Contacts of the helix formed by residues 252 - 265 (chain A) in PDB entry 2W9M
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 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLY* 4.2 2.0 - - - -
190A ARG* 3.8 13.9 - - - +
249A LEU 3.7 8.3 - - - -
250A ARG* 3.7 1.8 - - - -
251A SER* 1.3 87.2 + - - -
253A GLU* 1.3 54.9 + - - +
254A HIS 2.8 1.9 + - - -
255A PHE* 2.6 35.6 + - - +
256A ALA* 2.8 10.7 + - - -
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Residues in contact with GLU 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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190A ARG* 6.0 0.6 - - - +
196A ARG* 5.9 4.2 - - - -
249A LEU 4.7 0.8 + - - -
252A GLY* 1.3 67.2 - - - +
254A HIS* 1.3 64.5 + - - +
256A ALA* 3.3 5.5 + - - +
257A GLY 3.1 18.5 + - - -
407B ASP* 3.4 35.4 - - + +
437B ARG* 2.9 59.5 + - - +
440B GLU* 3.4 29.4 - - - +
441B ARG* 6.0 0.3 - - - -
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Residues in contact with HIS 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG* 6.1 1.9 - - - +
252A GLY 2.8 4.6 + - - -
253A GLU* 1.3 76.3 - - - +
255A PHE* 1.3 67.1 + - + +
257A GLY 3.5 0.5 + - - -
258A GLN* 3.2 35.2 + - + +
299A ARG* 5.4 0.7 - - - -
304A ARG 4.4 4.7 - - - +
305A GLU 4.2 3.1 - - - -
306A PRO* 3.5 37.7 - - + +
309A ASP* 2.9 36.6 + - - -
405B LEU* 5.5 0.8 - - + +
406B ASP* 2.7 41.0 + - - +
407B ASP* 3.8 20.3 + - - +
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Residues in contact with PHE 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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248A LEU* 3.7 40.4 - - + -
251A SER* 3.8 11.2 - - - -
252A GLY* 2.6 12.4 + - - +
254A HIS* 1.3 78.0 - - + +
256A ALA* 1.3 63.8 + - - +
258A GLN* 2.9 12.1 + - + +
259A VAL* 2.8 41.2 + - + +
291A PHE* 3.9 25.6 - + - -
299A ARG* 3.9 36.6 - - + -
304A ARG* 3.8 44.8 + - + +
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Residues in contact with ALA 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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248A LEU 4.6 1.3 - - - -
249A LEU* 3.4 38.8 - - + +
252A GLY 2.8 14.9 + - - +
253A GLU* 3.6 10.8 - - - +
255A PHE* 1.3 75.7 - - - +
257A GLY* 1.3 61.6 + - - +
259A VAL* 3.3 10.9 + - - +
260A GLN* 3.0 32.0 + - - +
437B ARG* 5.6 0.7 - - - +
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Residues in contact with GLY 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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253A GLU 3.1 11.0 + - - -
254A HIS 3.9 3.1 - - - -
256A ALA* 1.3 78.3 - - - +
258A GLN* 1.3 62.8 + - - +
260A GLN* 3.9 10.2 + - - +
261A ALA* 3.0 25.1 + - - +
406B ASP* 5.1 3.1 - - - -
437B ARG* 4.7 8.7 - - - +
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Residues in contact with GLN 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 HIS* 3.2 30.8 + - + +
255A PHE* 2.9 17.8 + - + +
257A GLY* 1.3 78.1 - - - +
259A VAL* 1.3 57.5 + - - +
261A ALA* 3.4 6.8 + - - +
262A ALA* 3.0 27.3 + - - +
299A ARG* 3.7 12.6 + - - +
309A ASP* 3.3 33.6 + - - +
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Residues in contact with VAL 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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248A LEU* 4.3 22.2 - - + +
249A LEU* 4.7 4.3 - - + -
255A PHE* 2.8 42.6 + - + +
256A ALA* 3.4 15.5 - - - +
258A GLN* 1.3 70.9 - - - +
260A GLN* 1.3 66.5 + - + +
262A ALA* 3.5 8.2 + - + +
263A ALA* 3.0 25.6 + - - +
270A LEU* 3.6 22.9 - - + +
291A PHE* 4.9 9.2 - - + -
294A LEU* 4.4 12.9 - - + +
296A LEU* 5.3 3.6 - - + -
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Residues in contact with GLN 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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249A LEU* 3.5 28.8 - - + +
256A ALA* 3.0 23.7 + - - +
257A GLY* 3.9 7.7 + - - +
259A VAL* 1.3 76.2 - - + +
261A ALA* 1.3 66.1 + - - +
263A ALA* 3.0 7.1 + - - +
264A GLN* 2.9 37.3 + - - +
270A LEU* 3.3 31.7 + - + +
271A THR* 5.0 1.2 + - - +
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Residues in contact with ALA 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 GLY 3.0 18.8 + - - +
258A GLN* 3.4 8.1 - - - +
260A GLN* 1.3 76.1 - - - +
262A ALA* 1.3 61.3 - - - +
264A GLN* 3.6 10.1 + - - +
265A ALA* 3.1 25.3 + - - +
75B ASP* 4.1 6.6 - - - +
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Residues in contact with ALA 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 GLN 3.0 17.0 + - - +
259A VAL* 3.6 9.6 - - - +
261A ALA* 1.3 76.9 - - - +
263A ALA* 1.3 60.8 + - - +
265A ALA* 3.6 6.3 + - - +
266A ARG* 3.1 38.1 + - - +
294A LEU* 4.8 1.1 - - + -
296A LEU* 4.1 24.7 - - + -
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Residues in contact with ALA 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 VAL 3.0 14.8 + - - +
260A GLN 3.0 7.4 + - - +
262A ALA* 1.3 74.9 - - - +
264A GLN* 1.3 60.2 + - + +
266A ARG* 2.9 19.4 + - - +
268A PHE* 3.1 34.8 + - + +
270A LEU* 4.0 24.9 - - + +
294A LEU* 4.0 20.9 - - + -
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Residues in contact with GLN 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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260A GLN* 2.9 30.9 + - - +
261A ALA* 4.0 7.7 + - - +
263A ALA* 1.3 71.2 - - + +
265A ALA* 1.3 58.1 + - - +
266A ARG 2.9 10.8 + - - -
267A GLY* 3.2 10.0 + - - -
268A PHE 3.3 16.4 - - - +
269A THR* 5.0 12.9 + - - +
270A LEU 5.8 0.9 - - - +
75B ASP* 5.0 3.1 - - - +
78B ARG* 3.4 14.8 - - - +
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Residues in contact with ALA 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 ALA 3.1 19.5 + - - +
262A ALA* 3.8 9.0 - - - +
263A ALA 3.2 0.4 - - - -
264A GLN* 1.3 75.7 - - - +
266A ARG* 1.3 65.6 + - + +
267A GLY 3.7 0.2 - - - -
71B ALA* 4.6 7.0 - - + +
74B SER* 3.9 11.3 - - - -
75B ASP* 3.5 36.2 + - + +
78B ARG* 2.9 20.2 + - - +
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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