Contacts of the helix formed by residues 300 - 312 (chain C) in PDB entry 6Q2J
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 GLU 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C LEU* 3.9 27.3 - - + +
225C ARG* 5.3 8.0 + - - -
296C ILE* 4.2 7.9 - - + +
297C THR* 3.6 30.0 + - + +
298C GLN 3.3 0.8 - - - -
299C SER* 1.3 84.0 - - - +
301C GLU* 1.3 60.6 + - - +
302C SER 3.7 1.6 - - - +
303C LEU* 4.2 15.6 + - + +
304C CYS* 3.6 19.4 + - - +
138E GLN* 5.9 0.9 + - - -
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Residues in contact with GLU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C CYS* 5.6 6.1 - - + +
296C ILE* 4.7 10.3 - - + -
297C THR 3.8 9.7 + - - +
298C GLN* 3.6 33.8 + - - +
299C SER 3.4 2.0 - - - -
300C GLU* 1.3 77.3 - - - +
302C SER* 1.3 61.9 + - - +
303C LEU 3.3 0.2 - - - -
304C CYS* 3.3 6.3 + - - +
305C LYS* 2.9 61.8 + - + +
236E LYS* 5.4 5.6 + - - -
261E THR* 5.9 0.9 - - - +
348E ARG* 4.6 14.1 + - - -
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Residues in contact with SER 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER* 3.9 19.1 + - - -
262C LEU 6.1 0.4 - - - -
299C SER 5.1 3.0 + - - -
301C GLU* 1.3 75.3 + - - +
303C LEU* 1.3 62.5 + - - +
305C LYS* 3.2 11.2 + - - +
306C ILE* 2.9 40.0 + - - +
34E ASP* 5.3 0.2 + - - -
173E SER* 6.0 2.0 - - - -
175E ARG* 4.7 12.1 + - - -
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C LEU* 3.7 26.2 - - + -
256C GLU* 3.6 42.4 - - + +
259C ILE* 4.1 9.2 - - + -
260C SER* 3.9 29.6 - - - +
300C GLU* 4.2 17.2 + - + +
301C GLU 3.3 0.4 - - - -
302C SER* 1.3 82.1 + - - +
304C CYS* 1.3 56.1 + - - +
306C ILE* 3.3 3.1 + - - -
307C PHE* 2.9 47.5 + - + +
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Residues in contact with CYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C THR* 4.9 0.9 - - - -
220C CYS* 3.8 21.5 - - - +
221C LEU* 4.3 16.8 - - + -
293C CYS* 2.0 60.7 - - + -
296C ILE* 4.5 11.9 - - + -
300C GLU 3.6 13.8 + - - +
301C GLU* 3.3 10.6 + - - +
303C LEU* 1.3 78.4 - - - +
305C LYS* 1.3 57.9 + - - +
307C PHE* 3.8 4.9 - - - +
308C GLN* 2.9 24.4 + - - +
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Residues in contact with LYS 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LYS* 4.4 17.9 + - + +
293C CYS* 4.7 9.8 + - + +
301C GLU* 2.9 51.6 + - + +
302C SER* 3.6 10.1 - - - +
303C LEU 3.2 0.2 - - - -
304C CYS* 1.3 78.3 - - - +
306C ILE* 1.3 58.8 + - + +
308C GLN* 3.5 11.1 + - - +
309C HIS* 2.9 28.5 + - - +
236E LYS* 5.4 10.4 - - - +
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Residues in contact with ILE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C VAL* 6.2 0.4 - - + -
259C ILE* 3.4 43.5 - - + +
260C SER* 5.0 3.1 - - - -
262C LEU* 3.5 29.2 - - + +
263C SER 4.3 9.2 - - - +
264C LYS* 4.7 11.4 - - + -
267C LEU* 4.0 21.3 - - + -
302C SER* 2.9 28.1 + - - +
303C LEU 3.9 3.6 - - - +
305C LYS* 1.3 74.4 - - + +
307C PHE* 1.3 61.7 + - - +
309C HIS* 3.2 7.0 + - - +
