Contacts of the helix formed by residues 258 - 266 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37G GLU* 4.6 6.3 - - - +
39G CYS 5.5 0.4 - - - -
40G ASN* 4.9 8.3 - - - +
213G THR 4.8 1.2 - - - +
214G LYS* 2.8 28.6 + - - -
106H HIS* 3.2 26.5 + - - -
110H ARG* 3.3 40.3 + - - +
256H ARG* 3.3 13.6 + - - +
257H TYR* 1.3 70.8 - - - +
259H ARG* 1.3 57.0 + - - +
260H ASP* 3.0 3.8 + - + +
261H ASP* 2.7 34.6 + - - +
262H ASP 2.9 10.4 + - - -
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Residues in contact with ARG 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G GLY* 3.1 22.8 + - - +
39G CYS* 3.9 27.9 + - + +
214G LYS* 4.3 2.4 - - - +
172H GLU* 5.4 0.4 + - - -
174H PHE* 3.1 53.6 - - + +
175H TYR* 2.5 40.8 + - - +
176H LEU* 3.0 18.6 + - - +
178H GLY* 3.9 11.8 - - - +
257H TYR 3.6 2.9 + - - -
258H ASP* 1.3 74.4 + - - +
260H ASP* 1.3 59.5 + - - +
262H ASP* 3.5 12.3 - - - +
263H MET* 3.0 61.4 + - + +
693H PRO* 4.4 3.1 - - + -
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Residues in contact with ASP 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G GLU* 3.2 22.3 - - - +
214G LYS* 3.6 24.0 + - + +
110H ARG* 5.9 2.2 - - - +
114H ARG* 5.8 5.2 - - - +
258H ASP* 3.0 3.7 - - + +
259H ARG* 1.3 79.0 - - - +
261H ASP* 1.3 69.2 + - - +
263H MET* 4.0 1.4 - - - +
264H VAL* 3.1 30.6 + - - +
691H HIS* 3.1 40.8 + - + +
692H ALA* 3.9 4.0 - - - +
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Residues in contact with ASP 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H ALA* 5.4 5.4 - - - +
37H PHE* 4.8 13.9 + - - +
39H LEU* 4.9 7.4 - - - +
110H ARG* 3.8 26.0 + - - -
114H ARG* 5.2 2.8 + - - -
257H TYR* 4.2 12.5 - - + -
258H ASP* 2.7 20.1 + - - +
260H ASP* 1.3 71.8 - - - +
262H ASP* 1.3 58.0 + - - +
264H VAL* 2.9 7.4 + - - -
265H ILE* 2.6 58.7 + - + +
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Residues in contact with ASP 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H GLU* 4.7 2.3 - - - +
175H TYR* 2.3 35.2 + - - -
178H GLY* 3.5 7.8 - - - -
179H GLN* 3.1 26.0 + - - +
257H TYR* 3.5 28.9 - - + +
258H ASP 2.9 10.5 + - - +
259H ARG* 3.5 19.9 - - - +
261H ASP* 1.3 75.2 - - - +
263H MET* 1.3 59.7 + - + +
266H THR* 2.7 43.1 + - - +
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Residues in contact with MET 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H GLU* 3.8 29.8 - - + +
174H PHE* 3.6 23.6 - - + -
259H ARG* 3.0 53.2 + - + +
261H ASP 3.2 0.2 - - - -
262H ASP* 1.3 82.9 - - + +
264H VAL* 1.3 62.0 + - - +
266H THR* 3.8 0.6 - - - +
268H LYS* 3.0 28.0 + - - +
688H LEU* 3.2 12.6 - - + +
690H THR 4.7 3.8 - - - +
691H HIS* 3.6 28.7 - - - +
692H ALA* 3.6 26.9 - - - +
693H PRO* 4.0 0.2 - - + -
696H TYR* 4.9 5.6 - - - -
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Residues in contact with VAL 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LEU* 3.7 13.2 - - + -
93H PHE* 3.8 3.5 - - - -
94H VAL* 3.7 8.7 - - + +
95H GLY* 3.3 31.0 - - - -
260H ASP* 3.1 16.0 + - + +
261H ASP* 2.9 8.3 + - - +
263H MET* 1.3 75.6 - - - +
265H ILE* 1.3 63.7 + - - +
336H GLN* 2.4 34.4 + - - +
688H LEU* 4.2 8.1 - - + +
691H HIS* 4.2 22.2 - - + -
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Residues in contact with ILE 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H PHE* 4.4 7.4 - - + -
39H LEU* 3.5 36.3 - - + -
93H PHE* 4.1 11.5 - - + -
95H GLY 3.7 10.1 - - - +
97H PRO* 4.6 15.5 - - + -
234H GLN* 5.2 0.2 - - - +
237H HIS* 5.8 6.5 - - + +
257H TYR* 3.7 38.4 - - + +
261H ASP* 2.6 45.4 + - + +
262H ASP 4.1 0.7 - - - +
264H VAL* 1.3 73.5 - - - +
266H THR* 1.3 67.4 + - + +
267H GLY 3.9 0.5 + - - -
336H GLN* 4.0 5.4 - - - +
337H SER 5.3 1.6 + - - -
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Residues in contact with THR 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H GLU* 4.0 3.3 + - - -
175H TYR* 3.7 5.4 - - - +
179H GLN* 4.0 8.3 - - + -
234H GLN* 4.1 17.3 - - + +
257H TYR* 3.7 25.8 - - + -
262H ASP* 2.7 46.1 + - - +
263H MET 3.8 0.2 - - - +
265H ILE* 1.3 78.5 - - + +
267H GLY* 1.3 59.4 + - - +
268H LYS* 3.1 23.0 + - - -
336H GLN* 3.3 5.0 - - - +
1779H CA 2.6 26.2 - - - -
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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