Contacts of the helix formed by residues 256 - 268 (chain A) in PDB entry 4O91
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 PRO 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ASN 3.3 7.0 - - - +
255A LEU* 1.3 94.4 - - + +
257A LYS* 1.3 57.0 + - - +
258A PRO* 4.1 5.8 - - + -
259A ILE* 2.8 35.8 + - + +
260A GLU* 2.9 11.0 + - - -
484A PHE* 3.7 23.6 - - + -
487A PHE* 3.5 41.7 - - + -
488A TYR* 3.2 20.6 - - + +
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Residues in contact with LYS 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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255A LEU 3.3 6.4 + - - +
256A PRO* 1.3 70.1 - - - +
258A PRO* 1.3 71.9 - - + +
260A GLU* 3.1 35.0 + - + +
261A SER* 2.9 28.3 + - - -
488A TYR* 5.6 0.2 - - - -
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Residues in contact with PRO 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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256A PRO* 3.4 10.5 - - + -
257A LYS* 1.3 93.8 - - + +
259A ILE* 1.3 60.0 + - + +
261A SER* 3.9 5.7 + - - -
262A LEU* 3.4 21.1 + - - +
283A ILE* 5.5 2.3 - - + +
287A LEU* 4.5 22.0 - - + +
487A PHE* 4.7 6.3 - - + -
488A TYR* 6.5 0.2 - - + -
491A TRP* 4.0 31.6 - - + -
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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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131A MET* 3.6 28.9 - - + -
219A LEU* 4.3 13.8 - - + +
223A ILE* 4.1 13.5 - - + -
255A LEU* 3.8 19.5 - - + -
256A PRO* 2.8 25.2 + - + +
258A PRO* 1.3 73.2 - - + +
260A GLU* 1.3 67.7 + - - +
261A SER 3.2 0.2 - - - -
262A LEU* 3.3 5.8 + - + +
263A MET* 2.9 23.5 + - + +
287A LEU* 4.0 21.1 - - + -
291A PHE* 4.0 19.7 - - + -
484A PHE* 4.0 14.6 - - + -
487A PHE* 5.2 2.0 - - + -
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Residues in contact with GLU 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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251A LEU* 3.7 30.6 - - + +
252A ILE 5.4 3.2 - - - +
255A LEU* 3.7 35.0 - - + +
256A PRO 2.9 11.0 + - - +
257A LYS* 3.1 35.8 + - - +
259A ILE* 1.3 77.4 - - - +
261A SER* 1.3 57.8 + - - +
263A MET* 3.7 2.8 - - - +
264A THR* 2.9 44.1 + - + +
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Residues in contact with SER 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 LYS* 2.9 19.4 + - - -
258A PRO* 3.9 6.7 + - - -
260A GLU* 1.3 78.1 - - - +
262A LEU* 1.3 62.2 + - - +
264A THR* 3.2 7.6 + - - -
265A ARG* 3.2 37.0 + - - +
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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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215A TRP* 3.7 32.1 - - + -
219A LEU* 4.9 3.1 - - + -
258A PRO 3.4 11.4 + - - +
259A ILE* 3.3 8.9 + - + +
261A SER* 1.3 80.1 + - - +
263A MET* 1.3 65.3 + - - +
265A ARG* 3.1 21.8 + - - +
266A CYS* 3.1 17.3 + - - -
275A PRO* 4.3 20.2 - - + -
280A ILE* 4.4 10.5 - - + -
283A ILE* 3.9 42.2 - - + -
284A MET* 3.9 19.3 - - + -
287A LEU* 5.2 2.7 - - + -
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Residues in contact with MET 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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216A GLY* 4.1 9.1 - - - +
219A LEU* 3.7 33.3 - - + +
220A TRP* 3.8 25.6 - - - +
223A ILE* 3.9 15.0 - - + -
251A LEU* 6.3 1.8 - - - -
252A ILE* 4.0 11.9 - - + -
255A LEU* 4.1 14.4 - - + -
259A ILE* 2.9 16.8 + - + +
260A GLU* 3.7 4.7 - - - +
262A LEU* 1.3 77.6 - - - +
264A THR* 1.3 65.7 + - + +
266A CYS* 3.2 15.8 + - - +
267A TRP* 3.3 51.0 + - + +
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Residues in contact with THR 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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251A LEU* 4.6 9.2 - - + -
260A GLU* 2.9 34.2 + - + +
261A SER* 3.2 11.1 + - - -
263A MET* 1.3 74.0 - - + +
265A ARG* 1.3 65.9 + - - +
267A TRP* 3.1 43.4 + - + +
268A SER* 3.4 10.2 + - - -
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Residues in contact with ARG 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 SER* 3.2 28.0 + - - +
262A LEU* 3.1 15.8 + - - +
264A THR* 1.3 77.2 + - - +
266A CYS* 1.3 58.5 + - - +
268A SER* 2.7 29.4 + - - -
273A GLN 3.9 10.3 + - - +
274A ARG* 3.5 8.3 - - - -
275A PRO* 3.6 29.9 - - + +
279A GLU* 2.7 37.5 + - - -
283A ILE* 4.3 13.5 - - - +
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Residues in contact with CYS 266 (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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212A VAL* 3.6 34.5 - - - +
213A PHE* 3.4 12.7 - - - -
215A TRP* 3.8 29.6 - - - -
216A GLY* 3.9 9.9 - - - -
262A LEU* 3.1 16.3 + - - -
263A MET* 3.4 9.4 - - - +
264A THR 3.2 0.2 - - - -
265A ARG* 1.3 80.8 - - - +
267A TRP* 1.3 57.2 + - - +
274A ARG* 3.3 22.6 + - - -
275A PRO* 3.9 10.3 - - - -
280A ILE* 3.9 9.6 - - - -
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Residues in contact with TRP 267 (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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213A PHE* 3.4 11.8 - + - -
216A GLY* 3.6 26.2 + - - -
217A ILE* 3.7 19.2 - - + +
220A TRP* 3.9 12.1 - + + -
248A ARG* 2.8 62.9 + - + +
249A PRO* 3.4 46.9 - - + -
250A PRO 4.7 1.6 - - - -
251A LEU* 4.7 11.7 - - + -
263A MET* 3.3 41.7 + - + -
264A THR* 3.1 31.8 + - + +
266A CYS* 1.3 75.0 - - - +
268A SER* 1.3 61.7 + - - +
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Residues in contact with SER 268 (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 ARG* 4.4 0.2 + - - -
264A THR 3.4 6.7 + - - -
265A ARG* 2.7 24.5 + - - -
266A CYS 3.3 0.6 - - - -
267A TRP* 1.3 78.8 - - - +
269A LYS* 1.3 61.9 + - - +
270A ASP 3.6 10.9 + - - -
273A GLN* 3.7 10.7 - - - -
274A ARG* 3.0 43.3 + - - +
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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