Contacts of the helix formed by residues 258 - 275 (chain B) in PDB entry 3GNI
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 ALA 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B HIS* 3.4 49.4 - - + +
191B TYR 4.7 2.2 - - - +
192B VAL* 4.1 10.8 - - + +
220B MET* 4.6 4.7 - - - -
257B ASP* 1.3 77.4 - - - +
259B LYS* 1.3 57.9 + - + +
260B SER 3.0 0.4 - - - -
261B ASP* 3.0 28.5 + - - +
262B ILE* 3.6 2.2 + - - +
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Residues in contact with LYS 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU* 4.7 0.2 - - - -
257B ASP* 3.0 21.6 + - - +
258B ALA* 1.3 77.7 - - + +
260B SER* 1.3 56.7 + - - +
261B ASP 3.3 0.2 - - - -
262B ILE* 3.3 16.3 + - + +
263B TYR 3.4 0.9 + - - -
364B PRO* 3.4 24.1 + - + +
365B ASP* 3.1 31.7 + - - +
367B ARG* 2.8 55.9 + - + +
368B PRO 4.4 8.1 - - - +
369B SER* 4.6 14.6 - - - +
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Residues in contact with SER 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B VAL* 3.7 13.9 - - - +
194B ARG* 5.6 0.7 - - - +
245B SER* 3.4 22.1 + - - -
247B GLU* 3.7 5.6 + - - -
248B VAL* 3.6 16.1 - - - +
256B TYR* 3.8 11.0 - - - -
257B ASP* 2.8 21.6 + - - -
259B LYS* 1.3 76.4 - - - +
261B ASP* 1.3 63.8 + - - +
262B ILE 3.1 1.0 + - - -
263B TYR* 3.3 7.3 + - - +
264B SER* 3.3 21.1 + - - -
367B ARG* 3.6 9.4 - - - +
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Residues in contact with ASP 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 4.2 8.8 - - + +
187B HIS* 2.6 31.3 + - + +
192B VAL* 3.3 13.3 - - - +
193B HIS* 2.9 29.9 + - - +
194B ARG* 2.9 28.1 + - - -
196B VAL* 4.5 5.8 - - + +
258B ALA 3.0 9.0 + - - +
260B SER* 1.3 80.2 + - - +
262B ILE* 1.3 58.3 + - - +
263B TYR 3.3 0.2 - - - -
264B SER* 3.3 10.8 + - - -
265B VAL* 3.1 30.4 + - - +
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 4.3 14.1 - - + -
183B LEU* 4.6 1.1 - - + -
187B HIS* 4.4 10.3 - - + +
258B ALA 3.9 11.0 - - - +
259B LYS* 3.3 16.5 + - + +
260B SER 3.1 0.8 - - - -
261B ASP* 1.3 78.9 - - - +
263B TYR* 1.3 63.8 + - - +
265B VAL* 3.2 20.1 + - + +
266B GLY 3.3 4.7 + - - -
359B CYS* 3.3 28.9 - - - +
367B ARG* 4.4 8.3 - - + -
368B PRO* 3.5 28.0 - - + +
369B SER* 4.7 0.9 - - - -
370B ALA* 3.9 34.8 - - + +
373B LEU* 4.2 8.1 - - + -
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Residues in contact with TYR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B TRP 4.0 1.8 - - - -
244B LEU 3.6 17.0 - - - -
245B SER* 3.5 18.4 - - - -
246B PRO* 3.8 16.6 - - + -
259B LYS 3.4 2.4 + - - -
260B SER 3.3 9.8 + - - +
262B ILE* 1.3 79.0 - - - +
264B SER* 1.3 63.2 + - - +
266B GLY 3.2 2.4 + - - -
267B ILE* 3.1 43.8 + - + +
279B PHE* 4.7 1.7 - - - -
290B GLU* 3.2 34.3 + - - +
359B CYS 3.3 17.4 + - - -
360B LEU* 3.6 37.9 - - + +
361B GLN 4.9 0.7 - - - -
362B ARG* 6.0 0.7 - - - -
367B ARG* 3.6 31.2 - - - -
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Residues in contact with SER 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ARG* 5.7 2.9 - - - -
196B VAL* 3.7 29.0 + - - +
243B TRP* 2.7 27.5 + - - +
244B LEU* 4.6 7.1 - - - +
245B SER 4.9 0.3 + - - -
260B SER 3.3 11.9 + - - -
261B ASP* 3.3 14.3 + - - -
262B ILE 3.2 0.6 - - - -
263B TYR* 1.3 74.9 - - - +
265B VAL* 1.3 56.0 + - - +
267B ILE* 3.4 3.6 + - - +
268B THR* 2.6 38.8 + - - -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 4.2 16.8 - - + +
179B VAL* 4.6 3.1 - - + -
180B LEU* 3.8 20.9 - - + -
183B LEU* 3.5 25.6 - - + -
196B VAL* 4.5 9.2 - - + -
261B ASP 3.1 16.2 + - - +
262B ILE* 3.2 13.9 - - + +
264B SER* 1.3 76.1 - - - +
266B GLY* 1.3 57.5 + - - +
268B THR* 3.3 9.4 + - - -
269B ALA* 2.8 26.0 + - - +
355B PHE* 3.9 27.6 - - + -
359B CYS* 4.2 3.8 - - - -
