Contacts of the helix formed by residues 316 - 326 (chain B) in PDB entry 3OPS
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 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B CYS* 6.3 0.2 - - + -
45B VAL* 4.0 7.6 - - + +
314B GLY 4.2 0.4 - - - -
315B ASN* 1.3 71.0 + - - +
317B TYR* 1.3 62.3 + - - +
319B ILE* 3.0 24.6 + - + +
320B TYR* 3.3 17.9 - - + -
340B ILE* 3.9 36.6 - - + +
342B ILE* 4.0 15.5 - - + -
345B MSE 3.8 20.4 - - + -
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Residues in contact with TYR 317 (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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45B VAL* 4.0 14.9 - - + +
47B ILE* 5.4 1.3 - - + -
58B TYR 3.7 2.6 + - - -
59B GLY* 3.5 25.9 - - - -
60B SER* 3.7 21.8 - - - -
97B TYR* 3.6 30.1 - + - +
101B ASP* 5.4 0.2 - - - -
287B ILE* 4.7 1.8 - - + -
315B ASN* 3.2 14.1 + - - +
316B ALA* 1.3 77.4 - - - +
318B GLY* 1.3 56.7 + - - +
320B TYR* 3.0 27.9 + - - +
321B ALA* 3.2 16.2 + - + -
345B MSE 4.2 12.0 - - - +
365B PHE* 3.2 37.6 - + + +
367B ILE* 4.0 16.6 - - + -
369B PHE* 3.8 25.4 - + - -
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Residues in contact with GLY 318 (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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286B ILE* 3.4 24.7 - - - +
287B ILE* 4.0 9.1 - - - +
312B CYS* 3.7 11.9 - - - -
315B ASN* 3.3 6.5 + - - -
316B ALA 3.0 1.8 + - - -
317B TYR* 1.3 75.5 - - - +
319B ILE* 1.3 58.4 + - - +
320B TYR 3.2 0.2 - - - -
321B ALA* 3.7 6.2 - - - +
322B SER* 2.9 34.0 + - - -
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Residues in contact with ILE 319 (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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312B CYS* 3.7 9.0 - - - -
316B ALA* 3.0 23.8 + - + +
318B GLY* 1.3 74.8 - - - +
320B TYR* 1.3 75.1 + - + +
322B SER* 3.5 5.8 - - - -
323B GLY* 3.4 15.2 + - - -
335B VAL* 3.5 20.9 - - + +
336B GLU 3.3 20.0 - - - +
337B TYR* 3.5 28.9 - - + -
338B ASP* 3.2 43.5 - - + +
350B TYR* 5.2 0.2 - - - -
357B ILE* 4.1 13.7 - - + +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA* 3.3 23.6 - - + +
317B TYR* 3.0 19.0 + - + +
319B ILE* 1.3 95.0 - - + +
321B ALA* 1.3 65.4 - - - +
322B SER 3.1 1.7 + - - -
323B GLY* 3.3 8.0 + - - -
324B HIS* 3.3 22.1 + - - -
337B TYR* 4.5 15.4 + + - -
338B ASP 5.5 0.5 + - - -
340B ILE 4.6 11.3 + - - -
345B MSE 4.4 6.4 - - + +
347B VAL* 3.2 41.4 - - + +
350B TYR* 3.3 56.1 + + + +
357B ILE* 4.7 2.5 - - + -
365B PHE* 4.8 1.8 - - + -
367B ILE* 3.6 19.7 - - + -
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Residues in contact with ALA 321 (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 TYR* 3.2 44.0 - - + +
286B ILE* 3.9 4.7 - - + -
291B PHE* 3.3 11.5 - - + -
317B TYR* 3.2 13.4 + - + +
318B GLY* 3.7 11.0 - - - +
320B TYR* 1.3 77.2 - - - +
322B SER* 1.3 62.5 + - - +
324B HIS* 3.3 2.3 + - - +
325B LEU* 3.2 18.7 + - - +
365B PHE* 3.9 14.6 - - + -
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Residues in contact with SER 322 (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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286B ILE* 3.4 25.2 - - - +
310B PRO* 4.4 13.7 + - - +
312B CYS* 5.0 2.3 - - - +
318B GLY 2.9 21.4 + - - -
319B ILE* 3.5 9.2 - - - -
320B TYR 3.1 0.4 - - - -
321B ALA* 1.3 74.4 - - - +
323B GLY* 1.3 65.6 + - - +
325B LEU* 3.3 4.8 + - - +
326B SER 3.3 16.1 + - - -
332B PHE* 3.5 15.7 - - - -
334B PHE 5.6 0.2 - - - -
335B VAL* 4.0 19.6 - - - -
336B GLU 5.3 1.5 + - - -
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Residues in contact with GLY 323 (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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126B LEU* 3.3 13.3 - - - +
128B VAL* 3.6 10.7 - - - +
319B ILE 3.4 6.5 + - - -
320B TYR* 3.3 7.2 + - - -
322B SER* 1.3 78.5 - - - +
324B HIS* 1.3 55.4 + - - +
326B SER* 2.7 29.1 + - - -
335B VAL* 3.8 15.4 - - - +
350B TYR* 5.7 0.4 - - - -
357B ILE* 5.4 1.1 - - - -
359B VAL* 4.1 11.4 - - - -
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Residues in contact with HIS 324 (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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110B PRO* 4.1 3.4 - - - +
111B VAL* 3.5 14.7 + - + -
112B TYR* 2.9 55.9 - + + +
115B VAL* 4.4 3.3 - - - +
126B LEU* 4.3 0.7 - - - -
291B PHE* 4.2 12.8 - - + -
320B TYR 3.3 15.6 + - - -
321B ALA 3.3 8.2 + - - +
322B SER 3.2 1.0 - - - -
323B GLY* 1.3 72.8 - - - +
325B LEU* 1.3 66.6 + - - +
327B ALA* 3.1 22.0 + - - +
350B TYR* 3.2 21.2 + - - -
359B VAL* 3.4 17.4 - - + +
360B PRO* 4.7 3.6 + - + -
364B GLY 3.3 13.3 + - - -
365B PHE* 3.8 21.0 - + + -
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Residues in contact with LEU 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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286B ILE* 4.1 9.0 - - + -
291B PHE* 3.6 37.1 - - + +
294B TRP* 3.6 37.0 - - + +
295B MSE 3.8 21.3 - - + +
310B PRO* 3.7 29.4 - - + -
321B ALA 3.2 5.5 + - - +
322B SER* 3.3 6.9 + - - +
324B HIS* 1.3 73.6 - - - +
326B SER* 1.3 52.5 + - - +
327B ALA 2.9 5.4 - - - -
328B ALA* 2.6 33.4 + - - +
329B VAL* 3.7 11.0 + - + +
332B PHE* 4.1 13.5 - - + -
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Residues in contact with SER 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.7 12.4 - - - +
128B VAL* 3.5 20.5 - - - +
322B SER 3.3 4.2 + - - -
323B GLY 2.7 21.2 + - - -
325B LEU* 1.3 77.4 - - - +
327B ALA* 1.3 61.4 + - - +
329B VAL 3.2 19.9 - - - +
332B PHE* 3.6 39.1 - - - +
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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