Contacts of the strand formed by residues 757 - 763 (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 LEU 757 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B ILE* 3.9 20.9 - - + -
407B LEU* 4.4 17.7 - - + -
753B CYS* 3.0 29.9 - - - +
754B THR* 3.0 12.6 + - - +
755B LYS* 5.3 0.3 - - - -
756B GLY* 1.3 81.0 + - - +
758B SER* 1.3 59.8 + - - +
789B MET* 4.6 4.9 - - + -
790B SER 3.9 6.3 - - - +
791B VAL* 4.5 7.4 - - + -
795B LEU* 4.3 15.9 - - + -
801B VAL* 3.8 26.2 - - + -
803B PHE* 3.3 37.0 - - + -
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Residues in contact with SER 758 (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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753B CYS* 4.7 0.4 - - - -
756B GLY 3.9 0.4 + - - -
757B LEU* 1.3 75.4 - - - +
759B ILE* 1.3 70.3 + - - +
760B HIS* 3.7 3.0 + - - +
789B MET* 3.2 5.8 - - - +
790B SER* 3.0 38.2 + - - +
792B GLU* 3.4 34.1 + - - -
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Residues in contact with ILE 759 (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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409B LEU* 5.3 0.9 - - + -
751B ILE* 3.7 46.9 - - + +
753B CYS* 3.9 12.5 - - - -
758B SER* 1.3 79.4 + - - +
760B HIS* 1.3 60.9 + - - +
761B THR 4.2 2.7 - - - +
762B PHE* 3.8 26.6 - - + -
771B THR* 4.3 15.9 - - + +
772B ASP* 3.9 9.9 - - - +
787B VAL* 3.0 39.7 - - + -
788B GLN 3.5 4.0 - - - +
789B MET* 3.7 17.7 - - + +
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Residues in contact with HIS 760 (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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758B SER* 4.1 1.8 + - - +
759B ILE* 1.3 75.8 - - - +
761B THR* 1.3 84.8 + - - +
762B PHE* 4.9 5.7 - - - -
771B THR* 6.2 0.2 - - - -
788B GLN* 2.7 56.6 + - + +
789B MET 3.5 24.4 - - - -
790B SER* 3.9 16.1 + - - +
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Residues in contact with THR 761 (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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759B ILE 3.9 0.4 - - - -
760B HIS* 1.3 97.2 + - - +
762B PHE* 1.3 71.0 + - - +
763B HIS* 3.4 29.9 - - + +
787B VAL* 3.5 8.0 - - - +
788B GLN* 3.0 39.0 + - - +
853B ASP* 4.5 6.3 - - - +
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Residues in contact with PHE 762 (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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751B ILE* 4.5 4.3 - - + -
759B ILE* 3.8 20.9 - - + -
760B HIS 4.9 2.9 - - - -
761B THR* 1.3 84.3 - - - +
763B HIS* 1.3 71.5 + - - +
764B GLY 4.4 0.5 + - - -
766B PHE* 3.6 20.6 - - + -
768B VAL* 4.2 18.2 - - + -
771B THR* 4.2 11.9 - - + -
772B ASP* 3.0 46.7 - - - -
774B LEU* 3.5 34.8 - - + -
786B ALA 3.8 2.2 - - - +
787B VAL* 3.8 15.7 - - + -
853B ASP* 5.0 0.9 - - - +
931B LYS* 4.1 3.8 + - - -
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Residues in contact with HIS 763 (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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761B THR* 3.4 29.5 - - + +
762B PHE* 1.3 75.7 + - - +
764B GLY* 1.3 58.2 + - - +
766B PHE* 3.6 7.9 - - - -
785B TYR* 3.4 6.9 - - - -
786B ALA* 2.7 59.3 + - + +
787B VAL* 4.3 1.1 - - - -
788B GLN* 4.5 4.2 + - - +
846B LEU* 4.2 17.5 - - + +
849B ASN* 3.0 38.0 - - + +
850B MET* 4.4 10.8 - - + +
853B ASP* 3.3 22.0 - - - -
931B LYS* 2.9 24.2 + - - +
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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