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ILE 3.3 4.4 + - - -
263B TYR 3.2 7.8 + - - -
265B VAL* 1.3 77.0 - - - +
267B ILE* 1.3 64.0 + - - +
269B ALA* 3.1 10.9 + - - +
270B CYS* 3.1 24.9 + - - -
356B VAL* 4.4 5.6 - - - +
359B CYS* 3.7 21.4 - - - +
360B LEU* 4.1 11.9 - - - -
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO 3.7 17.9 - - - +
243B TRP* 3.5 25.8 - - + +
263B TYR* 3.1 47.4 + - + +
264B SER 3.8 5.8 - - - +
265B VAL 3.4 0.2 - - - -
266B GLY* 1.3 74.0 - - - +
268B THR* 1.3 52.8 + - - +
270B CYS* 3.1 8.7 + - - +
271B GLU* 2.8 31.2 + - - +
277B VAL* 3.7 20.2 - - + -
278B PRO* 3.8 17.3 - - + +
279B PHE* 4.5 10.1 - - + -
360B LEU* 3.8 15.7 - - + +
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 4.4 5.8 - - + -
196B VAL* 3.3 22.5 + - + +
197B LYS* 3.6 2.0 - - - +
198B ALA 3.9 21.5 - - - +
201B ILE* 3.9 21.5 - - + -
243B TRP* 3.5 5.5 - - - -
264B SER 2.6 22.4 + - - -
265B VAL* 3.4 8.3 - - - -
267B ILE* 1.3 78.4 - - - +
269B ALA* 1.3 51.6 + - - +
271B GLU* 3.3 9.4 + - - +
272B LEU* 2.7 50.3 + - + +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 4.9 0.2 - - - -
176B LEU* 3.8 24.4 - - + +
265B VAL 2.8 13.9 + - - +
266B GLY* 3.1 12.8 + - - +
268B THR* 1.3 75.0 - - - +
270B CYS* 1.3 58.4 + - - +
272B LEU* 3.4 5.5 + - - +
273B ALA* 3.0 30.0 + - - +
352B PHE* 3.8 13.3 - - + -
355B PHE* 4.4 2.7 - - + -
356B VAL* 3.8 23.1 - - + -
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Residues in contact with CYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLY 3.1 14.6 + - - +
267B ILE* 3.1 9.6 + - - +
269B ALA* 1.3 74.3 - - - +
271B GLU* 1.3 59.0 + - - +
273B ALA* 4.5 3.1 - - - -
274B ASN* 2.9 47.8 + - - +
276B HIS 3.8 2.2 - - - +
278B PRO* 3.8 22.2 - - + -
356B VAL* 3.9 23.3 - - - -
360B LEU* 4.6 8.5 - - - -
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LYS* 3.0 29.4 + - - +
159B ILE* 3.8 5.8 - - + +
197B LYS* 3.9 0.9 - - - -
198B ALA* 2.9 44.7 + - + +
199B SER 4.9 0.9 + - - -
243B TRP* 3.1 32.9 + - - +
267B ILE 2.8 13.5 + - - +
268B THR* 3.5 9.6 - - - +
270B CYS* 1.3 77.8 - - - +
272B LEU* 1.3 56.3 + - - +
275B GLY* 2.8 30.7 + - - -
276B HIS* 3.4 11.2 + - - -
277B VAL* 4.1 20.9 - - - +
278B PRO* 4.5 0.4 - - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ALA* 3.7 29.8 - - + -
159B ILE* 4.2 11.7 - - + +
166B GLY* 3.4 2.8 - - - -
167B MET* 2.8 40.2 + - + +
172B ILE* 3.7 30.3 - - + +
175B ILE* 4.1 18.6 - - + -
176B LEU* 4.0 24.7 - - + -
198B ALA* 4.1 12.3 - - + -
201B ILE* 4.8 0.4 - - + -
268B THR* 2.7 34.7 + - + +
269B ALA 3.9 3.1 - - - +
270B CYS 3.3 0.2 - - - -
271B GLU* 1.3 70.7 - - - +
273B ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ASP 3.4 5.2 - - - +
166B GLY* 3.2 16.6 - - - -
167B MET 4.5 1.2 - - - +
172B ILE* 3.7 8.0 - - - +
269B ALA 3.0 18.2 + - - +
270B CYS* 3.9 6.3 - - - +
271B GLU 3.4 0.2 - - - -
272B LEU* 1.3 79.1 - - - +
274B ASN* 1.3 63.3 + - - +
348B PHE* 3.7 38.1 - - + -
352B PHE* 4.0 13.9 - - + -
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Residues in contact with ASN 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B MET 4.0 2.8 - - - +
165B ASP* 3.5 19.8 - - - +
270B CYS* 2.9 33.6 + - - +
273B ALA* 1.3 85.0 - - - +
275B GLY* 1.3 58.9 + - - +
276B HIS* 3.2 40.1 + - + +
278B PRO* 5.9 1.4 - - - +
348B PHE* 4.9 7.1 - - - -
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Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LYS* 4.3 9.0 + - - -
159B ILE* 3.8 26.3 - - - +
164B MET 3.8 16.8 - - - +
166B GLY* 3.8 9.0 - - - -
271B GLU 2.8 15.9 + - - -
273B ALA 3.6 1.8 - - - -
274B ASN* 1.3 76.8 - - - +
276B HIS* 1.3 59.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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