Contacts of the helix formed by residues 266 - 275 (chain B) in PDB entry 4OE4
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 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B GLN* 3.7 7.6 + - - +
97B ALA 5.1 2.2 + - - -
237B GLN* 4.2 3.1 - - - +
265B GLY* 1.3 68.4 - - - -
267B PRO* 1.3 70.6 - - - +
268B VAL* 3.3 10.4 + - - +
269B GLN* 2.9 45.2 + - + +
270B VAL* 2.9 34.7 + - - +
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Residues in contact with PRO 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LYS* 3.9 12.7 - - + +
237B GLN* 4.3 13.0 - - + +
265B GLY 3.4 7.4 - - - +
266B ASP* 1.3 93.0 - - - +
268B VAL* 1.3 60.3 + - + +
270B VAL* 4.2 0.5 - - - +
271B THR* 2.7 33.8 + - - -
1000B NAD 3.5 55.9 - - + +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASP* 3.3 8.1 + - - +
267B PRO* 1.3 74.8 - - + +
269B GLN* 1.3 62.1 - - - +
271B THR* 3.3 4.6 + - - -
272B ASP* 2.9 46.8 + - - +
298B LYS* 3.8 13.2 - - - +
1000B NAD 3.7 27.4 - - + +
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Residues in contact with GLN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA 5.1 11.8 + - - +
98B THR* 5.2 2.2 - - - +
99B GLU* 2.5 41.2 + - + +
266B ASP* 2.9 29.1 + - + +
268B VAL* 1.3 81.1 - - - +
270B VAL* 1.3 64.2 + - + +
272B ASP* 3.4 5.0 + - - +
273B GLN* 3.3 20.4 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA* 4.2 24.2 - - + +
102B VAL* 4.0 12.4 - - + +
206B TYR* 3.8 14.1 - - - +
234B LYS* 3.9 19.1 - - + -
263B ILE* 4.0 26.0 - - + +
265B GLY* 3.9 23.3 - - - +
266B ASP 2.9 23.0 + - - +
269B GLN* 1.3 76.3 - - + +
271B THR* 1.3 63.3 + - - +
273B GLN* 3.4 3.6 + - - +
274B VAL* 3.0 25.3 + - + +
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Residues in contact with THR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B TYR* 2.8 26.3 + - + -
208B VAL* 5.0 0.2 - - - +
234B LYS* 4.7 0.3 - - - -
267B PRO 2.7 23.2 + - - -
268B VAL* 3.6 3.4 - - - -
270B VAL* 1.3 75.5 - - - +
272B ASP* 1.3 72.7 + - - +
274B VAL* 3.3 1.4 + - - +
275B LEU* 3.0 41.6 + - + +
295B LEU* 3.5 26.1 - - + +
298B LYS* 4.5 6.7 - - + +
1000B NAD 3.4 17.4 + - + -
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B VAL* 2.9 33.0 + - - +
269B GLN* 3.4 6.3 + - - +
271B THR* 1.3 74.8 - - - +
273B GLN* 1.3 61.4 + - - +
275B LEU* 3.6 5.8 + - - +
276B ALA* 3.3 21.7 + - - +
298B LYS* 2.5 37.1 + - - +
307B LYS* 5.7 0.5 + - - -
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Residues in contact with GLN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 3.1 35.4 - - + +
102B VAL* 3.6 28.5 - - + -
103B MET* 3.4 31.7 - - + +
106B VAL* 5.5 1.4 - - + +
269B GLN 3.3 9.8 + - - +
270B VAL 3.8 7.2 - - - +
271B THR 3.2 0.6 - - - -
272B ASP* 1.3 77.7 - - - +
274B VAL* 1.3 66.1 + - - +
276B ALA* 3.1 22.2 + - - +
277B ASP* 4.0 5.1 + - - +
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B VAL* 3.6 18.2 - - + -
106B VAL* 4.7 7.4 - - + -
204B PHE* 3.6 29.3 - - + -
206B TYR* 3.6 49.8 - - + -
232B VAL* 4.0 8.5 - - + -
263B ILE* 4.6 2.5 - - + -
270B VAL* 3.0 26.3 + - + +
271B THR 3.8 3.6 - - - +
273B GLN* 1.3 76.0 - - - +
275B LEU* 1.3 59.5 + - - +
276B ALA 3.2 4.5 + - - -
277B ASP* 3.3 17.0 + - - +
280B PHE* 4.4 5.7 - - + +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B TYR* 4.5 9.2 - - + -
271B THR* 3.0 38.7 + - + +
272B ASP* 3.9 6.5 - - - +
274B VAL* 1.3 76.0 - - + +
276B ALA* 1.3 57.4 + - - +
277B ASP 3.3 0.7 - - - -
280B PHE* 3.5 44.6 - - + -
295B LEU* 4.5 6.3 - - + +
298B LYS* 3.9 27.4 - - + +
299B ILE* 3.9 18.4 - - + +
307B LYS* 3.2 11.8 + - - +
308B TYR* 2.6 36.3 + - - +
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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