Contacts of the helix formed by residues 258 - 266 (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 ASP 258 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E GLU* 3.5 19.5 - - - +
40E ASN* 4.9 4.6 - - - +
214E LYS* 2.5 34.9 + - - -
106F HIS* 3.3 22.5 + - + -
110F ARG* 3.4 37.1 + - - +
256F ARG* 3.4 6.6 + - - +
257F TYR* 1.3 75.6 - - - +
259F ARG* 1.3 66.7 + - - +
260F ASP* 3.1 3.8 + - - +
261F ASP* 3.2 13.6 + - - +
262F ASP* 2.9 18.4 + - - +
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Residues in contact with ARG 259 (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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37E GLU* 5.1 2.8 + - - -
38E GLY* 2.7 33.6 + - - +
39E CYS* 3.9 17.9 - - + +
214E LYS* 4.2 2.9 - - - +
172F GLU* 5.1 2.0 + - - -
174F PHE* 4.0 26.3 - - - +
175F TYR* 2.5 54.4 + - - +
176F LEU* 3.5 16.0 + - - +
178F GLY* 4.1 8.9 - - - +
257F TYR 3.7 1.2 + - - -
258F ASP* 1.3 75.9 + - - +
260F ASP* 1.3 63.5 + - - +
262F ASP* 3.1 12.9 + - - +
263F MET* 3.0 59.0 + - + +
693F PRO* 3.9 11.9 - - + -
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Residues in contact with ASP 260 (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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41E GLU* 3.2 25.3 - - - +
214E LYS* 3.3 27.8 + - + +
110F ARG* 5.5 4.5 - - - +
258F ASP* 3.2 3.2 - - + +
259F ARG* 1.3 76.1 - - - +
261F ASP* 1.3 64.8 - - - +
263F MET* 3.5 2.8 + - - +
264F VAL* 3.1 27.9 + - - +
691F HIS* 3.1 38.7 + - + +
692F ALA* 3.6 8.7 - - - +
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Residues in contact with ASP 261 (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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36F ALA* 5.4 3.8 - - - +
37F PHE* 5.4 5.6 + - - +
39F LEU* 3.9 18.1 - - - +
110F ARG* 3.6 37.3 + - - -
257F TYR* 4.5 7.9 - - + -
258F ASP* 3.2 18.9 + - - +
260F ASP* 1.3 74.7 - - - +
262F ASP* 1.3 58.8 + - - +
264F VAL* 4.4 4.7 - - - +
265F ILE* 2.7 55.2 + - + +
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Residues in contact with ASP 262 (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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172F GLU* 4.6 4.5 - - - +
175F TYR* 2.7 35.9 + - - -
178F GLY* 3.7 4.4 - - - -
179F GLN* 3.0 37.4 + - - +
257F TYR* 3.4 17.5 - - + +
258F ASP 2.9 11.9 + - - +
259F ARG* 3.1 20.0 - - - +
261F ASP* 1.3 76.5 - - - +
263F MET* 1.3 57.2 + - + +
266F THR* 2.5 40.2 + - - -
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Residues in contact with MET 263 (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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172F GLU* 4.1 27.1 - - - +
174F PHE* 3.2 34.3 - - + -
259F ARG* 3.0 30.3 + - + +
260F ASP 4.0 0.4 - - - +
262F ASP* 1.3 75.3 - - + +
264F VAL* 1.3 58.4 + - - +
268F LYS* 3.0 23.1 + - - +
680F LEU* 6.4 0.2 - - - -
688F LEU* 3.0 25.2 - - + +
690F THR 4.4 4.5 - - - +
691F HIS* 3.5 32.8 - - - +
692F ALA* 3.3 28.0 - - - -
696F TYR* 4.7 6.7 - - + -
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Residues in contact with VAL 264 (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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39F LEU* 4.1 14.4 - - + -
93F PHE* 3.3 6.8 - - - -
94F VAL* 3.9 7.0 - - + +
95F GLY* 3.4 28.9 - - - -
260F ASP 3.1 18.9 + - - +
261F ASP* 3.1 5.1 + - - +
263F MET* 1.3 78.6 - - - +
265F ILE* 1.3 63.6 + - - +
266F THR 3.6 0.2 - - - -
336F GLN* 2.8 26.0 + - - +
688F LEU* 4.8 11.0 - - + +
691F HIS* 3.9 24.7 - - + +
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Residues in contact with ILE 265 (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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37F PHE* 4.1 8.7 - - + -
39F LEU* 3.8 23.6 - - + -
93F PHE* 3.7 19.1 - - + -
95F GLY 3.7 16.2 - - - +
97F PRO* 4.4 19.1 - - + -
237F HIS* 5.5 7.6 - - + -
257F TYR* 3.9 41.3 - - + +
261F ASP* 2.7 40.6 + - + +
264F VAL* 1.3 74.9 - - - +
266F THR* 1.3 63.6 + - + +
336F GLN* 4.2 2.9 - - - +
337F SER 5.5 1.2 + - - -
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Residues in contact with THR 266 (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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175F TYR* 4.0 7.0 - - - +
179F GLN* 4.1 6.3 - - + -
234F GLN* 3.4 23.1 - - + +
257F TYR* 3.9 25.6 - - + -
262F ASP* 2.5 35.4 + - - +
265F ILE* 1.3 79.6 - - + +
267F GLY* 1.3 58.1 - - - +
268F LYS* 2.9 29.8 + - - -
336F GLN* 3.5 7.6 - - - +
337F SER 5.6 0.2 - - - -
1779F CA 2.9 22.7 - - - -
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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