Contacts of the helix formed by residues 256 - 265 (chain A) in PDB entry 1Q6Z
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 GLY 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A PRO 2.9 8.9 + - - -
255A ALA* 1.3 75.1 - - - +
257A ILE* 1.3 66.2 + - - +
258A ALA 3.5 2.0 - - - -
259A ALA* 3.4 1.6 + - - +
260A ILE* 3.0 25.8 + - - +
280A TYR* 3.5 7.5 - - - -
282A GLN* 3.8 7.5 - - - +
284A ASP* 3.5 24.5 - - - -
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Residues in contact with ILE 257 (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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256A GLY* 1.3 72.9 - - - +
258A ALA* 1.3 65.9 + - - +
260A ILE* 3.9 2.1 - - - +
261A SER* 3.1 20.6 + - - -
280A TYR* 3.5 37.9 + - + -
282A GLN 5.2 0.8 + - - +
284A ASP* 3.4 15.8 + - - +
285A PRO* 5.0 6.3 - - + -
286A GLY 3.6 20.2 - - - +
287A GLN 3.4 21.1 - - - +
288A TYR* 3.9 31.8 - - + +
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Residues in contact with ALA 258 (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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256A GLY 3.5 0.2 - - - -
257A ILE* 1.3 78.5 - - - +
259A ALA* 1.3 63.7 + - - +
261A SER* 3.2 8.8 + - - -
262A GLN* 3.0 25.3 + - - +
284A ASP* 3.0 30.0 + - - +
285A PRO 3.7 13.9 - - - +
286A GLY* 4.3 5.2 - - - -
287A GLN 4.5 0.9 - - - -
290A LYS* 5.4 0.5 - - - -
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Residues in contact with ALA 259 (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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254A PRO* 3.5 31.4 - - + -
256A GLY* 3.8 6.5 - - - +
257A ILE 3.3 0.2 - - - -
258A ALA* 1.3 76.0 - - - +
260A ILE* 1.3 57.8 + - - +
262A GLN* 3.4 5.6 + - - +
263A LEU* 3.0 32.6 + - - +
282A GLN* 5.8 0.7 - - - +
284A ASP* 3.0 18.3 + - - +
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Residues in contact with ILE 260 (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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235A PRO* 3.8 30.1 - - + -
253A MET* 3.8 26.0 - - + -
254A PRO* 3.3 27.8 - - + +
256A GLY 3.0 13.8 + - - +
257A ILE 4.0 2.9 - - - +
259A ALA* 1.3 75.6 - - - +
261A SER* 1.3 67.7 + - - +
263A LEU* 3.2 6.0 + - + +
264A LEU* 3.1 29.6 + - + +
278A PHE* 3.7 30.1 - - + -
280A TYR* 3.8 17.5 - - + +
288A TYR 5.1 3.4 - - - +
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Residues in contact with SER 261 (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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257A ILE 3.1 6.2 + - - -
258A ALA* 3.2 14.0 + - - -
260A ILE* 1.3 78.2 - - - +
262A GLN* 1.3 62.2 + - - +
264A LEU* 3.4 6.3 + - - +
265A GLU 3.0 17.5 + - - -
287A GLN* 2.8 32.0 + - - +
288A TYR 3.5 17.5 - - - -
289A LEU* 3.8 14.4 - - - +
290A LYS* 3.4 23.6 + - - +
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Residues in contact with GLN 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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258A ALA 3.0 18.4 + - - +
259A ALA* 3.7 5.6 - - - +
261A SER* 1.3 75.4 + - - +
263A LEU* 1.3 65.4 + - - +
265A GLU* 2.7 40.0 + - - +
290A LYS* 3.7 22.7 + - - +
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Residues in contact with LEU 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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232A TRP* 4.0 49.1 - - + +
253A MET* 4.3 13.9 - - + -
254A PRO* 3.6 32.8 - - + -
259A ALA 3.0 18.5 + - - +
260A ILE* 3.2 6.3 + - - +
262A GLN* 1.3 76.0 - - - +
264A LEU* 1.3 62.7 + - + +
265A GLU 3.6 2.4 + - - +
267A HIS* 3.9 12.1 + - - -
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Residues in contact with LEU 264 (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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204A ALA* 4.5 4.5 - - + -
206A VAL* 4.5 2.0 - - + -
232A TRP* 4.4 18.4 - - + -
253A MET* 4.2 18.4 - - + -
260A ILE* 3.1 34.3 + - + +
261A SER* 3.6 4.9 - - - +
263A LEU* 1.3 76.5 - - - +
265A GLU* 1.3 65.9 + - - +
267A HIS* 3.0 22.0 + - - +
270A VAL* 3.8 42.4 - - + -
278A PHE* 4.7 7.6 - - + -
289A LEU* 4.3 18.8 - - + -
293A THR* 3.2 15.1 + - + -
295A LEU* 5.1 0.4 - - + -
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Residues in contact with GLU 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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261A SER 3.0 12.0 + - - +
262A GLN* 2.7 42.4 + - - +
263A LEU 4.3 2.3 - - - +
264A LEU* 1.3 79.0 - - - +
266A GLY* 1.3 62.2 + - - +
267A HIS* 3.4 7.3 + - - -
290A LYS* 3.8 33.9 + - + +
291A PRO 5.7 1.6 - - - +
293A THR* 4.3 3.1 - - - -
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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
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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