Contacts of the helix formed by residues 317 - 327 (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 ALA 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B PHE* 4.0 29.8 - - + -
290B PRO* 4.4 11.0 - - + -
316B PHE* 1.3 97.5 - - + +
318B MSE 1.3 65.7 + - - +
319B GLU* 3.1 9.4 - - - -
320B LEU* 3.1 5.3 + - + -
321B HIS* 3.0 25.1 + - + -
337B PHE* 4.7 2.7 - - - -
340B LEU* 4.2 6.1 - - + -
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Residues in contact with MSE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE 3.0 7.7 + - - -
317B ALA* 1.3 72.5 - - - +
319B GLU* 1.3 79.5 + - - +
321B HIS* 4.3 1.8 - - - +
322B VAL* 2.9 33.1 + - - +
334B VAL* 3.9 16.4 - - + -
335B GLU 3.6 16.6 - - - +
336B HIS* 3.9 13.7 - - - +
337B PHE* 3.3 44.9 - - + +
338B GLU* 4.8 0.2 - - - -
341B GLU* 4.3 19.5 - - + +
348B ILE* 3.8 31.0 - - + +
355B MSE 3.7 21.5 - - + +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 5.1 4.7 - - + -
317B ALA 3.1 3.4 - - - -
318B MSE 1.3 104.6 + - + +
320B LEU* 1.3 56.8 + - - +
322B VAL* 3.9 2.2 - - - +
323B HIS* 3.5 21.1 + - - -
337B PHE* 4.4 3.6 - - - +
340B LEU* 3.9 27.1 - - - +
341B GLU* 4.2 12.0 + - - +
344B PHE* 4.1 18.5 - - + -
346B GLU 6.1 0.7 - - - +
348B ILE* 4.6 18.8 - - + +
358B PRO* 5.7 0.3 - - - +
363B LEU* 4.3 8.0 - - - +
365B LEU* 3.8 38.0 - - + +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 4.8 13.5 - - + +
124B VAL* 4.2 22.7 - - + -
138B LEU* 3.8 13.0 - - + -
289B ALA* 3.7 26.5 - - + -
290B PRO* 4.1 15.5 - - + -
295B ILE* 3.7 28.3 - - + -
317B ALA* 3.1 11.9 + - + +
318B MSE 3.0 0.2 - - - -
319B GLU* 1.3 79.3 - - - +
321B HIS* 1.3 65.2 - - + +
322B VAL 3.3 1.8 - - - -
323B HIS* 3.2 16.4 + - - +
324B LEU* 3.4 16.5 + - + +
363B LEU* 4.4 14.1 - - + -
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Residues in contact with HIS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B PRO 4.1 1.3 - - - -
288B ASP* 3.9 2.6 + - - -
289B ALA* 3.0 44.2 + - + -
290B PRO* 3.9 9.0 - - + +
298B PHE* 3.9 9.3 - + - -
314B PRO* 3.5 23.2 - - + +
315B HIS 3.1 21.1 + - - -
316B PHE 2.8 30.2 - - - +
317B ALA* 3.0 15.3 + - + +
318B MSE 4.4 3.8 - - - -
320B LEU* 1.3 72.7 - - + +
322B VAL* 1.3 60.9 + - - +
323B HIS 3.1 2.0 - - - -
324B LEU* 3.8 14.9 - - + +
325B ALA* 2.7 34.1 + - - +
334B VAL* 4.5 7.9 - - + -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 4.0 8.3 - - + +
318B MSE 2.9 23.5 + - - +
319B GLU 3.9 4.5 - - - +
321B HIS* 1.3 76.1 - - - +
323B HIS* 1.3 74.4 + - + +
325B ALA* 4.0 1.3 - - - +
326B ALA* 3.1 22.7 + - - +
334B VAL* 4.5 10.7 - - - +
348B ILE* 4.3 7.9 - - + -
355B MSE 3.9 26.2 - - + -
356B LEU 4.0 5.6 - - - +
357B VAL* 3.8 30.8 - - + +
358B PRO* 3.8 20.9 - - + -
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Residues in contact with HIS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 4.1 2.5 - - - -
138B LEU* 3.8 25.8 - - + -
139B ALA* 3.3 38.0 + - - +
142B LEU* 4.6 1.8 - - - +
319B GLU 3.5 22.9 + - - -
320B LEU* 3.2 8.7 + - - +
321B HIS 3.1 0.6 - - - -
322B VAL* 1.3 81.1 - - + +
324B LEU* 1.3 64.6 + - - +
326B ALA* 3.4 11.1 + - - +
327B ALA* 3.5 10.6 + - - +
357B VAL* 4.0 1.6 - - - +
358B PRO* 3.8 41.4 - - + +
360B ARG 5.1 0.2 - - - -
362B GLY 3.8 14.4 - - - -
363B LEU* 3.3 28.3 + - + -
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.6 4.0 - - + -
142B LEU* 3.8 25.1 - - + -
289B ALA* 3.9 15.7 - - + -
295B ILE* 4.0 25.1 - - + -
298B PHE* 3.7 40.4 - - + -
299B LEU* 4.4 5.2 - - + -
312B LEU* 5.0 2.1 - - - +
320B LEU* 3.4 21.5 + - + +
321B HIS* 3.2 27.7 + - + +
323B HIS* 1.3 74.0 - - - +
325B ALA* 1.3 65.6 + - - +
327B ALA* 3.1 16.3 + - - +
328B TYR* 3.6 7.1 + - - +
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Residues in contact with ALA 325 (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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146B ARG* 3.1 12.1 + - - -
149B VAL* 4.1 4.3 - - + -
312B LEU* 4.7 5.8 - - - -
314B PRO* 4.5 6.6 - - + +
321B HIS 2.7 21.7 + - - +
322B VAL 4.0 3.1 - - - +
324B LEU* 1.3 71.1 - - - +
326B ALA* 1.3 63.1 + - - +
328B TYR* 3.0 15.8 + - - +
332B PRO* 3.4 28.2 - - + +
334B VAL* 3.5 24.9 - - + -
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ALA* 4.1 13.2 - - + -
144B SER* 4.1 2.5 - - - -
145B TYR 2.8 26.8 + - - -
146B ARG* 3.5 29.0 + - - +
149B VAL* 4.2 1.9 - - - +
322B VAL 3.1 19.5 + - - +
323B HIS 3.5 7.2 - - - +
324B LEU 3.2 0.2 - - - -
325B ALA* 1.3 75.9 - - - +
327B ALA* 1.3 58.5 + - - +
357B VAL* 3.7 22.9 - - + -
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ALA 4.9 1.3 - - - +
142B LEU* 4.1 24.0 - - + +
143B GLY 3.3 24.4 - - - +
144B SER* 4.2 0.2 - - - +
145B TYR* 3.5 15.2 - - - -
299B LEU* 6.0 2.7 - - + -
323B HIS 3.5 8.2 + - - +
324B LEU* 3.1 10.9 + - - +
325B ALA 3.1 1.2 - - - -
326B ALA* 1.3 78.9 - - - +
328B TYR* 1.3 60.4 + - - +
329B PRO* 3.8 2.3 - - - +
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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