310C MET* 2.9 35.4 + - + +
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Residues in contact with PHE 307 (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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220C CYS* 4.4 12.6 - - + -
221C LEU* 3.9 21.5 - - + -
224C ILE* 3.7 44.2 - - + -
228C GLN* 6.0 1.1 - - - -
237C TYR* 3.8 20.0 - + - -
256C GLU* 4.5 18.2 - - + -
259C ILE* 3.9 27.8 - - + -
303C LEU* 2.9 36.2 + - + +
304C CYS 3.8 3.6 - - - +
306C ILE* 1.3 76.6 - - - +
308C GLN* 1.3 56.7 + - - +
310C MET* 3.2 14.7 + - + +
311C LEU* 2.9 37.7 + - + +
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Residues in contact with GLN 308 (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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220C CYS* 3.9 17.6 - - - -
291C CYS* 3.9 19.0 + - - +
292C THR* 4.6 6.3 - - - +
293C CYS* 3.3 26.0 + - - +
304C CYS 2.9 17.8 + - - +
305C LYS* 3.8 9.1 - - - +
307C PHE* 1.3 76.3 - - - +
309C HIS* 1.3 61.3 + - - +
311C LEU* 4.6 3.1 - - - +
312C HIS* 3.3 33.6 + - + +
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Residues in contact with HIS 309 (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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245C TRP* 4.1 21.2 - + - -
264C LYS* 3.1 33.4 + - - +
267C LEU* 3.6 34.5 + - + +
305C LYS 2.9 18.3 + - - +
306C ILE* 3.2 8.0 + - - +
308C GLN* 1.3 78.0 - - - +
310C MET* 1.3 62.4 + - + +
312C HIS* 3.7 1.4 + - - -
315C SER* 2.7 48.6 + - - -
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Residues in contact with MET 310 (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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237C TYR* 4.1 3.6 - - + +
240C PHE* 3.7 22.6 - - + -
241C GLN* 3.7 27.6 - - - +
245C TRP* 3.8 48.0 + - + +
248C VAL* 4.7 9.6 - - - -
259C ILE* 4.1 20.0 - - + -
267C LEU* 5.2 2.9 - - + -
306C ILE* 2.9 22.9 + - + +
307C PHE* 3.7 36.8 - - + +
309C HIS* 1.3 83.6 - - + +
311C LEU* 1.3 65.1 + - + +
312C HIS 3.3 6.1 + - - +
315C SER* 5.1 0.3 - - - -
316C CYS* 6.0 0.7 - - - -
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C CYS* 5.0 1.1 - - + -
223C VAL* 4.7 7.2 - - + -
224C ILE* 3.8 31.0 - - + -
237C TYR* 4.3 16.2 - - + +
240C PHE* 4.5 11.2 - - + -
279C TYR* 4.3 16.5 + - - -
282C ILE* 5.0 3.8 - - + -
287C LEU* 4.3 39.9 - - + +
291C CYS* 4.6 20.0 - - - -
307C PHE* 2.9 24.4 + - + +
308C GLN* 4.6 3.6 - - - +
310C MET* 1.3 78.3 - - + +
312C HIS* 1.3 63.5 + - - +
313C ARG 3.8 0.2 + - - -
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Residues in contact with HIS 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 5.9 0.2 - - - -
279C TYR* 5.1 2.9 - - - -
308C GLN* 3.3 27.0 + - + +
309C HIS* 4.5 0.7 - - - -
310C MET 3.2 8.6 - - - +
311C LEU* 1.3 82.3 - - - +
313C ARG* 1.3 65.1 + - + +
314C LYS* 3.0 51.7 + - + +
315C SER* 3.3 25.7 + - - +
316C CYS* 5.1 1.7 + - - -
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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