Contacts of the helix formed by residues 251 - 262 (chain A) in PDB entry 4BPW
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 ILE 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A VAL* 3.8 26.5 - - + -
248A PRO* 3.3 14.8 - - + +
249A GLU 3.0 1.0 - - - -
250A THR* 1.3 84.1 - - - +
252A HIS* 1.3 64.4 + - - +
253A ASP 3.4 2.0 - - - -
254A GLU* 3.7 10.0 + - - +
255A LEU* 3.2 43.0 + - + +
272A LEU* 6.1 0.2 - - + -
275A VAL* 3.8 23.8 - - + +
276A ALA* 4.7 8.1 - - + +
279A TYR* 3.6 32.3 - - + -
292A LEU* 4.1 15.7 - - + -
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Residues in contact with HIS 252 (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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244A LEU* 2.7 53.2 + - + +
245A ALA* 4.8 2.9 - - - -
247A VAL* 2.9 23.5 + - + -
248A PRO 3.0 21.8 + - - -
249A GLU* 3.0 35.1 + - + +
251A ILE* 1.3 79.2 - - - +
253A ASP* 1.3 58.8 + - - +
255A LEU* 3.3 2.4 + - - +
256A GLN* 2.7 39.0 + - - +
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Residues in contact with ASP 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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249A GLU* 4.4 12.9 + - - +
250A THR 5.4 1.4 + - - +
252A HIS* 1.3 78.0 - - - +
254A GLU* 1.3 67.7 + - - +
256A GLN* 3.1 8.0 + - - +
257A GLN* 3.1 33.0 + - - +
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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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250A THR 5.6 1.0 + - - +
251A ILE* 3.7 14.5 + - - +
252A HIS 3.4 0.4 - - - -
253A ASP* 1.3 79.5 - - - +
255A LEU* 1.3 63.0 + - - +
257A GLN* 3.5 7.0 + - - +
258A SER* 3.2 27.5 + - - +
275A VAL* 3.9 25.2 - - + +
278A ARG* 3.0 31.1 + - - -
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Residues in contact with LEU 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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244A LEU* 3.7 27.8 - - + -
247A VAL* 4.6 2.7 - - + -
251A ILE* 3.2 40.8 + - + +
252A HIS 3.7 3.1 - - - +
253A ASP 3.2 0.4 - - - -
254A GLU* 1.3 78.3 - - - +
256A GLN* 1.3 59.0 + - - +
258A SER* 3.2 3.5 + - - -
259A PHE* 2.8 51.2 + - + -
271A HIS* 3.9 5.6 - - + +
272A LEU* 3.7 35.7 - - + +
275A VAL* 3.6 30.1 - - + -
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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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237A LYS* 3.4 27.3 - - - +
240A TRP* 2.6 30.4 + - - -
241A ASP* 3.7 8.1 + - - -
244A LEU* 3.6 19.7 - - - +
252A HIS* 2.7 21.4 + - - +
253A ASP* 3.1 9.4 + - - +
255A LEU* 1.3 72.6 - - - +
257A GLN* 1.3 62.3 + - + +
259A PHE* 3.4 8.6 + - - +
260A GLN* 3.2 38.0 + - - +
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Residues in contact with GLN 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 ASP* 3.1 19.0 + - - +
254A GLU* 3.8 9.1 - - - +
256A GLN* 1.3 75.2 - - + +
258A SER* 1.3 66.0 + - - +
260A GLN* 3.0 23.3 + - - +
261A LYS* 3.0 44.2 + - - +
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Residues in contact with SER 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 GLU* 3.2 18.1 + - - +
255A LEU* 3.2 11.5 + - - -
257A GLN* 1.3 77.8 - - - +
259A PHE* 1.3 63.5 + - - +
261A LYS* 3.6 6.9 + - - +
262A SER* 3.0 30.0 + - - -
271A HIS* 3.7 40.0 + - - -
275A VAL* 5.4 2.4 - - - +
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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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234A LEU* 4.6 7.4 - - + -
240A TRP* 3.5 49.8 - + + -
243A ILE* 5.9 0.4 - - + -
244A LEU* 3.9 22.9 - - + -
255A LEU* 2.8 50.0 + - + +
256A GLN* 3.6 6.3 - - - +
258A SER* 1.3 80.2 - - - +
260A GLN* 1.3 62.5 + - - +
262A SER 3.4 2.8 + - - -
268A ARG* 2.7 85.3 + - + +
271A HIS* 4.5 1.8 - - + -
272A LEU* 4.5 13.7 - - + -
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Residues in contact with GLN 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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237A LYS* 4.9 7.9 - - - +
240A TRP* 4.2 17.5 - - + -
256A GLN* 3.2 37.4 + - - +
257A GLN* 3.0 18.0 + - - +
259A PHE* 1.3 77.1 - - - +
261A LYS* 1.3 62.7 + - + +
262A SER 3.5 7.1 + - - +
268A ARG* 4.9 0.3 + - - -
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Residues in contact with LYS 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 GLN* 3.0 39.6 + - - +
258A SER* 4.2 6.1 - - - +
260A GLN* 1.3 79.8 - - + +
262A SER* 1.3 60.2 + - - +
263A HIS* 4.2 14.0 + - - -
267A GLN* 4.7 0.2 - - - +
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Residues in contact with SER 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 SER 3.0 21.0 + - - -
259A PHE 3.4 1.4 + - - +
260A GLN 3.3 6.5 - - - +
261A LYS* 1.3 80.5 - - - +
263A HIS* 1.3 62.2 + - - +
267A GLN* 3.1 21.9 + - - +
268A ARG* 2.9 39.5 + - - -
271A HIS* 3.2 25.5 + - - -
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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