Contacts of the helix formed by residues 703 - 708 (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 703 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689B LEU* 4.5 3.4 - - - -
699B LEU* 2.7 34.9 + - - +
700B ALA 5.3 0.2 - - - -
702B LEU* 1.3 74.1 - - - +
704B CYS* 1.3 56.7 + - - +
706B SER* 2.8 22.7 + - - -
707B ARG* 2.9 23.4 + - - +
713B VAL* 4.9 8.5 - - - +
928B CYS* 4.9 5.6 - - - -
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Residues in contact with CYS 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B PRO* 3.8 30.5 - - - -
670B THR 5.6 0.7 - - - -
673B TYR* 3.7 2.0 - - + -
674B LYS* 3.8 28.3 - - + +
677B ALA* 3.4 9.0 - - - +
700B ALA 4.1 5.1 + - - -
701B SER 3.0 16.1 + - - +
703B GLY* 1.3 76.9 - - - +
705B ILE* 1.3 61.3 + - - +
706B SER 3.3 0.5 + - - -
707B ARG* 4.3 12.3 - - - -
708B TYR* 3.3 36.1 + - + -
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Residues in contact with ILE 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B LEU* 4.1 16.4 - - + -
634B MET* 5.2 0.9 - - + -
673B TYR* 3.6 25.0 + - + +
676B LEU* 3.8 36.6 - - + -
677B ALA* 3.6 10.7 - - - +
680B CYS* 5.0 0.9 - - - -
687B VAL* 3.6 33.5 - - + +
689B LEU* 4.2 15.7 - - + -
702B LEU* 2.9 25.4 + - + +
703B GLY 3.0 0.8 + - - -
704B CYS* 1.3 79.0 - - - +
706B SER* 1.3 68.8 + - - +
709B SER* 2.8 22.9 + - - -
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Residues in contact with SER 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B VAL 2.5 25.0 + - - -
689B LEU* 3.2 25.7 + - - +
703B GLY 2.8 8.9 + - - -
705B ILE* 1.3 84.3 - - - +
707B ARG* 1.3 64.8 + - - -
708B TYR 3.3 0.4 - - - -
709B SER* 3.3 3.7 + - - -
710B ALA 3.4 0.2 + - - -
711B GLY 2.9 25.7 + - - -
712B SER 3.5 19.4 + - - -
713B VAL* 4.1 10.1 - - - -
765B ASN* 3.8 4.1 + - - -
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Residues in contact with ARG 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B GLY* 2.9 23.3 + - - +
704B CYS* 4.2 12.1 - - - +
706B SER* 1.3 76.9 - - - +
708B TYR* 1.3 71.2 + - + +
713B VAL* 5.5 1.3 - - + -
764B GLY 4.1 2.9 - - - +
765B ASN* 3.2 26.0 - - - +
766B PHE 3.0 26.5 + - - +
852B VAL* 4.5 8.9 - - - +
856B MET* 5.1 12.7 - - - +
924B ILE* 3.9 15.0 + - - +
927B MET* 4.0 10.4 - - - +
928B CYS* 3.2 50.2 - - - +
931B LYS* 4.4 21.8 - - - +
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Residues in contact with TYR 708 (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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674B LYS* 3.9 32.4 - - + +
677B ALA* 3.8 18.6 - - + +
678B LEU* 3.9 20.7 - - + +
681B SER* 4.0 9.4 - - - -
704B CYS* 3.3 32.2 + - + -
707B ARG* 1.3 88.5 - - + +
709B SER* 1.3 57.7 + - - +
710B ALA 3.5 0.9 - - - -
766B PHE 3.7 17.9 - - - +
767B PHE* 3.9 23.3 - + - +
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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