Contacts of the helix formed by residues 276 - 288 (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 SER 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A LYS* 3.9 18.2 - - - +
212A VAL* 4.4 1.1 - - - -
274A ARG 3.8 1.2 + - - -
275A PRO* 1.3 77.7 - - - +
277A MET* 1.3 62.1 + - - +
278A GLU* 3.6 9.4 + - - +
279A GLU* 3.3 23.7 + - - +
280A ILE* 3.1 20.4 + - - +
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Residues in contact with MET 277 (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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138A SER* 3.8 29.4 - - - -
141A VAL* 3.7 37.0 - - + -
142A ALA* 3.8 19.3 - - + -
145A HIS* 3.8 19.5 + - + +
157A LEU* 4.7 0.4 - - + -
211A ASP 3.8 13.2 - - - +
212A VAL* 4.0 15.4 - - + +
215A TRP* 3.7 32.8 - - + -
275A PRO 4.0 0.2 + - - -
276A SER* 1.3 71.2 - - - +
278A GLU* 1.3 60.2 + - + +
280A ILE* 3.1 13.1 + - + +
281A VAL* 2.8 34.8 + - - +
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Residues in contact with GLU 278 (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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142A ALA* 3.8 28.1 - - + +
146A SER* 4.6 9.6 - - - -
276A SER* 3.2 9.2 + - - +
277A MET* 1.3 78.3 - - - +
279A GLU* 1.3 62.9 + - - +
281A VAL* 3.5 12.0 + - - +
282A LYS* 3.1 27.5 + - - +
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ARG* 2.7 40.7 + - - -
275A PRO* 3.8 12.3 - - + +
276A SER* 3.3 19.6 + - - +
277A MET 3.2 0.6 - - - -
278A GLU* 1.3 77.8 - - - +
280A ILE* 1.3 58.7 + - - +
282A LYS* 3.1 7.5 + - + +
283A ILE* 2.9 49.6 + - + +
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Residues in contact with ILE 280 (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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138A SER* 3.6 14.1 - - - -
212A VAL* 4.0 15.3 - - + -
215A TRP* 3.5 41.1 - - + -
262A LEU* 4.4 8.3 - - + -
266A CYS* 3.9 23.3 - - - -
275A PRO* 4.0 14.4 - - + -
276A SER 3.1 14.4 + - - +
277A MET* 3.1 25.2 + - + +
279A GLU* 1.3 76.2 - - - +
281A VAL* 1.3 57.2 + - - +
283A ILE* 3.7 6.8 - - - +
284A MET* 2.8 31.7 + - + +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.7 2.7 - - + +
138A SER* 3.4 40.8 - - - +
139A GLN* 3.7 23.3 - - + +
142A ALA* 3.9 10.1 - - + -
277A MET 2.8 23.9 + - - +
278A GLU* 3.6 13.0 - - - +
280A ILE* 1.3 72.6 - - - +
282A LYS* 1.3 59.8 + - + +
284A MET 3.4 0.2 + - - -
285A THR* 2.7 46.7 + - - +
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Residues in contact with LYS 282 (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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278A GLU* 3.1 14.5 + - - +
279A GLU* 3.1 12.5 + - + +
281A VAL* 1.3 82.0 - - + +
283A ILE* 1.3 63.4 + - + +
285A THR* 3.3 6.7 + - - -
286A HIS* 3.1 51.1 + - + +
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Residues in contact with ILE 283 (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 PRO 5.5 2.5 - - - +
262A LEU* 3.9 42.2 - - + -
265A ARG* 4.3 5.8 - - - +
279A GLU* 2.9 47.3 + - + +
280A ILE 3.8 2.5 - - - +
282A LYS* 1.3 78.0 - - + +
284A MET* 1.3 57.8 + - - +
286A HIS* 3.2 9.5 + - + +
287A LEU* 2.9 41.4 + - + +
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Residues in contact with MET 284 (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* 3.3 60.6 - - + +
134A CYS* 3.9 18.6 - - + -
135A LEU* 3.7 24.5 - - + +
138A SER* 4.7 0.2 - - - +
215A TRP* 3.8 28.5 - - + -
219A LEU* 4.7 2.7 - - + -
262A LEU* 3.9 13.0 - - + -
280A ILE* 2.8 26.8 + - + +
281A VAL* 4.7 0.2 - - - -
283A ILE* 1.3 72.5 - - - +
285A THR* 1.3 60.2 + - - +
287A LEU* 3.3 7.2 + - - +
288A MET* 3.1 28.8 + - - +
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Residues in contact with THR 285 (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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135A LEU* 3.6 22.1 - - + +
139A GLN* 4.4 4.2 + - - -
281A VAL* 2.7 31.9 + - - +
282A LYS* 3.6 7.6 - - - -
283A ILE 3.2 0.2 - - - -
284A MET* 1.3 77.9 - - - +
286A HIS* 1.3 72.7 + - + +
288A MET* 3.4 15.1 + - - +
289A ARG* 4.1 2.6 + - - +
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Residues in contact with HIS 286 (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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282A LYS* 3.1 42.5 + - + +
283A ILE* 3.7 9.9 - - + +
285A THR* 1.3 86.8 - - + +
287A LEU* 1.3 63.1 + - + +
288A MET 3.4 0.2 + - - -
289A ARG* 3.4 21.6 - - - +
290A TYR* 4.1 7.9 - - - -
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Residues in contact with LEU 287 (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* 3.9 28.0 - - + -
258A PRO* 4.5 19.1 - - + +
259A ILE* 4.0 15.3 - - + -
262A LEU* 5.2 2.0 - - + -
283A ILE* 2.9 35.3 + - + +
284A MET* 3.7 12.3 - - - +
285A THR 3.2 0.4 - - - -
286A HIS* 1.3 75.3 - - + +
288A MET* 1.3 56.1 + - - +
289A ARG 3.0 5.2 - - - -
290A TYR* 2.9 27.4 + - + +
291A PHE* 3.4 13.0 - - + -
487A PHE* 4.3 22.4 - - + -
491A TRP* 4.4 15.5 - - + -
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Residues in contact with MET 288 (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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128A ALA 3.9 5.6 - - - +
131A MET* 3.7 30.3 - - - +
132A SER* 3.7 33.2 - - - +
135A LEU* 3.6 22.4 - - + -
284A MET* 3.1 21.9 + - - +
285A THR* 3.6 10.3 - - - +
286A HIS 3.3 0.8 - - - -
287A LEU* 1.3 76.2 - - - +
289A ARG* 1.3 56.5 + - - +
291A PHE* 2.8 51.9 + - + +
292A PRO* 4.0 1.6 - - - +
294A ALA* 4.1 7.0 - - + -
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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