Contacts of the helix formed by residues 261 - 275 (chain C) in PDB entry 6QPA
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 SER 261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C ARG* 5.3 0.4 - - - +
159C THR* 3.2 8.9 + - - -
259C TRP* 3.2 2.6 - - - +
260C GLU* 1.3 82.5 - - - +
262C PRO* 1.3 76.8 - - - +
263C GLU* 3.1 16.3 + - - +
264C HIS* 2.6 34.9 + - - -
265C ALA* 3.0 22.7 + - - +
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Residues in contact with PRO 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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51C THR* 5.6 6.1 - - - +
65C VAL* 3.7 24.9 - - + +
66C ASP* 6.4 0.2 - - + -
159C THR* 3.0 17.7 - - + +
261C SER* 1.3 88.7 - - - +
263C GLU* 1.3 69.9 + - - +
265C ALA 3.3 0.3 + - - -
266C HIS* 2.9 31.2 + - - +
298C PHE* 3.6 15.9 - - + -
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Residues in contact with GLU 263 (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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65C VAL* 5.7 0.8 - - - +
261C SER* 3.1 21.0 + - - +
262C PRO* 1.3 87.0 - - - +
264C HIS* 1.3 65.0 + - + +
266C HIS* 3.4 4.4 + - - +
267C GLN* 3.0 33.6 + - - +
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Residues in contact with HIS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C PRO* 4.1 29.6 - - + +
192C GLY* 4.2 9.9 - - - -
259C TRP* 3.4 13.0 - - + -
260C GLU* 3.3 36.5 + - + +
261C SER* 2.6 35.2 + - - +
263C GLU* 1.3 81.0 - - + +
265C ALA* 1.3 57.0 + - - +
267C GLN* 4.3 5.1 - - - +
268C GLY* 2.7 28.6 + - - -
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Residues in contact with ALA 265 (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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159C THR* 4.1 4.5 - - + -
161C VAL* 3.8 9.9 - - + -
259C TRP* 3.4 36.2 - - + +
261C SER 3.0 12.2 + - - +
262C PRO 3.6 6.3 - - - +
264C HIS* 1.3 74.5 - - - +
266C HIS* 1.3 66.6 + - - +
269C LEU* 2.9 30.1 + - - +
298C PHE* 3.7 18.2 - - + -
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Residues in contact with HIS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C HIS* 3.0 61.4 + + - -
55C PRO* 4.0 12.5 - - + +
56C MET 5.3 0.2 + - - -
57C ALA 5.8 1.4 + - - -
65C VAL* 3.4 31.9 - - + +
262C PRO 2.9 17.4 + - - +
263C GLU* 3.9 5.6 + - - +
265C ALA* 1.3 78.7 - - - +
267C GLN* 1.3 65.8 + - - +
270C GLY* 3.2 8.5 + - - -
298C PHE* 3.9 1.5 - - + -
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Residues in contact with GLN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C GLU* 3.0 20.4 + - - +
264C HIS* 4.3 5.7 - - - +
266C HIS* 1.3 81.5 + - - +
268C GLY* 1.3 61.1 + - - +
270C GLY* 3.2 9.2 + - - -
271C HIS* 3.0 28.6 + - + -
274C VAL* 5.7 0.5 - - - +
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Residues in contact with GLY 268 (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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186C MET* 3.8 9.2 - - - +
190C VAL* 3.6 17.0 - - - +
259C TRP* 3.5 20.4 - - - -
264C HIS 2.7 24.3 + - - -
267C GLN* 1.3 71.8 - - - +
269C LEU* 1.3 64.5 + - - +
271C HIS* 3.1 21.9 + - - +
272C VAL 4.6 0.3 + - - -
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Residues in contact with LEU 269 (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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54C HIS* 3.7 26.0 - - + +
161C VAL* 3.6 28.5 - - + -
186C MET* 4.3 13.2 - - + -
257C ILE* 3.7 29.4 - - + -
259C TRP* 4.0 6.9 - - + +
265C ALA 2.9 21.0 + - - +
268C GLY* 1.3 74.4 - - - +
270C GLY* 1.3 61.9 + - - +
271C HIS 3.0 1.6 + - - -
272C VAL* 3.3 28.3 + - + +
296C TYR* 4.0 28.3 - - + +
298C PHE* 4.2 6.5 - - + -
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Residues in contact with GLY 270 (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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54C HIS* 4.1 4.9 + - - -
266C HIS 3.2 14.4 + - - -
267C GLN* 3.2 6.9 + - - -
268C GLY 3.1 1.6 - - - -
269C LEU* 1.3 76.3 - - - +
271C HIS* 1.3 56.7 + - - +
272C VAL 3.2 0.2 - - - -
273C MET* 2.9 38.9 + - - +
274C VAL* 3.2 19.4 + - - +
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Residues in contact with HIS 271 (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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185C TRP* 4.7 6.3 - + - -
189C ASN 5.4 2.4 + - - -
190C VAL* 4.0 31.7 - - + +
191C PRO* 5.0 9.9 - - + +
267C GLN* 3.0 37.4 + - + -
268C GLY* 3.1 14.1 + - - +
269C LEU 3.0 1.4 + - - -
270C GLY* 1.3 73.1 - - - +
272C VAL* 1.3 61.2 + - - +
273C MET 3.0 5.6 - - - -
274C VAL* 3.8 14.5 - - + +
275C ASP* 3.0 42.8 + - + +
278C LEU* 3.6 17.6 - - + +
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Residues in contact with VAL 272 (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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182C THR* 4.3 7.6 - - + -
186C MET* 4.7 8.3 - - + -
269C LEU* 3.3 19.9 + - + +
270C GLY* 5.1 0.2 - - - -
271C HIS* 1.3 76.0 - - - +
273C MET* 1.3 71.5 + - + +
278C LEU* 3.7 23.1 - - + -
279C ARG* 3.3 27.0 - - - +
282C HIS* 3.6 49.8 + - + +
283C ASN* 4.8 2.3 - - - +
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Residues in contact with MET 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C HIS* 5.1 4.0 - - + -
56C MET* 4.4 27.6 - - + +
57C ALA* 4.2 26.2 - - + +
270C GLY* 2.9 22.1 + - - +
272C VAL* 1.3 92.8 - - + +
274C VAL* 1.3 67.3 + - + +
275C ASP 3.6 1.7 - - - -
279C ARG* 3.0 37.6 + - - +
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C GLN 5.7 0.2 - - - +
270C GLY* 3.2 18.6 + - - +
271C HIS* 3.8 19.1 - - + +
273C MET* 1.3 85.6 - - + +
275C ASP* 1.3 60.3 + - - +
276C TYR 4.1 1.1 + - - -
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Residues in contact with ASP 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TRP* 3.5 29.6 - - + -
271C HIS* 3.0 27.9 + - + +
273C MET 5.1 0.4 - - - -
274C VAL* 1.3 78.6 - - - +
276C TYR* 1.3 66.5 + - - +
277C GLU* 2.9 13.5 + - - +
278C LEU* 2.9 19.9 + - + -
279C ARG* 2.9 25.7 + - - +
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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