Contacts of the helix formed by residues 252 - 264 (chain A) in PDB entry 2C3E
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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237A MET* 3.7 9.5 - - - +
250A TYR 3.9 0.2 - - - -
251A THR* 1.3 85.2 + - - +
253A THR* 1.3 66.4 + - - -
254A VAL 3.3 2.9 - - - -
255A ASP* 2.8 6.6 + - - +
256A CYS* 2.8 22.5 + - - +
802A CDL 3.6 21.3 - - - -
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Residues in contact with THR 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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175A GLY* 5.8 0.9 - - - -
177A ASN* 4.6 3.3 - - - +
178A VAL* 3.6 30.9 + - + +
181A GLN* 5.0 3.1 - - - +
233A VAL* 4.6 3.1 - - + -
237A MET* 4.1 15.7 - - + +
252A GLY* 1.3 69.2 - - - -
254A VAL* 1.3 58.3 + - - +
256A CYS* 2.8 18.8 + - - +
257A TRP* 2.9 39.4 + - + +
802A CDL 2.9 54.4 + - - +
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Residues in contact with VAL 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 GLY 3.3 0.4 - - - -
253A THR* 1.3 69.9 - - - +
255A ASP* 1.3 57.9 + - - +
256A CYS 2.9 5.4 - - - -
257A TRP* 3.4 10.6 + - + +
258A ARG* 2.9 33.9 + - + +
802A CDL 3.1 52.0 - - - +
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Residues in contact with ASP 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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250A TYR* 3.1 12.2 - - - -
251A THR* 2.7 36.2 + - - +
252A GLY* 2.8 24.3 + - - +
254A VAL* 1.3 78.8 - - - +
256A CYS* 1.3 55.6 + - - +
258A ARG* 4.1 11.1 - - - +
259A LYS* 2.9 61.9 + - - +
802A CDL 4.4 0.6 + - - -
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Residues in contact with CYS 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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233A VAL* 3.7 30.1 - - + -
236A ARG* 3.8 16.4 - - - -
237A MET* 3.2 33.2 - - - -
250A TYR* 3.5 14.8 - - + -
252A GLY 2.8 3.4 + - - -
253A THR* 2.8 13.3 + - - +
255A ASP* 1.3 75.9 - - - +
257A TRP* 1.3 64.2 + - - +
258A ARG 2.9 1.8 + - - -
260A ILE* 3.1 36.8 + - - +
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Residues in contact with TRP 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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178A VAL* 4.0 8.1 - - + +
181A GLN* 4.8 1.7 + - - -
229A PRO* 4.0 19.1 - - + -
230A PHE* 3.3 61.7 - + - -
233A VAL* 3.8 11.9 - - + +
253A THR* 2.9 53.3 + - + +
254A VAL* 3.4 7.8 + - + +
256A CYS* 1.3 73.4 - - - +
258A ARG* 1.3 59.6 + - - +
261A ALA* 3.4 25.8 + - - +
269A PHE* 3.5 33.3 - + - -
802A CDL 3.9 23.7 + - + +
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Residues in contact with ARG 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 VAL* 2.9 23.6 + - + +
255A ASP* 3.5 15.9 - - - +
256A CYS 2.9 0.4 - - - -
257A TRP* 1.3 78.0 - - - +
259A LYS* 1.3 79.9 + - + +
260A ILE 3.3 0.2 + - - -
261A ALA* 4.0 2.4 - - - +
262A LYS* 2.9 57.5 + - - +
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Residues in contact with LYS 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 ILE 5.3 1.0 + - - -
249A MET* 2.8 33.3 + - + +
250A TYR* 3.1 20.4 - - + +
255A ASP* 2.9 45.5 + - - +
258A ARG* 1.3 86.8 - - + +
260A ILE* 1.3 58.7 + - - +
262A LYS* 2.9 8.2 + - + +
263A ASP* 2.7 52.8 + - - +
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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 THR* 4.4 4.7 - - + -
233A VAL* 4.2 4.3 - - + -
236A ARG* 3.4 24.5 - - + +
250A TYR* 3.6 16.3 + - - +
256A CYS* 3.1 31.8 + - - +
259A LYS* 1.3 73.7 - - - +
261A ALA* 1.3 57.3 + - - +
262A LYS 2.6 9.2 + - - -
263A ASP* 5.3 0.2 - - - -
264A GLU* 2.6 38.5 + - + +
265A GLY 3.1 2.6 + - - +
268A ALA* 3.6 28.5 - - + -
269A PHE* 3.3 42.6 - - + +
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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 TRP 3.4 17.4 + - - +
258A ARG* 4.1 2.5 - - - +
260A ILE* 1.3 78.4 - - - +
262A LYS* 1.3 60.7 + - - +
265A GLY* 3.2 29.2 - - - +
266A PRO* 4.2 5.1 - - + +
269A PHE* 3.8 11.4 - - + -
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Residues in contact with LYS 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 ARG* 2.9 44.2 + - - +
259A LYS* 2.9 9.2 + - + +
260A ILE 2.6 5.1 + - - -
261A ALA* 1.3 75.7 - - - +
263A ASP* 1.3 84.9 + - - +
264A GLU 3.5 0.3 + - - -
265A GLY* 3.6 4.5 + - - -
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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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39A HIS* 5.0 10.6 - - + +
259A LYS* 2.7 45.6 + - - +
262A LYS* 1.3 92.8 - - - +
264A GLU* 1.3 63.2 + - + +
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Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 2.8 44.6 - - + +
236A ARG* 2.7 36.4 + - - -
250A TYR* 3.4 9.2 + - - -
260A ILE* 2.6 20.5 + - - +
263A ASP* 1.3 73.2 - - + +
265A GLY* 1.3 58.9 + - - +
267A LYS 4.7 0.2 + - - -
268A ALA* 3.0 32.5 + - + +
271A LYS* 2.9 26.6 + - - +
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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