Contacts of the helix formed by residues 257 - 269 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188D PHE* 5.8 0.9 - - - +
226D TYR* 2.8 27.5 + - + +
255D ASN 3.5 3.5 + - - +
256D PRO* 1.3 67.5 - - - +
258D MSE 1.3 63.8 + - - +
259D ASN* 3.1 21.9 + - - +
260D LYS* 3.2 33.8 + - + +
261D LEU* 3.0 22.0 + - - +
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Residues in contact with MSE 258 (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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233D TRP* 5.5 7.0 - - + +
248D PHE* 5.3 1.1 - - + -
256D PRO* 3.0 43.1 + - + +
257D ASP* 1.3 73.5 + - - +
259D ASN* 1.3 57.7 + - - +
261D LEU* 3.6 27.3 - - + +
262D GLN* 3.0 37.9 + - + +
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Residues in contact with ASN 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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185D LEU* 3.2 54.1 + - - +
187D PRO 4.9 1.0 + - - -
188D PHE* 4.2 19.6 - - - +
257D ASP* 3.1 10.8 + - - +
258D MSE 1.3 75.9 - - - +
260D LYS* 1.3 61.7 + - - +
262D GLN* 3.4 4.6 + - - +
263D PHE* 2.9 28.8 + - - +
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Residues in contact with LYS 260 (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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188D PHE* 3.6 26.9 - - + -
189D SER 3.4 18.9 + - - -
191D ASP* 3.4 22.0 + - - +
224D ASP* 2.8 29.2 + - - +
226D TYR* 3.5 37.9 - - + +
257D ASP* 3.1 29.1 + - + +
259D ASN* 1.3 78.3 - - + +
261D LEU* 1.3 66.9 + - - +
263D PHE* 3.5 4.2 + - - -
264D HIS* 2.8 34.6 + - - +
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Residues in contact with LEU 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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226D TYR* 3.8 12.9 - - + -
230D ALA* 3.6 31.3 - - + +
233D TRP* 3.9 43.1 - - + +
248D PHE* 4.7 9.4 - - + -
257D ASP 3.0 12.8 + - - +
258D MSE 3.6 36.8 - - + +
260D LYS* 1.3 80.7 - - - +
262D GLN* 1.3 67.1 + - + +
264D HIS 3.3 0.2 + - - -
265D LEU* 3.0 42.5 + - + +
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Residues in contact with GLN 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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169D GLU* 3.2 37.0 + - - +
170D ARG* 3.8 10.5 + - - +
185D LEU* 3.9 15.9 - - + -
233D TRP* 5.6 1.8 - - - -
258D MSE 3.0 23.6 + - + +
259D ASN* 3.9 4.3 - - - +
261D LEU* 1.3 78.3 - - + +
263D PHE* 1.3 66.1 + - - +
265D LEU* 3.4 18.5 + - - +
266D MSE 3.0 33.7 + - - +
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Residues in contact with PHE 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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145D ARG* 4.0 25.4 - - + -
149D LEU* 4.1 18.6 - - + -
182D MSE 3.6 35.4 - - + -
185D LEU* 3.5 14.3 - - + +
186D LEU* 3.6 29.6 - - + -
188D PHE* 3.7 30.7 - + + -
259D ASN 2.9 17.5 + - - +
260D LYS 3.8 3.4 - - - +
261D LEU 3.3 0.2 - - - -
262D GLN* 1.3 77.8 - - - +
264D HIS* 1.3 71.2 + + - +
266D MSE 3.4 3.6 + - - +
267D LEU* 2.9 44.1 + - + +
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Residues in contact with HIS 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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145D ARG* 5.7 2.8 - - - +
188D PHE* 3.9 11.2 - + - -
223D ALA* 5.8 0.4 - - - +
224D ASP* 3.7 40.2 + - + +
226D TYR* 3.5 24.4 - - + +
227D GLN* 3.4 39.8 + - + +
230D ALA* 3.7 11.7 - - + -
231D ILE* 5.2 2.8 - - + +
260D LYS* 2.8 23.2 + - + +
263D PHE* 1.3 98.3 - + - +
265D LEU* 1.3 65.3 + - - +
267D LEU* 3.8 8.1 - - + +
268D ASP* 3.1 24.3 + - - +
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Residues in contact with LEU 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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167D ASP* 4.2 4.4 - - - +
169D GLU* 4.7 4.5 - - - +
170D ARG* 3.9 15.8 + - - +
230D ALA* 3.3 33.2 - - + +
231D ILE* 4.3 4.7 - - + +
233D TRP* 4.0 17.9 - - + -
234D ASN* 3.6 26.0 - - + +
261D LEU* 3.0 31.2 + - + +
262D GLN* 3.7 26.7 - - - +
264D HIS* 1.3 77.0 - - - +
266D MSE 1.3 63.1 + - - +
268D ASP* 3.3 14.8 + - + +
269D GLU* 3.4 15.9 + - - +
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Residues in contact with MSE 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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170D ARG* 3.5 31.0 - - - +
173D TRP* 4.0 6.1 - - + -
178D VAL* 3.3 42.4 - - + +
181D GLU* 3.6 16.4 - - + -
182D MSE 3.5 33.4 - - + +
185D LEU* 4.3 11.9 - - - -
262D GLN* 3.0 23.5 + - - +
263D PHE 3.8 3.1 - - - +
265D LEU* 1.3 73.7 - - - +
267D LEU* 1.3 65.3 + - - +
269D GLU* 3.0 27.7 + - - +
270D PHE* 3.3 10.2 - - - -
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Residues in contact with LEU 267 (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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145D ARG* 5.4 4.5 - - + -
148D ARG* 3.9 28.3 - - + +
149D LEU* 4.0 24.7 - - + +
152D ALA* 4.1 12.1 - - + -
182D MSE 3.5 11.8 - - - -
219D ARG* 6.0 0.2 - - - +
227D GLN* 4.3 17.3 - - - +
263D PHE* 2.9 37.3 + - + +
264D HIS* 3.8 8.3 - - + +
265D LEU 3.3 0.2 - - - -
266D MSE 1.3 76.2 - - - +
268D ASP* 1.3 61.8 + - - +
270D PHE* 3.1 15.9 + - - +
271D PHE* 3.2 34.0 - - + -
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Residues in contact with ASP 268 (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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197D GLY 5.0 0.5 - - - +
198D ASP* 5.0 5.5 - - - +
219D ARG* 4.9 7.4 + - - -
227D GLN* 4.9 2.5 + - - +
231D ILE* 3.6 38.7 - - + +
264D HIS 3.1 17.6 + - - +
265D LEU* 3.8 7.2 - - + +
266D MSE 3.2 0.4 - - - -
267D LEU* 1.3 75.8 - - - +
269D GLU* 1.3 63.2 + - - +
270D PHE 3.0 1.3 + - - -
271D PHE* 3.1 32.2 + - - +
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Residues in contact with GLU 269 (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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161D VAL* 3.6 6.4 - - - +
162D ASP* 4.8 3.8 + - - +
165D ASP 4.0 4.2 - - - +
166D PHE* 3.3 53.8 - - + +
167D ASP* 2.9 31.4 + - - +
170D ARG* 2.7 36.2 + - - +
178D VAL* 4.3 8.3 - - + -
265D LEU 3.4 9.9 + - - +
266D MSE 3.0 19.1 + - - +
268D ASP* 1.3 76.9 - - - +
270D PHE* 1.3 59.6 + - + +
271D PHE* 3.3 3.6 + - - +
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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