Contacts of the helix formed by residues 253 - 265 (chain A) in PDB entry 5J3V
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 HIS 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ILE* 5.3 2.8 - - + +
221A PHE* 3.6 39.9 - + + -
249A ARG 4.4 15.9 - - - -
250A LEU* 3.3 7.8 + - - +
252A PRO* 1.3 90.0 - - + +
254A MET* 1.3 62.5 + - - +
255A HIS 3.6 1.6 - - - -
256A ASN* 3.6 18.8 + - + +
257A ILE* 3.1 25.6 + - + +
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Residues in contact with MET 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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243A LEU* 4.5 17.7 - - + -
247A MET* 5.1 1.6 - - - +
250A LEU* 3.0 17.6 + - - +
251A LEU* 3.2 22.2 - - + +
252A PRO 3.2 4.2 + - - -
253A HIS* 1.3 77.1 - - - +
255A HIS* 1.3 65.7 + - + +
257A ILE* 3.0 22.3 + - - +
258A VAL* 3.0 22.4 + - + +
279A PHE* 4.9 4.9 - - + -
283A LEU* 3.7 40.2 - - + -
288A ILE* 4.5 12.8 - - + -
292A VAL* 3.9 35.2 - - + -
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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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252A PRO 5.2 0.4 + - - -
254A MET* 1.3 86.2 - - + +
256A ASN* 1.3 63.2 + - - +
258A VAL* 3.6 6.1 + - - +
259A GLU* 3.2 33.7 + - - +
291A ASP 5.4 1.1 - - - -
292A VAL* 3.7 38.9 - - + +
295A ARG* 3.4 34.6 + - + +
296A HIS* 3.1 22.9 + - + +
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Residues in contact with ASN 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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252A PRO 4.9 2.4 - - - +
253A HIS* 3.6 22.5 + - + +
254A MET 3.2 0.2 - - - -
255A HIS* 1.3 80.2 - - - +
257A ILE* 1.3 62.1 + - + +
259A GLU* 3.8 14.1 + - - +
260A TYR* 3.2 21.3 + - - +
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Residues in contact with ILE 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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221A PHE* 4.2 24.7 - - + -
239A LEU* 4.5 20.0 - - + -
243A LEU* 6.4 0.2 - - + -
250A LEU* 3.9 37.0 - - + +
253A HIS* 3.1 18.8 + - + +
254A MET* 3.0 11.7 + - - +
256A ASN* 1.3 76.6 - - + +
258A VAL* 1.3 55.6 + - - +
260A TYR* 3.0 8.9 + - + +
261A MET* 2.7 39.6 + - + +
279A PHE* 3.7 31.9 - - + -
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Residues in contact with VAL 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 MET* 3.0 30.0 + - + +
255A HIS* 3.9 6.1 - - - +
257A ILE* 1.3 76.9 - - - +
259A GLU* 1.3 56.9 + - - +
261A MET* 3.4 2.0 + - - -
262A LEU* 2.9 29.2 + - + +
279A PHE* 4.8 10.1 - - + -
280A TRP* 3.5 27.1 - - + -
283A LEU* 4.8 3.4 - - + -
292A VAL* 4.1 21.5 - - + -
293A LEU* 4.2 4.0 - - + -
296A HIS* 3.5 35.4 - - + +
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Residues in contact with GLU 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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255A HIS* 3.2 20.3 + - - +
256A ASN* 4.0 15.9 + - - +
257A ILE 3.2 0.6 - - - -
258A VAL* 1.3 73.3 - - - +
260A TYR* 1.3 65.2 + - - +
262A LEU* 3.2 9.9 + - - +
263A GLN* 3.2 30.4 + - - +
295A ARG* 5.7 0.7 - - - -
296A HIS* 3.7 24.4 - - + +
299A LYS* 4.7 12.8 + - - +
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Residues in contact with TYR 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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224A ALA* 2.7 53.1 + - + -
225A GLY* 5.3 0.4 - - - -
232A ARG* 4.5 5.2 - - - +
235A VAL* 4.1 8.3 - - + +
236A CYS* 4.2 16.7 - - - -
239A LEU* 4.3 22.7 - - + -
256A ASN 3.2 12.9 + - - +
257A ILE* 3.0 12.5 + - - +
259A GLU* 1.3 79.3 - - - +
261A MET* 1.3 66.3 + - - +
263A GLN* 3.3 11.7 + - - +
264A ARG* 3.1 63.3 + - + +
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Residues in contact with MET 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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236A CYS* 3.6 29.4 - - + +
239A LEU* 3.6 42.4 - - + -
240A VAL* 4.5 0.4 - - + -
257A ILE* 2.7 24.4 + - + +
258A VAL 3.8 4.0 - - - +
260A TYR* 1.3 78.0 - - + +
262A LEU* 1.3 52.7 + - - +
264A ARG* 3.7 2.2 - - - +
265A THR* 2.6 38.9 + - - -
276A ALA* 4.1 27.9 - - - +
279A PHE* 3.7 34.8 - - + -
280A TRP* 3.8 15.5 - - + -
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Residues in contact with LEU 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 VAL 2.9 18.5 + - - +
259A GLU* 3.2 8.3 + - - +
261A MET* 1.3 77.3 - - - +
263A GLN* 1.3 62.3 + - + +
265A THR* 3.9 4.6 - - - +
266A GLN* 3.1 31.8 + - - +
280A TRP* 3.7 8.3 - - + -
296A HIS* 4.7 10.1 - - + +
299A LYS* 3.6 49.8 - - + +
300A LEU* 3.7 39.3 - - + +
303A VAL* 4.0 16.4 - - + -
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Residues in contact with GLN 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 GLU* 3.2 16.1 + - - +
260A TYR* 3.8 11.6 - - - +
262A LEU* 1.3 78.3 - - + +
264A ARG* 1.3 82.1 + - - +
265A THR 3.1 4.7 - - - -
266A GLN* 3.1 30.7 + - - +
267A ASP* 3.9 0.3 - - - -
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Residues in contact with ARG 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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224A ALA 5.1 1.0 + - - -
225A GLY* 5.7 4.0 - - - -
232A ARG* 3.9 21.6 - - - +
236A CYS* 4.0 7.2 - - - -
260A TYR* 3.1 59.5 + - + +
261A MET* 3.3 3.5 + - - +
263A GLN* 1.3 117.9 + - - +
265A THR* 1.3 62.9 + - - +
267A ASP* 3.2 41.8 + - - +
272A VAL* 3.9 6.2 - - + +
273A ALA* 3.3 14.0 + - - -
276A ALA* 3.5 20.7 - - + +
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Residues in contact with THR 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 MET 2.6 21.5 + - - -
262A LEU* 3.9 9.1 - - - -
263A GLN 3.1 0.4 - - - -
264A ARG* 1.3 78.6 - - - +
266A GLN* 1.3 58.1 + - - +
267A ASP 3.3 0.9 - - - -
273A ALA* 3.4 23.4 - - - +
276A ALA* 3.9 6.4 + - - -
277A CYS* 4.4 21.5 - - + -
280A TRP* 3.2 26.2 + - + +
303A VAL* 3.8 24.0 - - + +
304A LEU* 5.2 3.6 - - + -
375A LEU* 4.7 11.5 - - + +
379A SER* 5.6 0.9 - - - +
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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