Contacts of the helix formed by residues 261 - 272 (chain A) in PDB entry 1QCY
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 ARG 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ALA* 3.7 11.7 - - + -
258A ASP* 3.0 13.8 + - + +
260A HIS* 1.3 118.3 + - + +
262A LEU* 1.3 64.3 + - - +
263A LYS 3.2 2.9 - - - -
264A LYS* 3.1 48.5 + - - +
265A VAL* 2.9 32.0 + - + +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A THR* 4.5 3.6 - - + +
223A ALA* 4.0 26.5 - - + +
226A THR* 5.3 3.4 - - + +
256A SER* 4.0 5.8 - - - +
258A ASP 3.9 0.6 + - - -
259A ASN* 3.4 20.7 + - + +
261A ARG* 1.3 79.1 - - - +
263A LYS* 1.3 63.1 + - - +
265A VAL* 4.4 5.6 - - + -
266A ILE* 2.9 40.2 + - + +
298A GLU* 3.5 41.1 - - + +
301A SER* 4.6 4.0 - - - +
302A ILE* 4.3 31.4 - - + -
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ASN 4.6 1.4 + - - -
260A HIS 4.7 6.0 + - - +
261A ARG 3.1 1.7 + - - -
262A LEU* 1.3 77.7 - - - +
264A LYS* 1.3 63.6 + - - +
266A ILE* 3.9 5.1 - - - +
267A GLN* 3.1 33.2 + - + +
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A HIS 5.4 0.2 + - - -
261A ARG* 3.1 43.5 + - - +
263A LYS* 1.3 78.1 - - - +
265A VAL* 1.3 68.0 + - + +
267A GLN* 3.2 7.1 + - + +
268A ASP* 2.9 53.6 + - - +
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA* 3.9 22.2 - - + +
226A THR* 3.7 30.3 - - + -
227A ASP* 3.7 36.8 - - + +
230A ARG* 4.5 0.3 + - - -
261A ARG* 2.9 35.5 + - + +
262A LEU* 3.9 7.2 - - + +
264A LYS* 1.3 75.2 - - + +
266A ILE* 1.3 64.9 + - + +
268A ASP* 3.4 7.8 + - - +
269A CYS* 3.1 22.1 + - - -
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Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A THR* 5.9 2.7 - - + -
262A LEU* 2.9 34.1 + - + +
263A LYS* 3.9 4.9 - - - +
265A VAL* 1.3 76.6 - - + +
267A GLN* 1.3 59.9 + - - +
269A CYS* 2.7 28.6 + - - +
270A GLU* 2.8 11.9 + - + +
276A ARG* 2.6 37.6 + - - +
301A SER* 3.2 33.4 - - - +
302A ILE* 3.6 25.4 - - + +
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LYS* 3.1 24.7 + - + +
264A LYS* 3.2 8.7 + - + +
266A ILE* 1.3 79.1 - - - +
268A ASP* 1.3 61.3 + - - +
270A GLU* 3.1 17.8 + - - +
271A ASP* 2.6 66.4 + - - +
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASP* 5.0 0.3 - - - +
230A ARG* 3.6 35.2 + - - +
264A LYS* 2.9 57.8 + - - +
265A VAL* 3.6 4.3 - - - +
267A GLN* 1.3 78.3 - - - +
269A CYS* 1.3 61.2 + - - +
271A ASP* 3.5 13.0 + - - +
272A GLU* 3.2 31.6 + - - +
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Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A THR* 4.1 15.9 - - - -
230A ARG* 3.9 21.5 - - - +
248A MET* 3.9 26.7 - - - -
265A VAL* 3.1 21.7 + - - +
266A ILE* 2.7 14.6 + - - +
268A ASP* 1.3 73.3 - - - +
270A GLU* 1.3 59.1 + - - +
272A GLU 3.4 2.1 + - - +
273A ASN 3.3 3.5 + - - -
274A ILE* 2.9 37.4 + - + +
276A ARG* 3.9 21.3 - - - -
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ILE* 2.8 10.5 + - + +
267A GLN* 3.4 25.1 - - - +
269A CYS* 1.3 75.1 - - - +
271A ASP* 1.3 61.9 + - - +
272A GLU 3.1 1.3 - - - -
273A ASN* 2.9 26.7 + - - +
274A ILE 4.7 4.0 - - - +
276A ARG* 2.7 32.7 + - - +
304A SER* 4.6 5.4 + - - -
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLN* 2.6 51.1 + - - +
268A ASP* 3.9 13.2 - - - +
269A CYS 3.4 0.2 - - - -
270A GLU* 1.3 76.9 - - - +
272A GLU* 1.3 61.7 + - + +
273A ASN* 3.1 13.9 + - - +
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ARG* 2.7 53.0 + - - +
234A PHE* 5.9 0.3 - - - +
246A LYS* 4.5 20.0 + - - +
268A ASP* 3.2 15.0 + - - +
269A CYS 4.0 3.6 - - - +
270A GLU 3.1 1.2 - - - -
271A ASP* 1.3 79.8 - - + +
273A ASN* 1.3 73.4 + - - +
274A ILE* 3.2 18.4 + - + +
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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