622A ARG* 4.7 2.5 - - - -
637A GLU* 3.4 39.5 - - + +
638A LEU* 1.3 80.2 - - - +
640A ALA* 1.3 63.2 + - - +
647A ASN* 2.6 41.3 + - + +
649A VAL 3.2 9.6 - - - -
650A SER* 4.0 6.3 - - - +
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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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618A SER 3.6 8.3 - - - +
619A GLY* 4.1 0.4 - - - -
639A THR* 1.3 76.1 - - - +
641A LEU* 1.3 66.2 + - - +
642A SER 3.7 0.2 + - - -
647A ASN 4.4 3.6 - - - -
648A ALA 3.2 8.3 + - - -
649A VAL* 2.9 42.6 + - + +
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Residues in contact with LEU 641 (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 LEU* 4.0 31.2 - - + -
613A SER* 5.4 1.8 - - - -
616A LEU* 4.4 19.5 - - + +
617A ASP 3.7 20.4 - - - +
618A SER* 2.9 22.3 + - - +
619A GLY* 4.6 0.2 - - - -
640A ALA* 1.3 76.9 - - - +
642A SER* 1.3 63.2 + - - +
644A SER* 3.7 13.0 - - - +
645A THR 3.5 40.2 - - - +
646A PRO* 3.6 7.6 - - + -
647A ASN 4.6 2.4 - - - +
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Residues in contact with SER 642 (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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641A LEU* 1.3 77.5 - - - +
643A GLY* 1.3 65.2 + - - +
644A SER 3.1 2.0 - - - +
645A THR* 2.9 31.2 + - - +
648A ALA* 3.7 17.8 - - - +
649A VAL* 4.1 16.1 - - - +
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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