Contacts of the helix formed by residues 251 - 262 (chain C) in PDB entry 6G2T
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 ASN 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195C ARG* 4.1 9.0 + - - -
226C MET* 4.4 13.5 + - - +
229C ALA* 3.5 26.6 - - + +
232C SER* 5.6 1.0 + - - -
235C LEU* 4.7 2.7 - - - +
250C GLY* 1.3 70.7 - - - -
252C GLU* 1.3 76.5 + - - +
253C ARG 3.4 0.2 - - - -
254C PHE* 3.2 40.6 - - + -
255C ARG* 3.5 37.6 + - - +
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Residues in contact with GLU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU* 4.9 1.4 - - + +
191C ILE* 2.9 53.0 - - + +
192C LEU* 3.3 29.2 - - + +
194C GLU* 3.7 7.8 - - - +
195C ARG* 3.6 41.3 + - - +
249C ILE* 3.4 15.4 - - + +
250C GLY 3.1 2.4 - - - +
251C ASN* 1.3 82.9 + - - +
253C ARG* 1.3 62.5 + - - +
255C ARG* 3.3 26.0 + - - +
256C CYS* 3.7 5.9 + - - +
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Residues in contact with ARG 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU* 5.2 4.3 - - + -
211C ILE* 6.3 0.7 - - + -
215C LEU* 3.3 27.3 + - + +
216C CYS* 3.4 30.1 - - - +
217C TYR* 3.6 24.6 + - + -
234C SER 3.8 5.5 + - - -
235C LEU* 2.8 35.0 + - - +
237C LYS* 3.1 54.8 - - - +
249C ILE* 3.4 30.9 - - + +
250C GLY 3.6 11.9 + - - +
252C GLU* 1.3 81.0 - - - +
254C PHE* 1.3 62.2 + - + +
256C CYS* 3.5 3.1 + - - +
257C PRO* 3.1 21.0 - - - +
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Residues in contact with PHE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C TYR* 3.4 40.9 - + + +
218C VAL* 4.8 0.2 - - - -
219C ALA* 3.6 22.5 + - + +
222C PHE* 4.0 26.2 - + - -
225C GLU* 3.7 26.2 - - + +
226C MET* 3.5 33.4 - - + -
235C LEU* 4.3 16.6 - - + -
250C GLY 4.3 1.8 - - - -
251C ASN* 3.2 43.7 - - + -
253C ARG* 1.3 83.9 - - + +
255C ARG* 1.3 63.2 + - + +
257C PRO* 3.0 14.6 - - - +
258C GLU* 3.6 8.0 + - - +
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Residues in contact with ARG 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C TYR* 4.4 20.6 + - + +
191C ILE* 3.6 13.7 - - + +
194C GLU* 2.6 36.4 + - - -
222C PHE* 3.5 31.2 - - + -
226C MET* 5.1 11.6 - - - -
251C ASN* 3.5 33.7 + - - +
252C GLU* 3.3 24.5 - - - +
254C PHE* 1.3 82.8 - - + +
256C CYS* 1.3 65.9 + - - +
258C GLU* 2.9 22.2 + - - +
259C ALA 3.3 4.2 + - - -
265C PHE* 4.9 3.8 - - + -
112D LYS* 5.2 4.8 - - - +
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Residues in contact with CYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 3.1 56.3 - - + +
187C TYR* 3.5 19.3 - - + -
188C LEU* 3.3 39.9 - - + -
191C ILE* 5.2 0.4 - - + -
212C LYS* 5.5 4.0 - - + -
216C CYS* 4.6 4.3 - - - -
252C GLU 3.7 3.4 + - - +
253C ARG 3.5 8.3 + - - +
254C PHE 3.4 0.2 - - - -
255C ARG* 1.3 80.1 - - - +
257C PRO* 1.4 67.2 - - + +
259C ALA* 3.2 10.6 + - - +
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Residues in contact with PRO 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 4.7 5.8 - - + -
212C LYS* 6.3 0.2 - - + -
216C CYS* 4.1 12.6 - - + -
217C TYR 3.4 21.5 - - - +
218C VAL* 3.4 26.9 - - + -
253C ARG 3.1 13.7 - - - +
254C PHE 3.0 12.6 - - - +
256C CYS* 1.4 92.8 - - + +
258C GLU* 1.3 62.7 + - - +
260C LEU* 3.3 18.7 + - + +
261C PHE* 3.5 15.1 - - - -
305C TYR* 4.2 20.2 - - + -
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C VAL* 5.0 3.3 - - - +
219C ALA* 5.1 3.6 + - - +
222C PHE* 3.2 38.2 - - + +
254C PHE 3.6 3.9 + - - +
255C ARG* 2.9 27.2 + - - +
257C PRO* 1.3 77.2 - - - +
259C ALA* 1.3 50.8 + - - +
261C PHE* 2.8 14.9 + - - +
262C GLN* 2.7 47.3 + - + +
265C PHE* 3.7 13.0 - - + -
311C ARG* 2.9 44.8 + - - -
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C LEU* 4.5 0.5 - - - +
184C LEU* 4.1 7.2 - - + -
187C TYR* 4.8 8.7 - - + -
255C ARG 3.3 3.6 + - - +
256C CYS 3.2 15.6 + - - +
258C GLU* 1.3 78.9 - - - +
260C LEU* 1.3 60.9 + - - +
262C GLN 3.0 29.2 - - - +
263C PRO* 3.1 8.7 - - - +
265C PHE* 4.3 13.6 - - + -
266C LEU* 4.0 30.6 - - + +
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C SER* 6.3 0.2 - - - -
159C THR* 4.9 3.1 - - - +
179C LEU* 3.4 40.3 - - + +
180C ALA 4.4 7.2 - - - +
184C LEU* 3.7 38.6 - - + +
257C PRO* 3.3 14.5 + - + +
258C GLU 3.1 0.8 - - - -
259C ALA* 1.3 77.2 - - - +
261C PHE* 1.3 64.3 + - + +
263C PRO* 4.1 0.2 - - - +
272C GLY* 3.2 8.3 - - - -
273C ILE* 3.1 45.1 + - + -
302C THR* 4.4 23.3 - - + +
305C TYR* 4.8 5.8 - - + -
308C ILE* 5.7 4.9 - - + -
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Residues in contact with PHE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C VAL* 3.7 24.0 - - + -
257C PRO 3.5 17.5 - - - -
258C GLU* 2.8 20.3 + - - +
260C LEU* 1.3 81.9 - - + +
262C GLN* 1.3 64.0 + - + +
263C PRO* 3.5 7.1 - - - +
272C GLY* 3.6 9.3 + - - -
273C ILE* 3.7 20.6 - - + +
274C HIS* 3.6 23.0 - - + -
275C GLU* 4.3 1.4 - - - +
308C ILE* 4.4 7.6 - - + -
311C ARG* 3.4 40.8 - - + +
312C MET* 3.4 26.5 - - + -
315C GLU* 3.0 28.9 - - - -
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Residues in contact with GLN 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLU* 2.7 36.5 + - + +
259C ALA* 3.0 16.0 - - - +
261C PHE* 1.3 80.5 + - - +
263C PRO* 1.3 63.1 - - - +
264C SER* 3.0 24.0 + - - +
265C PHE* 3.1 35.9 + - + +
274C HIS* 5.3 5.5 + - - -
275C GLU* 5.6 1.8 + - - -
311C ARG* 5.3 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