Contacts of the strand formed by residues 751 - 757 (chain B) in PDB entry 2W77
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 ARG 751 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B GLY 5.0 2.2 + - - -
745B TYR* 3.6 13.2 - - - -
746B ASN* 2.9 44.3 + - + +
749B ARG* 3.9 32.0 - - - +
750B SER* 1.3 78.1 - - - +
752B TRP* 1.3 71.4 + - - +
753B GLU* 3.3 33.1 + - - +
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Residues in contact with TRP 752 (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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743B MET* 3.8 28.0 - - + -
744B VAL* 3.4 25.4 - - - -
745B TYR* 3.6 43.6 - + + -
751B ARG* 1.3 86.2 - - - +
753B GLU* 1.3 66.6 + - - +
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Residues in contact with GLU 753 (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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369B PHE* 3.3 12.2 - - - -
375B ARG* 3.0 37.8 + - - +
742B GLN 3.7 0.3 - - - +
743B MET* 3.5 6.7 - - - -
744B VAL* 2.9 37.0 + - + +
746B ASN* 2.9 37.9 + - - +
751B ARG* 3.3 26.6 + - - +
752B TRP* 1.3 80.5 - - - +
754B LYS* 1.3 59.6 + - - +
755B PHE* 3.9 12.2 + - + -
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Residues in contact with LYS 754 (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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375B ARG* 3.4 17.9 + - - +
741B TRP* 4.4 19.4 - - + +
742B GLN 3.6 5.4 - - - +
743B MET* 3.9 27.1 - - + -
753B GLU* 1.3 71.1 - - - +
755B PHE* 1.3 63.4 + - - +
756B SER* 4.1 20.5 + - - +
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Residues in contact with PHE 755 (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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368B LEU* 4.1 20.6 - - + -
369B PHE* 3.6 20.0 - + - -
375B ARG* 3.0 45.8 - - + +
707B TRP* 5.1 1.9 - - - -
741B TRP* 3.1 6.6 - - - +
742B GLN 2.7 35.0 + - - +
744B VAL* 2.7 47.1 - - + -
753B GLU* 3.9 12.1 - - + -
754B LYS* 1.3 77.0 - - - +
756B SER* 1.3 61.8 + - - +
793B ILE* 3.6 31.2 - - + -
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Residues in contact with SER 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739B LYS* 5.7 6.4 - - - +
740B SER 3.9 5.4 - - - -
741B TRP* 4.1 5.5 - - - +
754B LYS* 4.1 20.9 + - - +
755B PHE* 1.3 77.9 + - - +
757B GLN* 1.3 67.2 + - - +
758B GLU* 3.9 7.9 + - - +
790B TYR* 5.3 3.8 - - - -
793B ILE* 4.7 8.8 - - - +
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Residues in contact with GLN 757 (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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707B TRP* 3.8 15.1 - - + -
738B GLY 4.5 0.7 - - - +
739B LYS* 3.5 5.8 - - - +
740B SER* 2.9 46.8 + - - +
755B PHE 4.2 0.4 + - - -
756B SER* 1.3 73.4 - - - +
758B GLU* 1.3 92.0 + - - +
760B TYR* 4.1 22.2 - - + +
787B LYS* 5.2 3.8 - - - +
788B THR 4.9 1.6 + - - -
789B TYR* 3.6 18.4 - - - +
790B TYR* 2.7 52.7 + - - +
793B ILE* 5.0 0.7 - - + -
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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