Contacts of the helix formed by residues 700 - 704 (chain F) in PDB entry 2W3S
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 700 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E ALA* 4.3 9.9 - - - +
133E LEU* 4.0 7.9 - - + -
139E TYR* 3.6 11.1 - - - -
356E ARG* 3.8 28.3 - - - +
358E ASP* 4.5 16.4 - - + +
698F ILE 3.3 0.6 + - - -
699F PRO* 1.3 74.4 - - - +
701F PHE* 1.3 68.6 + - - +
702F SER* 3.2 1.6 - - - +
703F ASP* 2.6 31.9 + - - +
704F ARG 4.0 0.5 + - - -
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Residues in contact with PHE 701 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E PHE* 3.8 11.0 - + - -
125E TYR* 4.6 9.0 - - + -
126E ASP* 3.1 27.8 - - - +
129E LEU* 3.8 44.6 - - + +
130E ALA* 4.4 8.0 + - - +
132E ASN 4.9 0.2 + - - -
139E TYR* 3.2 42.8 - + + +
142E ILE* 3.6 25.4 - - + -
143E LEU* 3.9 33.7 - - + -
700F ALA* 1.3 72.7 - - - +
702F SER* 1.3 58.0 + - - +
703F ASP 3.3 0.2 + - - -
704F ARG* 2.8 53.0 + - - +
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Residues in contact with SER 702 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ASP* 3.5 29.1 + - - -
130E ALA* 5.7 0.4 - - - +
357E PHE* 5.1 4.5 - - - +
358E ASP* 2.6 34.0 + - - +
458E LEU* 6.1 0.9 - - - +
641F ARG* 4.6 8.8 + - - -
700F ALA* 3.0 3.5 + - - +
701F PHE* 1.3 78.0 - - - +
703F ASP* 1.3 63.8 + - - +
704F ARG 3.0 8.1 + - - +
706F ARG* 2.9 29.7 + - - +
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Residues in contact with ASP 703 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E ARG* 3.7 23.0 - - - +
357E PHE* 5.0 12.8 + - - +
358E ASP* 5.6 1.1 + - - +
641F ARG* 6.1 3.7 - - - +
642F ILE* 4.9 12.8 + - - +
669F VAL* 5.8 1.8 - - - +
677F THR* 5.3 5.3 + - - +
699F PRO* 3.4 18.3 - - + +
700F ALA* 2.6 43.3 + - - +
702F SER* 1.3 73.0 + - - +
704F ARG* 1.3 63.0 + - - +
705F PRO* 3.5 5.7 - - - +
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Residues in contact with ARG 704 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ASP* 2.5 35.1 + - - -
138E GLY 3.7 19.1 - - - +
139E TYR* 4.0 19.1 - - + -
140E ALA* 4.3 15.0 - - - +
143E LEU* 3.7 30.1 - - - +
641F ARG* 5.9 0.3 - - - -
642F ILE 4.5 1.3 - - - +
669F VAL* 4.9 4.9 - - - +
700F ALA 4.0 1.4 + - - -
701F PHE* 2.8 38.6 + - - +
702F SER 3.2 9.2 - - - +
703F ASP* 1.3 75.4 - - - +
705F PRO* 1.4 83.0 + - + +
706F ARG* 2.8 44.1 + - - +
708F PHE* 5.0 3.8 - - + -
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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