Contacts of the helix formed by residues 257 - 272 (chain A) in PDB entry 4GWR
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 THR 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.7 7.6 - - - -
255A GLY* 3.4 1.6 - - - -
256A ARG* 1.3 83.0 - - - +
258A ARG* 1.3 64.6 + - - +
259A SER* 3.5 8.5 + - - -
260A ASP* 3.0 37.6 + - - +
261A ILE* 3.1 21.3 + - - +
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 3.5 18.0 + - - +
202A ALA* 3.0 40.4 + - + +
203A ALA* 4.0 23.8 - - - +
205A SER* 4.2 7.9 - - - -
206A GLU* 2.9 42.6 + - - +
256A ARG 4.5 0.2 - - - -
257A THR* 1.3 72.6 - - - +
259A SER* 1.3 59.2 + - - +
260A ASP 3.3 0.2 + - - -
261A ILE* 3.4 0.9 + - - +
262A VAL* 2.8 35.6 + - + +
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Residues in contact with SER 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 5.7 0.4 - - - -
257A THR* 3.2 9.2 + - - -
258A ARG* 1.3 79.3 - - - +
260A ASP* 1.3 57.8 + - - +
262A VAL* 4.7 3.8 - - - -
263A SER* 2.9 31.0 + - - -
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Residues in contact with ASP 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A TYR* 3.3 19.8 + - - +
254A GLY* 5.2 1.6 - - - -
255A GLY* 3.2 31.7 + - - +
257A THR* 3.0 31.7 + - - +
259A SER* 1.3 79.8 - - - +
261A ILE* 1.3 63.0 + - - +
263A SER* 3.4 6.7 + - - -
264A ARG* 3.1 19.8 + - - +
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A MET* 4.2 12.9 - - + +
196A LEU* 4.9 1.6 - - + -
199A GLU 4.4 5.8 - - - +
200A TRP* 3.9 28.0 - - + -
203A ALA* 3.6 34.1 - - + -
207A VAL* 4.9 3.6 - - + -
217A LEU* 4.0 15.9 - - + -
240A ILE* 5.9 0.4 - - + -
252A TYR* 3.7 21.8 - - + +
255A GLY 3.8 3.8 - - - +
256A ARG* 3.6 30.7 - - + +
257A THR 3.1 8.3 + - - +
258A ARG 4.0 0.4 - - - +
260A ASP* 1.3 81.4 - - - +
262A VAL* 1.3 57.9 + - - +
264A ARG* 3.2 5.4 + - - +
265A ALA* 2.9 25.5 + - - +
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ALA* 4.2 4.7 - - - +
206A GLU* 3.4 49.6 - - + +
207A VAL* 4.0 15.7 - - + -
210A GLN* 4.6 8.7 - - + -
258A ARG* 2.8 28.7 + - + +
259A SER* 4.2 3.6 - - - +
261A ILE* 1.3 68.9 - - - +
263A SER* 1.3 60.5 + - - +
265A ALA* 3.2 6.6 + - - +
266A LEU* 2.9 49.1 + - + +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A SER 2.9 20.7 + - - -
260A ASP* 3.4 8.3 - - - -
261A ILE 3.3 0.2 - - - -
262A VAL* 1.3 78.4 - - - +
264A ARG* 1.3 64.2 + - - +
266A LEU* 3.3 7.7 + - - +
267A ASP* 3.1 23.4 + - - +
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A MET* 3.9 6.7 - - + -
242A ILE* 3.4 36.9 - - + +
244A GLN* 5.6 0.6 + - - -
250A VAL* 3.8 19.2 - - - +
251A ASP 5.5 1.6 + - - -
252A TYR* 3.7 29.9 - - + +
253A ASP* 5.7 3.9 + - - -
260A ASP 3.1 4.7 + - - +
261A ILE 3.2 7.4 + - - +
263A SER* 1.3 78.4 - - - +
265A ALA* 1.3 63.3 + - - +
267A ASP* 2.7 39.6 + - - +
268A LEU* 3.0 54.1 + - + +
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A MET* 4.1 17.2 - - - -
207A VAL* 3.5 39.9 - - + -
211A THR* 5.2 2.2 - - + -
215A VAL* 3.6 8.9 - - + +
261A ILE 2.9 11.2 + - - +
262A VAL* 3.2 8.5 + - + +
264A ARG* 1.3 77.2 - - - +
266A LEU* 1.3 58.2 + - + +
268A LEU* 3.3 7.4 + - - +
269A PHE* 2.9 26.9 + - - +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLN* 3.8 42.6 - - + +
211A THR* 4.4 11.0 - - + -
262A VAL* 2.9 33.1 + - + +
263A SER* 3.3 6.9 + - - +
265A ALA* 1.3 74.9 - - + +
267A ASP* 1.3 60.4 + - - +
269A PHE* 3.5 13.6 - - + +
270A SER* 2.8 31.5 + - - -
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Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A SER* 3.1 13.5 + - - +
264A ARG* 2.7 41.3 + - - +
266A LEU* 1.3 74.3 - - - +
268A LEU* 1.3 61.5 + - - +
270A SER* 3.4 14.8 + - - -
271A ASP* 3.5 14.9 + - - +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 3.7 21.0 - - + +
182A MET* 4.1 20.4 - - - -
215A VAL* 4.4 3.4 - - + -
242A ILE* 3.6 29.8 - - + -
244A GLN* 3.5 33.9 + - - +
264A ARG* 3.0 49.0 + - + +
265A ALA* 3.5 7.0 - - - +
267A ASP* 1.3 72.8 - - - +
269A PHE* 1.3 65.7 + - - +
271A ASP* 3.5 3.6 + - - +
272A ASN* 3.1 27.6 + - - +
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Residues in contact with PHE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLN 5.0 5.8 - - - -
211A THR* 3.8 29.4 - - + -
214A LYS* 3.6 42.0 - - + -
215A VAL* 4.0 9.9 - - + -
265A ALA 2.9 16.4 + - - +
266A LEU* 3.5 18.6 - - + +
268A LEU* 1.3 73.8 - - - +
270A SER* 1.3 72.3 + - - +
271A ASP 3.1 0.9 + - - -
272A ASN* 3.1 18.0 + - - -
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU 2.8 17.0 + - - -
267A ASP* 3.7 8.7 - - - -
268A LEU 3.3 0.2 - - - -
269A PHE* 1.3 84.4 - - - +
271A ASP* 1.3 59.0 + - - +
272A ASN 3.8 1.0 + - - -
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLN* 5.2 5.8 + - - +
267A ASP* 3.5 12.9 + - - +
268A LEU* 3.5 3.3 + - - +
269A PHE 3.2 0.6 - - - -
270A SER* 1.3 77.7 - - - +
272A ASN* 1.3 59.6 + - - +
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Residues in contact with ASN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU 5.0 4.8 - - - +
180A VAL* 3.6 24.5 - - + -
214A LYS* 4.1 26.5 - - + +
244A GLN* 4.2 8.3 - - - +
268A LEU 3.1 18.5 + - - +
269A PHE* 3.1 14.0 + - - +
270A SER 3.5 1.3 - - - -
271A ASP* 1.3 80.4 - - - +
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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