Contacts of the helix formed by residues 258 - 266 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C GLU* 4.4 7.0 - - - +
40C ASN* 5.4 0.7 - - - +
214C LYS* 2.4 34.8 + - - -
106D HIS* 3.5 18.9 + - + -
110D ARG* 3.0 44.9 + - - +
256D ARG* 3.5 12.3 + - - +
257D TYR* 1.3 74.9 - - - +
259D ARG* 1.3 54.0 + - - +
260D ASP* 3.1 3.4 - - - +
261D ASP* 3.1 11.8 + - + +
262D ASP* 2.6 33.7 + - - +
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Residues in contact with ARG 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLU* 5.6 1.6 + - - -
38C GLY* 2.9 28.9 + - - -
39C CYS* 4.3 15.6 + - + +
214C LYS* 4.3 6.9 - - - +
172D GLU* 5.4 1.2 + - - -
174D PHE* 3.8 35.8 - - - +
175D TYR* 2.4 45.1 + - - -
176D LEU* 3.3 22.6 + - - +
178D GLY* 4.3 9.9 - - - +
257D TYR 3.8 1.2 + - - -
258D ASP* 1.3 75.9 + - - +
260D ASP* 1.3 56.9 + - - +
262D ASP* 3.1 11.4 + - - +
263D MET* 2.9 57.5 + - + +
691D HIS 4.1 1.6 - - - +
692D ALA* 5.6 1.3 - - + -
693D PRO* 4.1 9.6 - - + -
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Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 3.8 9.9 - - - +
214C LYS* 3.2 23.1 + - - +
110D ARG* 3.1 28.6 + - - +
114D ARG* 5.3 2.1 + - - -
258D ASP* 3.1 8.0 - - - +
259D ARG* 1.3 71.6 - - - +
261D ASP* 1.3 68.9 + - - +
263D MET* 3.2 2.1 + - - +
264D VAL* 2.9 32.6 + - + +
691D HIS* 3.5 34.4 + - + +
692D ALA* 4.7 1.0 - - - +
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Residues in contact with ASP 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ALA* 5.3 4.0 - - - +
37D PHE* 5.0 9.7 + - - +
39D LEU* 3.9 16.5 - - - +
110D ARG* 3.5 38.3 + - - -
257D TYR* 4.4 9.6 - - + -
258D ASP* 3.1 16.5 + - - +
260D ASP* 1.3 80.6 - - - +
262D ASP* 1.3 64.4 + - - +
264D VAL* 4.6 3.4 - - - +
265D ILE* 2.9 48.8 + - + +
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Residues in contact with ASP 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLU* 4.4 5.5 - - - +
175D TYR* 2.6 35.9 + - - -
178D GLY* 3.7 3.7 - - - -
179D GLN* 3.2 35.1 + - - +
257D TYR* 3.9 14.9 - - + +
258D ASP 2.6 17.8 + - - +
259D ARG* 3.3 20.5 + - - +
261D ASP* 1.3 72.6 - - - +
263D MET* 1.3 56.5 + - + +
266D THR* 2.6 42.8 + - - +
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Residues in contact with MET 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLU* 3.9 31.2 - - - +
174D PHE* 3.2 33.0 - - + -
259D ARG* 2.9 37.1 + - + +
260D ASP 3.9 0.7 - - - +
262D ASP* 1.3 73.0 - - + +
264D VAL* 1.3 61.8 + - - +
268D LYS* 2.6 29.6 + - - +
336D GLN* 4.3 0.3 + - - -
688D LEU* 3.2 12.7 - - + +
690D THR 4.3 5.8 - - - +
691D HIS* 3.5 27.4 - - - +
692D ALA* 3.3 31.0 - - - -
696D TYR* 4.7 5.4 - - - -
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Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.5 9.0 - - + -
93D PHE* 3.3 5.2 - - - -
94D VAL* 3.4 25.1 - - + +
95D GLY* 3.5 13.5 - - - -
260D ASP* 2.9 23.1 + - + +
261D ASP* 4.1 3.8 - - - +
263D MET* 1.3 78.7 - - - +
265D ILE* 1.3 60.8 + - - +
336D GLN* 2.7 34.6 + - - +
688D LEU* 4.4 10.3 - - + +
691D HIS* 3.8 25.4 - - + +
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Residues in contact with ILE 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.1 7.4 - - + -
39D LEU* 3.8 25.8 - - + -
93D PHE* 3.8 18.3 - - + -
95D GLY 3.5 15.3 - - - +
97D PRO* 4.1 22.0 - - + -
234D GLN* 4.8 1.4 - - - +
237D HIS* 5.6 7.6 - - + +
257D TYR* 3.9 43.5 - - + +
261D ASP* 2.9 31.2 + - + +
264D VAL* 1.3 80.4 - - - +
266D THR* 1.3 64.0 + - + +
336D GLN* 4.4 1.9 - - - +
337D SER 5.4 1.2 + - - -
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Residues in contact with THR 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLU* 4.0 3.6 + - - -
175D TYR* 4.1 2.5 - - - +
179D GLN* 4.0 12.1 - - + -
234D GLN* 3.7 22.9 - - + +
257D TYR* 4.0 24.5 - - + -
262D ASP* 2.6 37.7 + - - +
265D ILE* 1.3 81.5 - - + +
267D GLY* 1.3 59.9 + - - +
268D LYS* 3.0 21.0 + - - -
336D GLN* 3.2 11.9 - - - +
337D SER 5.5 0.4 - - - -
1779D CA 2.9 22.5 - - - -
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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