Contacts of the helix formed by residues 315 - 327 (chain A) in PDB entry 2OKC
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 GLY 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ALA* 1.3 73.1 - - - +
316A ALA* 1.3 65.3 + - - -
317A GLY 3.1 0.9 - - - -
318A GLU* 3.1 19.9 + - - +
319A THR* 3.3 15.2 + - - -
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Residues in contact with ALA 316 (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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279A VAL* 3.7 29.4 - - + +
280A GLU 4.2 2.2 - - - +
281A THR* 3.7 31.2 - - - +
286A LEU* 3.9 8.5 - - + -
313A GLU* 5.6 1.3 - - - +
314A ALA 3.8 2.0 + - - -
315A GLY* 1.3 70.3 - - - -
317A GLY* 1.3 63.3 + - - +
319A THR* 3.3 4.8 + - - -
320A ILE* 3.1 27.5 + - - +
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Residues in contact with GLY 317 (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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286A LEU* 3.5 26.8 - - - +
313A GLU* 3.5 15.9 + - - -
314A ALA 4.2 2.8 + - - -
315A GLY 3.1 1.4 - - - -
316A ALA* 1.3 79.0 - - - +
318A GLU* 1.3 57.2 + - - +
320A ILE* 3.4 2.9 + - - +
321A ARG* 2.9 45.2 + - - +
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Residues in contact with GLU 318 (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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313A GLU 3.6 5.3 + - - -
314A ALA* 5.0 0.6 - - - +
315A GLY 3.1 16.9 + - - +
317A GLY* 1.3 73.4 - - - +
319A THR* 1.3 55.7 - - - +
321A ARG* 3.6 13.8 - - - +
322A LYS* 2.7 59.4 + - + +
422A LYS* 3.1 44.6 + - - +
423A THR* 2.9 20.6 + - - +
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Residues in contact with THR 319 (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 TYR* 4.5 13.2 - - + +
279A VAL* 4.2 22.3 - - + +
315A GLY 3.3 12.0 + - - -
316A ALA* 3.5 12.8 - - - -
318A GLU* 1.3 78.8 - - - +
320A ILE* 1.3 58.8 + - - +
322A LYS* 3.4 10.4 + - - +
323A ARG* 3.0 27.9 + - + +
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Residues in contact with ILE 320 (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 TYR* 4.6 6.5 - - + -
279A VAL* 3.5 21.1 - - + -
286A LEU* 3.9 29.2 - - + +
289A LEU* 3.7 31.0 - - + -
290A GLN* 3.5 30.5 - - + +
293A MSE 3.9 17.7 - - + +
316A ALA 3.1 18.8 + - - +
317A GLY 3.7 4.0 - - - +
319A THR* 1.3 74.3 - - - +
321A ARG* 1.3 56.0 + - + +
323A ARG* 3.1 7.0 + - - +
324A LEU* 2.7 33.8 + - + +
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Residues in contact with ARG 321 (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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286A LEU* 6.1 0.4 - - + -
289A LEU* 6.0 1.3 - - + -
309A ASN 4.5 0.2 + - - -
310A VAL* 3.1 29.3 + - + +
311A LEU* 3.4 20.1 + - - +
312A PHE 3.6 9.5 + - - -
313A GLU 3.0 36.5 + - - +
317A GLY* 2.9 31.2 + - - +
318A GLU* 3.6 9.4 - - - +
320A ILE* 1.3 74.4 - - + +
322A LYS* 1.3 66.6 + - - +
324A LEU* 3.3 12.3 + - + +
325A LEU* 3.0 31.3 + - + +
422A LYS* 2.6 29.1 + - - +
423A THR* 3.0 29.5 + - + +
424A SER* 4.6 0.2 - - - +
425A LEU* 3.6 25.9 - - + +
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Residues in contact with LYS 322 (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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318A GLU* 2.7 52.6 + - + +
319A THR* 3.5 9.2 - - - +
321A ARG* 1.3 73.2 - - - +
323A ARG* 1.3 61.6 + - - +
325A LEU* 3.3 9.1 + - + +
326A GLN* 3.1 23.4 + - - +
418A ILE* 6.4 2.2 - - + -
423A THR* 3.7 15.9 - - + +
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Residues in contact with ARG 323 (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 TYR* 3.6 57.4 - - + +
293A MSE 4.0 6.5 - - + -
319A THR* 3.0 17.4 + - + +
320A ILE* 3.1 9.2 + - - +
322A LYS* 1.3 74.4 - - - +
324A LEU* 1.3 64.4 + - - +
326A GLN* 4.5 3.8 - - - -
327A ASP* 3.1 55.8 + - - +
328A PHE* 3.9 1.6 - - + -
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Residues in contact with LEU 324 (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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289A LEU* 4.7 15.9 - - + -
293A MSE 3.6 32.9 - - + +
320A ILE 2.7 19.7 + - - +
321A ARG* 3.6 12.1 - - + +
322A LYS 3.3 0.2 - - - -
323A ARG* 1.3 71.6 - - - +
325A LEU* 1.3 58.3 + - - +
328A PHE* 3.0 51.5 + - + +
330A LEU* 3.9 33.9 - - + -
351A LEU* 4.3 19.3 - - + -
353A PHE* 4.0 17.7 - - + -
359A THR* 4.0 1.6 + - - -
425A LEU* 5.3 2.9 - - + -
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Residues in contact with LEU 325 (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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321A ARG* 3.0 23.2 + - + +
322A LYS* 3.3 6.0 + - - +
323A ARG 3.3 0.2 - - - -
324A LEU* 1.3 75.3 - - - +
326A GLN* 1.3 58.5 + - - +
330A LEU* 4.3 13.5 - - + -
358A PRO* 3.7 1.7 - - - +
359A THR* 2.9 49.4 + - + +
362A ILE* 3.7 28.9 - - + -
414A VAL* 4.1 15.9 - - + -
417A ILE* 4.1 15.0 - - + -
418A ILE* 4.2 13.5 - - + -
423A THR* 4.0 23.3 - - + -
425A LEU* 5.0 3.1 - - + -
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Residues in contact with GLN 326 (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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322A LYS 3.1 16.8 + - - +
323A ARG* 3.3 7.6 + - - +
325A LEU* 1.3 77.6 - - - +
327A ASP* 1.3 73.6 + - - +
328A PHE 3.5 0.2 - - - -
356A GLY 5.1 0.3 - - - +
358A PRO* 3.3 37.8 - - - +
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Residues in contact with ASP 327 (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 TYR* 5.6 0.3 - - - -
323A ARG* 3.1 35.9 + - - +
326A GLN* 1.3 94.1 + - - +
328A PHE* 1.3 79.8 + - + +
355A LYS* 4.5 2.0 - - - +
356A GLY* 3.0 30.3 + - - -
357A GLN 3.9 3.6 - - - -
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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