Contacts of the helix formed by residues 252 - 262 (chain A) in PDB entry 2Q2U
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 ASP 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A PHE* 1.3 75.4 - - - +
253A ALA* 1.3 65.6 + - - +
254A ASP* 2.9 14.3 + - - +
255A GLN* 2.7 55.9 + - - +
256A ARG* 3.0 13.6 + - - +
35F T 3.7 13.9 - - - +
36F A 3.2 17.5 - - - +
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Residues in contact with ALA 253 (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 VAL* 5.8 0.5 - - - +
252A ASP* 1.3 70.3 - - - +
254A ASP* 1.3 66.5 + - - +
256A ARG* 3.3 11.1 + - - +
257A ARG* 3.1 34.9 + - - +
35F T 3.9 1.4 + - - -
36F A 2.8 33.1 + - - +
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Residues in contact with ASP 254 (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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252A ASP* 2.9 13.3 + - - +
253A ALA* 1.3 76.9 - - - +
255A GLN* 1.3 58.3 + - + +
257A ARG* 3.1 30.1 + - - +
258A ASP* 2.9 28.3 + - - +
36F A 5.3 1.2 + - - -
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Residues in contact with GLN 255 (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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233A MET* 5.1 0.4 - - - -
250A GLY 3.8 4.9 + - - +
251A PHE* 3.4 17.9 - - + -
252A ASP* 2.7 59.8 + - - +
254A ASP* 1.3 70.1 - - + +
256A ARG* 1.3 58.9 + - - +
258A ASP* 3.0 6.2 + - - -
259A PHE* 2.8 47.7 + - + +
289A PHE* 3.8 25.4 - - - -
290A ILE 5.3 2.2 + - - -
291A GLY* 5.7 0.6 - - - -
292A ILE* 6.3 0.8 - - - +
35F T 5.6 0.2 + - - -
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Residues in contact with ARG 256 (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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203A LEU* 3.6 16.4 - - - +
232A VAL* 3.6 10.7 - - + +
233A MET* 2.9 69.3 + - + +
234A GLY* 3.1 23.0 + - - -
248A GLY 2.6 26.4 + - - -
249A THR* 4.5 3.4 - - - +
251A PHE* 3.7 28.5 + - + +
252A ASP 3.0 18.0 + - - +
253A ALA* 3.6 9.9 - - - +
255A GLN* 1.3 76.0 - - - +
257A ARG* 1.3 60.7 + - - +
259A PHE 4.2 0.2 - - - -
260A TRP* 3.3 9.9 + - - +
10E T 4.8 8.5 + - - -
11E G 4.1 9.3 + - - -
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Residues in contact with ARG 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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231A ASP 5.5 0.5 - - - +
232A VAL* 4.1 22.0 - - + +
253A ALA* 3.1 17.7 + - - +
254A ASP* 3.1 43.7 + - - +
255A GLN 3.0 0.2 - - - -
256A ARG* 1.3 76.2 - - - +
258A ASP* 1.3 58.6 + - - +
260A TRP* 3.9 1.9 - - - +
261A GLN* 2.9 44.9 + - + +
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Residues in contact with ASP 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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254A ASP 2.9 13.4 + - - +
255A GLN* 3.6 8.5 - - - +
257A ARG* 1.3 74.2 - - - +
259A PHE* 1.3 60.2 + - + +
261A GLN* 2.7 29.8 + - - +
262A ASN* 2.8 38.1 + - - -
266A TYR* 2.6 29.0 + - - -
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ILE* 4.4 9.4 - - + -
200A MET* 3.1 38.4 - - + +
233A MET* 3.8 25.6 - - + -
236A ILE* 4.3 10.8 - - + -
251A PHE* 3.6 15.5 - + - -
255A GLN* 2.8 35.1 + - + +
258A ASP* 1.3 74.4 - - + +
260A TRP* 1.3 58.0 + - - +
262A ASN 3.3 2.1 - - - +
263A LYS* 3.0 22.5 + - - -
266A TYR* 3.7 34.5 - + - -
271A VAL* 4.9 1.6 - - + -
289A PHE* 3.9 28.0 - + - -
292A ILE* 3.8 19.1 - - + -
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Residues in contact with TRP 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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200A MET* 4.1 20.6 - - + -
201A THR* 3.7 7.6 - - - -
202A ALA* 3.6 36.8 - - + -
229A GLU* 4.9 6.7 - - - -
230A GLU 5.4 0.7 - - - -
231A ASP* 3.2 44.7 + - - +
232A VAL* 3.5 6.5 - - - -
233A MET* 3.0 40.9 - - + +
256A ARG 3.3 7.5 + - - +
257A ARG 3.9 2.0 - - - +
258A ASP 3.1 0.8 - - - -
259A PHE* 1.3 76.1 - - - +
261A GLN* 1.3 69.6 + - + +
263A LYS* 3.0 63.6 + - + +
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Residues in contact with GLN 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 ARG* 2.9 34.1 + - + +
258A ASP* 2.7 21.4 + - - +
260A TRP* 1.3 76.9 - - + +
262A ASN* 1.3 67.3 + - - +
263A LYS* 3.5 4.9 + - - +
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Residues in contact with ASN 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 ASP* 2.8 34.4 + - - -
259A PHE 3.3 4.0 - - - -
261A GLN* 1.3 85.9 - - - +
263A LYS* 1.3 65.5 + - - +
264A GLU 3.1 3.3 + - - +
265A SER* 3.2 20.3 + - - +
266A TYR* 3.0 36.9 + - + +
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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