Contacts of the helix formed by residues 288 - 293 (chain B) in PDB entry 2OG9
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 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B TYR* 2.5 31.5 + - - -
264B GLY 5.1 0.8 + - - -
265B GLU 4.2 13.0 - - - +
267B LEU 5.3 0.6 + - - +
273B HIS* 4.8 0.6 + - - -
286B MSE 3.7 1.1 + - - +
287B PRO* 1.3 72.7 - - - +
289B ALA* 1.3 65.2 + - - +
290B PRO* 2.8 24.1 - - - +
291B ARG* 3.0 23.5 + - + -
292B VAL* 2.9 28.1 + - + +
315B HIS* 3.5 24.4 + - + +
316B PHE* 3.8 3.9 - - - +
321B HIS* 3.9 4.3 - - - -
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Residues in contact with ALA 289 (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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288B ASP* 1.3 72.3 - - - +
290B PRO* 1.3 69.0 - - + +
292B VAL* 3.2 9.4 + - - +
293B GLY 3.2 0.2 + - - -
294B GLY* 2.8 37.1 + - - +
295B ILE 4.6 0.2 - - - +
298B PHE* 3.6 20.6 - - + -
320B LEU* 3.7 16.4 - - + -
321B HIS* 3.0 24.5 - - + -
324B LEU* 3.9 7.6 - - + -
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Residues in contact with PRO 290 (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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65B PHE* 4.2 17.0 - - + +
66B SER* 3.4 30.6 + - - +
67B TYR* 3.7 25.1 - - + -
117B GLN* 3.8 8.7 - - - +
120B GLY* 5.3 1.5 - - - -
124B VAL* 5.8 1.1 - - + -
288B ASP* 2.8 19.5 - - - +
289B ALA* 1.3 89.7 - - + +
291B ARG* 1.3 58.3 - - - +
292B VAL 3.5 0.2 + - - -
293B GLY* 3.6 7.3 + - - -
294B GLY* 4.3 4.9 + - - +
317B ALA* 4.4 13.7 - - + -
320B LEU* 4.1 14.6 - - + -
321B HIS* 3.9 9.2 - - - +
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Residues in contact with ARG 291 (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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108A SER* 3.7 30.4 + - - +
67B TYR* 2.6 39.2 + - + +
69B LYS* 4.4 12.9 - - - +
117B GLN* 3.2 30.0 + - - +
265B GLU 3.3 22.0 + - - -
266B MSE 3.3 45.3 + - - +
267B LEU 3.5 16.4 - - - +
268B THR* 3.5 19.2 - - + +
288B ASP* 3.0 21.7 + - + +
290B PRO* 1.3 80.5 - - - +
292B VAL* 1.3 58.1 + - - +
293B GLY 3.4 0.2 - - - -
315B HIS* 5.2 7.1 - - - -
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B TRP* 4.7 3.6 - - - -
111B ARG 5.4 1.0 - - - +
116B THR* 4.7 4.3 + - - -
267B LEU 3.7 18.8 - - - +
268B THR 3.6 15.2 - - - +
269B SER* 4.0 12.3 - - - +
273B HIS* 3.8 26.9 - - + +
288B ASP 2.9 20.3 + - - +
289B ALA* 3.4 19.1 - - - +
291B ARG* 1.3 76.9 - - - +
293B GLY* 1.3 57.5 + - - +
294B GLY 4.0 10.1 - - - +
297B PRO* 3.4 17.9 - - + +
298B PHE* 4.1 5.6 - - + +
301B ILE* 4.0 20.4 - - + -
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Residues in contact with GLY 293 (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 TRP* 2.8 27.8 + - - -
116B THR* 3.2 27.3 - - - -
117B GLN* 4.8 0.2 - - - +
120B GLY* 3.1 16.7 - - - -
123B ASP* 4.1 0.2 - - - +
289B ALA 3.2 0.8 + - - -
290B PRO 3.6 3.6 + - - -
291B ARG 3.4 3.6 + - - -
292B VAL* 1.3 80.0 - - - +
294B GLY* 1.3 57.5 + - - +
297B PRO* 3.3 10.3 - - - +
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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