Contacts of the strand formed by residues 632 - 638 (chain B) in PDB entry 2NUP
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 GLY 632 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B GLN* 3.7 8.6 + - - -
505B VAL* 3.6 7.2 - - - -
627B MET* 3.2 11.7 - - - +
631B GLY* 1.3 74.4 - - - -
633B ARG* 1.3 59.7 + - - -
684B GLN 2.9 10.8 + - - +
685B VAL* 3.5 0.4 - - - +
686B ALA 3.1 25.5 + - - -
745B PHE* 4.0 12.3 - - - -
778B ASN* 3.8 9.3 - - - +
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Residues in contact with ARG 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B VAL 2.9 15.1 + - - +
506B TYR* 3.6 35.1 - - + -
507B LEU 2.9 26.7 + - - +
508B PHE* 4.2 9.9 - - - -
536B LEU* 5.5 3.0 - - - +
537B PRO* 6.2 2.6 - - - +
627B MET* 3.4 4.5 - - - +
632B GLY* 1.3 71.7 - - - -
634B MET* 1.3 62.7 + - - +
635B SER* 3.9 4.0 + - - -
686B ALA 3.9 1.8 - - - +
688B ASP* 3.2 26.9 - - - +
738B TYR* 3.2 53.2 + - - +
739B LEU* 4.2 17.4 + - - +
741B ARG* 5.1 6.2 - - - +
743B ILE* 4.2 20.2 - - + +
745B PHE* 4.2 1.2 - - + -
778B ASN* 3.2 23.6 - - - +
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Residues in contact with MET 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B LEU* 3.4 9.6 - - + +
509B VAL* 4.1 6.5 - - + -
620B LEU* 3.1 41.1 - - + +
623B ALA* 3.2 35.0 - - + +
624B PHE* 4.7 1.3 - - - -
627B MET* 3.8 15.5 - - - +
632B GLY 4.0 0.2 + - - -
633B ARG* 1.3 74.6 - - - +
635B SER* 1.3 60.3 + - - +
636B VAL* 3.2 16.2 + - + -
676B LEU* 6.3 0.2 - - + -
680B CYS* 5.3 2.7 - - - -
685B VAL* 4.6 4.0 - - + -
686B ALA 3.1 15.8 + - - +
687B VAL* 3.3 29.1 - - + +
688B ASP 2.9 26.2 + - - -
705B ILE* 5.0 1.1 - - + -
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Residues in contact with SER 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU 3.0 6.1 + - - -
508B PHE* 3.6 23.1 - - - -
509B VAL* 2.7 34.8 + - - +
633B ARG* 3.9 6.5 + - - -
634B MET* 1.3 70.7 - - - +
636B VAL* 1.3 57.6 + - - +
637B PHE* 3.5 22.5 - - - -
688B ASP* 3.9 4.5 - - - -
690B PHE* 4.1 4.0 - - - -
738B TYR* 2.8 32.7 + - - -
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Residues in contact with VAL 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B VAL* 3.5 13.7 - - + +
549B PHE* 5.2 0.7 - - + -
616B LEU* 3.9 18.4 - - + -
620B LEU* 3.5 19.1 - - + -
634B MET* 3.2 40.8 - - + -
635B SER* 1.3 76.5 - - - +
637B PHE* 1.3 64.8 + - - +
638B GLN* 4.0 0.8 + - + +
687B VAL* 3.8 8.5 - - + -
688B ASP 2.9 11.6 + - - +
689B LEU* 4.1 16.2 - - + -
690B PHE* 2.8 34.5 + - - +
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Residues in contact with PHE 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B PHE* 4.2 5.8 - + - -
509B VAL 2.8 14.4 + - - +
510B PHE* 3.6 26.5 - + + -
511B ASP* 3.1 27.2 + - - +
521B TYR* 3.5 37.2 + + + +
525B VAL* 3.7 29.4 - - + -
549B PHE* 4.6 1.0 - - - -
635B SER* 3.5 27.6 - - - -
636B VAL* 1.3 76.7 - - - +
638B GLN* 1.3 60.2 + - - +
690B PHE* 3.4 45.5 - + + +
692B LEU* 4.7 5.2 - - + -
731B LEU* 5.1 3.8 - - + -
735B LEU* 4.3 14.1 - - + -
738B TYR* 5.6 0.2 - + - -
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Residues in contact with GLN 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B ASP* 2.7 28.0 + - - -
549B PHE* 3.4 19.4 - - - -
614B SER* 3.4 24.4 + - - -
616B LEU* 3.4 34.4 - - + +
636B VAL* 4.0 1.4 - - + -
637B PHE* 1.3 75.0 - - - +
639B THR* 1.3 65.4 + - - +
640B GLN* 3.2 31.7 + - - +
642B PRO* 5.3 0.4 - - - -
689B LEU* 4.8 10.1 - - + -
690B PHE 2.9 9.8 + - - +
691B LEU* 3.2 17.2 - - + +
692B LEU* 3.0 23.0 + - - +
702B LEU* 5.0 2.9 - - + -
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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