Contacts of the helix formed by residues 252 - 264 (chain A) in PDB entry 2J2C
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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215A LYS* 5.5 7.2 - - - +
250A ASN 3.8 0.6 + - - -
251A SER* 1.3 73.6 - - - +
253A TYR* 1.3 62.3 + - - +
254A LYS* 3.3 9.3 + - - +
255A TYR* 3.0 28.9 + - - +
256A THR* 2.6 32.8 + - - -
288A VAL* 4.2 1.1 - - - -
289A ASP* 3.3 22.4 - - - +
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Residues in contact with TYR 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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252A ASP* 1.3 75.2 - - - +
254A LYS* 1.3 61.9 + - + +
256A THR* 3.4 0.8 + - - -
257A ASP* 2.8 49.0 + - + +
279A TRP* 4.2 19.7 - + - -
280A GLN* 3.1 26.9 + - - +
288A VAL* 3.9 23.3 - - + +
289A ASP* 4.7 1.0 + - - -
305A VAL* 3.7 26.2 - - + -
307A THR* 3.9 36.9 + - + +
310A GLY* 4.4 18.8 + - - +
326A VAL* 3.8 34.6 - - + +
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Residues in contact with LYS 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* 3.3 8.5 + - - +
253A TYR* 1.3 81.5 - - + +
255A TYR* 1.3 57.7 + - - +
257A ASP* 3.7 4.4 - - - +
258A LYS* 3.1 47.4 + - - +
309A THR 3.2 27.7 + - - -
310A GLY* 4.1 19.6 + - - +
311A LYS* 5.6 5.3 - - - +
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Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 3.9 11.0 - - + -
54A ASP* 3.7 13.2 - - - -
60A TYR* 2.6 39.0 + - - -
65A TYR* 4.5 5.7 + - - -
215A LYS* 3.6 55.6 - - + +
218A THR* 3.8 8.3 + - - +
219A VAL* 4.0 19.5 - - + -
251A SER* 4.1 8.5 - - - -
252A ASP* 3.0 20.5 + - - +
254A LYS* 1.3 75.1 - - - +
256A THR* 1.3 64.9 + - - +
258A LYS* 3.3 8.6 + - + +
259A ILE* 3.0 47.9 + - + +
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Residues in contact with THR 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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53A MET* 3.8 15.5 - - - -
247A LEU* 3.7 29.8 - - + -
249A THR* 4.3 3.8 - - + -
251A SER* 2.7 21.1 + - - -
252A ASP 2.6 25.8 + - - -
253A TYR* 3.6 3.8 - - - -
255A TYR* 1.3 76.4 - - - +
257A ASP* 1.3 56.7 + - - +
260A MET* 2.8 45.6 + - + +
279A TRP* 4.1 10.3 - - + -
288A VAL* 3.8 11.1 - - + +
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Residues in contact with ASP 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TYR* 2.8 48.5 + - + +
254A LYS* 3.7 5.8 - - - +
256A THR* 1.3 74.2 - - - +
258A LYS* 1.3 55.6 + - - +
261A THR* 2.5 45.5 + - - -
279A TRP* 2.9 29.1 + - - +
280A GLN* 3.8 5.9 + - - -
307A THR 5.6 0.5 - - - +
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Residues in contact with LYS 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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219A VAL* 3.4 46.2 - - + -
222A LEU* 4.3 6.1 - - + +
254A LYS* 3.1 34.8 + - - +
255A TYR* 3.3 8.9 + - - +
257A ASP* 1.3 75.8 - - + +
259A ILE* 1.3 63.9 + - - +
261A THR* 3.8 4.3 - - - -
262A TYR* 3.3 21.7 + - - +
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Residues in contact with ILE 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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53A MET* 3.9 15.5 - - + -
58A ALA* 3.3 33.2 - - + -
60A TYR* 4.0 4.0 - - - +
218A THR* 4.7 3.4 - - + -
219A VAL* 4.4 4.9 - - + -
222A LEU* 3.7 27.8 - - + -
226A VAL* 4.7 7.2 - - + -
255A TYR* 3.0 61.2 + - + +
258A LYS* 1.3 76.6 - - - +
260A MET* 1.3 59.5 + - - +
262A TYR* 3.2 8.2 + - - +
263A LEU* 2.9 32.6 + - + +
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Residues in contact with MET 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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53A MET* 3.9 18.4 - - - -
57A LEU* 3.8 24.0 - - + -
247A LEU* 4.5 5.2 - - + -
256A THR* 2.8 41.9 + - + +
259A ILE* 1.3 69.9 - - - +
261A THR* 1.3 63.6 + - - +
263A LEU* 3.2 14.1 + - + -
264A PHE* 3.2 44.5 + - + +
279A TRP* 3.4 33.7 - - + +
283A PHE* 3.6 38.1 - - + -
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Residues in contact with THR 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 ASP* 2.5 39.9 + - - -
258A LYS* 3.8 6.0 - - - -
260A MET* 1.3 70.7 - - - +
262A TYR* 1.3 63.5 + - - +
264A PHE* 3.2 5.6 + - - +
265A ASP* 3.1 25.2 + - + +
276A HIS* 5.4 2.4 + - + -
279A TRP* 3.6 12.9 - - + -
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Residues in contact with TYR 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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61A LYS* 5.3 0.9 + - - -
222A LEU* 3.4 53.4 + - + -
223A GLU* 3.4 32.2 - - + +
226A VAL* 3.1 49.2 + - + -
227A VAL 4.5 0.7 - - - -
228A LYS* 3.0 67.9 + - + +
258A LYS 3.3 4.5 + - - +
259A ILE* 3.2 11.3 + - + +
261A THR* 1.3 80.5 - - - +
263A LEU* 1.3 65.2 + - + +
265A ASP* 3.1 12.1 + - - -
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Residues in contact with LEU 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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57A LEU* 3.5 44.0 - - + +
58A ALA* 4.0 9.6 - - + -
226A VAL* 4.1 14.8 - - + -
227A VAL 3.4 25.1 - - - +
228A LYS* 4.4 8.2 - - - +
229A ASP 4.6 4.2 + - - +
232A LEU* 4.1 18.1 - - + +
233A PRO* 4.9 0.9 - - - +
259A ILE* 2.9 19.7 + - + +
260A MET* 3.2 24.2 + - - +
262A TYR* 1.3 79.6 - - + +
264A PHE* 1.3 67.4 + - + +
265A ASP 3.4 0.2 - - - -
266A PHE* 3.3 19.6 - - - -
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Residues in contact with PHE 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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232A LEU* 3.6 20.9 - - + -
233A PRO* 3.9 24.6 - - + +
236A LEU* 3.7 24.7 - - + -
260A MET* 3.2 42.5 + - + +
261A THR* 3.2 4.7 + - - +
262A TYR 3.1 0.6 - - - -
263A LEU* 1.3 80.0 - - + +
265A ASP* 1.3 59.6 + - - +
266A PHE* 2.9 18.4 + - - +
268A HIS 4.6 0.9 - - - +
276A HIS* 2.9 26.1 + - - +
277A ARG 4.7 0.9 - - - +
279A TRP* 3.5 20.4 - - + +
282A TYR* 3.4 49.8 - + + -
283A PHE* 4.6 1.6 - + - -
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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