Contacts of the helix formed by residues 257 - 269 (chain A) in PDB entry 4GKH
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A PHE* 6.0 0.3 - - - +
226A TYR* 2.9 28.1 + - + +
255A ASN 3.4 3.2 + - - +
256A PRO* 1.3 69.3 - - - +
258A MSE 1.3 58.5 + - - +
259A ASN* 3.2 13.2 + - - +
260A LYS* 3.1 39.6 + - + +
261A LEU* 2.9 27.9 + - - +
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Residues in contact with MSE 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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233A TRP* 5.1 9.4 - - + -
256A PRO* 3.3 23.4 + - - +
257A ASP* 1.3 73.7 + - - +
259A ASN* 1.3 57.2 + - - +
261A LEU* 3.5 30.9 - - + +
262A GLN* 2.9 32.6 + - - +
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Residues in contact with ASN 259 (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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185A LEU* 3.4 49.5 + - - +
187A PRO 5.5 0.4 + - - -
188A PHE* 3.9 25.3 - - - +
257A ASP* 3.2 9.2 + - - +
258A MSE 1.3 80.4 - - - +
260A LYS* 1.3 59.0 + - - +
262A GLN* 3.9 4.9 - - - +
263A PHE* 2.9 27.9 + - - +
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Residues in contact with LYS 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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188A PHE* 3.4 43.5 - - + -
189A SER 4.2 6.4 + - - +
191A ASP* 3.6 20.4 + - - +
224A ASP* 2.8 25.6 + - - +
226A TYR* 3.6 35.7 - - + -
257A ASP* 3.1 34.8 + - - +
259A ASN* 1.3 74.9 - - - +
261A LEU* 1.3 67.6 + - - +
263A PHE* 3.5 4.2 + - - -
264A HIS* 2.8 35.2 + - - +
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Residues in contact with LEU 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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226A TYR* 3.8 10.4 - - + -
230A ALA* 3.6 32.7 - - + +
233A TRP* 4.0 39.5 - - + -
248A PHE* 4.3 21.5 - - + -
256A PRO* 5.3 0.9 - - + -
257A ASP 2.9 13.4 + - - +
258A MSE 3.5 39.7 - - + +
260A LYS* 1.3 78.9 - - - +
262A GLN* 1.3 62.6 + - - +
264A HIS* 3.2 1.0 + - - -
265A LEU* 3.0 35.8 + - + +
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Residues in contact with GLN 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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169A GLU* 4.8 8.0 - - - +
170A ARG* 4.0 23.4 + - - +
185A LEU* 3.9 24.6 - - + +
258A MSE 2.9 17.6 + - - +
259A ASN* 3.9 4.9 - - - +
261A LEU* 1.3 76.4 - - - +
263A PHE* 1.3 65.3 - - - +
265A LEU* 3.3 15.2 + - - +
266A MSE 2.9 38.6 + - - +
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Residues in contact with PHE 263 (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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145A ARG* 3.9 28.9 - - + -
149A LEU* 4.1 18.4 - - + -
182A MSE 3.8 32.3 - - + -
185A LEU* 3.6 15.1 - - + +
186A LEU* 3.7 29.2 - - + -
188A PHE* 3.9 15.9 - + + -
259A ASN 2.9 19.3 + - - +
260A LYS 3.9 3.1 - - - +
262A GLN* 1.3 78.0 - - - +
264A HIS* 1.3 82.4 + + - +
266A MSE 3.3 3.3 + - - +
267A LEU* 2.9 49.2 + - + +
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Residues in contact with HIS 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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145A ARG* 5.6 3.4 - - - +
188A PHE* 3.9 17.2 - + - -
223A ALA* 6.0 0.2 - - - +
224A ASP* 3.8 19.8 + - + +
226A TYR* 3.6 24.1 - - + +
227A GLN* 3.3 41.3 + - + +
230A ALA* 3.6 22.9 - - + -
231A ILE* 5.2 2.8 - - + +
260A LYS* 2.8 26.6 + - + +
263A PHE* 1.3 96.2 - + - +
265A LEU* 1.3 64.1 + - - +
267A LEU* 3.4 8.7 + - + +
268A ASP* 3.1 24.1 + - - +
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Residues in contact with LEU 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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167A ASP* 4.3 4.8 - - - +
169A GLU* 4.9 10.5 - - - +
170A ARG* 4.0 13.8 + - - +
230A ALA* 3.5 31.4 - - + +
231A ILE* 5.0 2.0 - - + -
233A TRP* 3.9 24.5 - - + -
234A ASN* 3.6 28.9 - - + +
261A LEU* 3.0 29.9 + - + +
262A GLN* 3.6 16.4 - - - +
264A HIS* 1.3 72.3 - - - +
266A MSE 1.3 67.9 + - - +
268A ASP* 3.3 15.0 + - + +
269A GLU* 3.5 15.8 + - - +
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Residues in contact with MSE 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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170A ARG* 3.6 35.4 - - - +
173A TRP* 4.3 6.7 - - + -
178A VAL* 3.6 29.3 - - + +
181A GLU* 3.6 15.3 - - + -
182A MSE 3.6 26.0 - - + +
185A LEU* 3.7 26.7 - - - -
262A GLN* 2.9 31.8 + - + +
263A PHE 3.7 3.6 - - - +
265A LEU* 1.3 76.8 - - - +
267A LEU* 1.3 63.6 + - - +
269A GLU* 3.1 26.4 + - - +
270A PHE* 3.4 10.2 - - - -
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Residues in contact with LEU 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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145A ARG* 5.3 3.6 - - - -
148A ARG* 3.8 36.3 - - + +
149A LEU* 3.8 27.1 - - + +
152A ALA* 4.1 7.4 - - + -
182A MSE 3.6 10.2 - - - -
227A GLN* 4.4 15.7 - - - +
263A PHE* 2.9 36.4 + - + +
264A HIS* 3.8 8.7 - - + +
265A LEU 3.3 0.2 - - - -
266A MSE 1.3 75.3 - - - +
268A ASP* 1.3 63.0 + - - +
270A PHE* 3.1 16.1 + - - +
271A PHE* 3.3 31.9 - - + -
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Residues in contact with ASP 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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148A ARG* 5.0 2.3 + - - -
197A GLY 4.9 0.9 - - - +
198A ASP* 5.0 3.7 - - - +
219A ARG* 4.7 7.8 + - - -
227A GLN* 4.8 5.8 + - - +
231A ILE* 3.5 40.0 - - + +
264A HIS 3.1 16.7 + - - +
265A LEU* 3.9 6.7 - - + +
266A MSE 3.2 0.8 - - - -
267A LEU* 1.3 71.7 - - - +
269A GLU* 1.3 62.2 + - - +
270A PHE 3.0 6.7 + - - -
271A PHE* 3.2 31.5 + - - +
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Residues in contact with GLU 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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161A VAL* 3.6 14.6 - - - +
162A ASP 4.7 3.8 + - - +
165A ASP 3.9 4.7 - - - +
166A PHE* 3.3 43.2 - - + +
167A ASP* 2.7 37.0 + - - +
170A ARG* 2.9 31.9 + - - +
178A VAL* 4.3 11.4 - - + -
265A LEU 3.5 8.4 + - - +
266A MSE 3.1 16.8 + - - +
268A ASP* 1.3 78.3 - - - +
270A PHE* 1.3 61.5 + - + +
271A PHE* 3.5 4.5 + - - +
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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