Contacts of the helix formed by residues 252 - 263 (chain A) in PDB entry 2V3D
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 THR 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A LEU* 3.9 23.2 - - + +
251A PHE* 1.3 79.0 - - - +
253A PRO* 1.4 75.7 - - - +
254A GLU* 3.6 13.7 + - - +
255A HIS* 3.1 25.8 + - + +
256A GLN* 3.0 17.7 + - - +
291A TRP* 3.8 1.1 - - - -
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Residues in contact with PRO 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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240A LEU* 5.9 1.1 - - + -
252A THR* 1.4 87.9 - - - +
254A GLU* 1.3 74.4 - - - +
256A GLN* 3.8 0.9 - - - +
257A ARG* 2.9 28.2 + - - +
290A HIS* 4.1 18.6 - - + +
291A TRP* 3.5 54.3 - - + +
294A VAL* 3.7 19.0 - - + +
295A VAL* 3.8 3.6 - - - +
319B PRO* 5.4 8.5 - - + -
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Residues in contact with GLU 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 THR* 3.6 16.2 + - - +
253A PRO* 1.3 88.2 - - - +
255A HIS* 1.3 66.7 + - - +
257A ARG* 3.4 32.6 + - - +
258A ASP* 3.0 31.3 + - - +
290A HIS* 4.5 5.0 + - - -
294A VAL* 3.8 21.9 - - + +
319B PRO* 6.0 1.0 - - - +
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Residues in contact with HIS 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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196A SER* 4.0 25.4 - - - -
197A LEU* 4.2 9.6 - - + -
199A GLY 5.3 2.9 - - - -
201A PRO* 3.6 21.9 - - + +
206A HIS* 2.9 28.1 + + - -
250A GLY 4.1 6.8 + - - -
251A PHE* 3.7 24.2 - + + -
252A THR* 3.1 28.1 + - + +
254A GLU* 1.3 76.9 - - - +
256A GLN* 1.3 58.7 + - - +
258A ASP* 3.3 1.8 + - - -
259A PHE* 2.9 27.4 + - + +
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Residues in contact with GLN 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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232A ALA* 3.5 30.2 - - + +
233A GLU* 4.6 3.2 - - - +
236A PRO* 4.0 17.4 - - - +
251A PHE* 4.0 17.4 - - + +
252A THR 3.0 16.9 + - - +
253A PRO 3.8 3.8 - - - +
255A HIS* 1.3 75.3 - - - +
257A ARG* 1.3 66.4 + - - +
259A PHE* 3.7 4.0 - - + +
260A ILE* 2.8 38.3 + - + +
280A MET* 3.4 10.9 - - - +
281A LEU 2.9 27.4 + - - +
291A TRP* 3.6 25.7 - - + -
295A VAL* 4.5 4.5 - - + -
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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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253A PRO 2.9 21.9 + - - +
254A GLU* 3.5 36.8 - - - +
256A GLN* 1.3 73.5 - - - +
258A ASP* 1.3 87.4 + - - +
260A ILE* 3.7 0.2 - - - +
261A ALA* 2.9 29.1 + - - +
294A VAL* 3.3 28.5 + - - +
295A VAL* 4.0 24.2 - - - +
298A ASP* 3.5 32.6 + - + +
301A ALA* 3.6 6.8 - - + +
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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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201A PRO* 3.6 23.8 - - + +
254A GLU* 3.0 15.3 + - - +
255A HIS* 5.1 0.3 - - - -
257A ARG* 1.3 113.9 + - - +
259A PHE* 1.3 58.8 + - - +
261A ALA* 4.3 4.8 - - - +
262A ARG* 2.9 61.1 + - - +
298A ASP* 4.2 5.5 - - - +
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Residues in contact with PHE 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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197A LEU* 4.6 0.2 - - + -
201A PRO* 3.6 8.4 - - + +
206A HIS* 3.7 34.3 - + + -
209A TRP* 3.3 35.4 - + - -
210A ALA* 4.1 9.4 - - - -
213A PHE* 4.5 1.6 - + - -
232A ALA* 4.3 12.1 - - + -
251A PHE* 3.8 23.3 - + + -
255A HIS 2.9 18.3 + - - +
256A GLN* 3.7 6.3 - - + +
258A ASP* 1.3 72.8 - - - +
260A ILE* 1.3 57.3 + - + +
263A ASP* 2.8 36.3 + - + +
264A LEU* 2.8 63.5 + - + -
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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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232A ALA* 4.2 13.0 - - + -
256A GLN* 2.8 42.1 + - + +
257A ARG 3.7 3.1 - - - +
259A PHE* 1.3 75.0 - - + +
261A ALA* 1.3 65.0 + - - +
264A LEU* 4.1 7.2 - - + -
265A GLY* 2.9 28.2 + - - +
266A PRO* 3.3 2.8 - - - +
278A LEU* 3.8 29.2 - - + -
280A MET* 4.2 13.2 - - + -
295A VAL* 4.4 5.8 - - + -
301A ALA* 3.8 26.5 - - + +
304A TYR* 3.8 6.1 - - + -
305A VAL* 4.0 20.6 - - + -
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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 ARG 2.9 20.9 + - - +
258A ASP* 3.9 7.2 - - - +
260A ILE* 1.3 73.8 - - - +
262A ARG* 1.3 62.8 + - + +
266A PRO* 3.2 19.6 - - - +
298A ASP* 4.4 7.0 - - - +
300A GLU* 3.8 26.3 - - + +
301A ALA* 3.7 20.2 - - + +
304A TYR* 3.8 6.1 - - - -
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Residues in contact with ARG 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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200A GLN* 4.2 14.3 + - - +
201A PRO* 2.9 38.0 + - - +
202A GLY* 3.9 10.7 - - - +
207A GLN* 4.2 6.8 + - - +
258A ASP* 2.9 42.9 + - - +
261A ALA* 1.3 84.2 - - + +
263A ASP* 1.3 72.7 + - - +
266A PRO* 3.6 12.8 - - - +
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Residues in contact with ASP 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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201A PRO* 3.3 11.4 - - - +
202A GLY* 2.8 37.8 + - - -
206A HIS* 3.1 25.2 - - - +
207A GLN* 3.3 27.3 + - - +
210A ALA* 3.7 5.2 - - + -
259A PHE* 2.8 26.8 + - + +
261A ALA 3.7 0.4 - - - -
262A ARG* 1.3 78.8 - - - +
264A LEU* 1.3 64.9 + - - +
265A GLY 3.6 0.9 - - - -
266A PRO* 3.6 1.6 - - - +
267A THR* 2.7 31.2 + - - -
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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