Contacts of the helix formed by residues 252 - 262 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B PHE* 1.3 74.6 - - - +
253B ALA* 1.3 66.5 - - - +
254B ASP* 2.9 15.0 + - - +
255B GLN* 2.6 57.3 + - - +
256B ARG* 3.0 14.9 + - - +
35H T 3.7 14.1 - - - +
36H A 3.2 17.0 - - - +
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B VAL* 5.8 0.7 - - - +
252B ASP* 1.3 70.8 - - - +
254B ASP* 1.3 67.2 + - - +
256B ARG* 3.3 10.9 + - - +
257B ARG* 3.1 34.4 + - - +
35H T 3.9 1.6 + - - -
36H A 2.8 32.6 + - - +
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Residues in contact with ASP 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ASP* 2.9 13.7 + - - +
253B ALA* 1.3 76.5 - - - +
255B GLN* 1.3 58.6 + - + +
257B ARG* 3.2 29.9 + - - +
258B ASP* 2.9 28.8 + - - +
36H A 5.3 1.2 + - - -
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Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B MET* 5.2 0.4 - - - -
250B GLY 3.8 4.6 + - - +
251B PHE* 3.4 18.8 - - + -
252B ASP* 2.6 58.9 + - - +
254B ASP* 1.3 73.5 - - + +
256B ARG* 1.3 59.2 + - - +
258B ASP* 3.0 6.2 + - - +
259B PHE* 2.8 45.3 + - + +
289B PHE* 3.8 24.3 - - - -
290B ILE 5.3 2.4 + - - -
291B GLY* 5.8 0.8 - - - -
292B ILE* 6.3 0.8 - - - +
35H T 5.6 0.2 + - - -
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Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B LEU* 3.6 17.3 - - - +
232B VAL* 4.1 10.3 - - + -
233B MET* 2.9 68.8 + - + +
234B GLY* 3.1 22.6 + - - -
248B GLY 2.6 27.2 + - - -
249B THR* 4.5 3.4 - - - +
251B PHE* 3.7 28.3 + - + +
252B ASP 3.0 19.9 + - - +
253B ALA* 3.6 9.9 - - - +
255B GLN* 1.3 76.0 - - - +
257B ARG* 1.3 61.6 + - - +
260B TRP* 3.3 10.2 + - - +
10G T 4.8 8.4 + - - -
11G G 4.0 8.7 + - - -
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Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ASP 5.5 0.3 - - - +
232B VAL* 4.1 22.4 - - + +
253B ALA* 3.1 27.2 + - - +
254B ASP* 3.2 35.0 + - - +
255B GLN 3.0 0.2 - - - -
256B ARG* 1.3 76.4 - - - +
258B ASP* 1.3 58.9 + - - +
260B TRP* 3.9 2.3 - - - +
261B GLN* 2.9 44.0 + - + +
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Residues in contact with ASP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ASP 2.9 12.9 + - - +
255B GLN* 3.6 8.5 - - - +
257B ARG* 1.3 73.4 - - - +
259B PHE* 1.3 61.5 + - + +
261B GLN* 2.7 29.6 + - - +
262B ASN* 2.8 37.6 + - - -
266B TYR* 2.6 29.8 + - - -
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Residues in contact with PHE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ILE* 4.4 9.6 - - + -
200B MET* 3.0 38.5 - - + +
233B MET* 3.8 26.0 - - + -
236B ILE* 4.3 13.2 - - + -
251B PHE* 3.7 15.5 - + - -
255B GLN* 2.8 35.4 + - + +
258B ASP* 1.3 74.7 - - + +
260B TRP* 1.3 56.7 + - - +
262B ASN 3.3 2.1 - - - +
263B LYS* 3.0 21.8 + - - -
266B TYR* 3.6 34.8 - + - -
271B VAL* 4.9 2.0 - - + -
289B PHE* 3.9 26.2 - + - -
292B ILE* 3.8 19.7 - - + -
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Residues in contact with TRP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B MET* 4.0 22.2 - - + -
201B THR* 3.7 6.5 - - - -
202B ALA* 3.6 36.8 - - + -
229B GLU* 4.9 5.8 - - - -
230B GLU 5.4 0.4 - - - -
231B ASP* 3.2 44.0 + - - +
232B VAL* 3.5 6.7 - - - -
233B MET* 3.0 41.6 - - + +
256B ARG 3.3 7.5 + - - +
257B ARG 3.9 1.3 - - - +
258B ASP 3.1 0.8 - - - -
259B PHE* 1.3 76.1 - - - +
261B GLN* 1.3 69.3 + - + +
262B ASN 3.1 0.2 - - - -
263B LYS* 3.0 64.1 + - + +
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Residues in contact with GLN 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ARG* 2.9 34.1 + - + +
258B ASP* 2.7 21.2 + - - +
260B TRP* 1.3 76.9 - - + +
262B ASN* 1.3 67.3 + - - +
263B LYS* 3.5 5.1 + - - +
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Residues in contact with ASN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ASP* 2.8 34.2 + - - -
259B PHE 3.3 3.8 - - - -
261B GLN* 1.3 85.5 + - - +
263B LYS* 1.3 65.1 + - - +
264B GLU 3.1 3.5 + - - +
265B SER* 3.2 20.0 + - - +
266B TYR* 3.0 37.9 + - + +
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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