Contacts of the helix formed by residues 315 - 334 (chain A) in PDB entry 3OX4
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LYS* 4.2 0.6 - - - +
314A LEU* 1.3 78.7 - - - +
316A ASP* 1.3 60.9 + - - -
317A LYS 3.2 3.3 + - - -
318A GLU* 3.3 18.3 + - - -
319A GLY* 2.8 26.2 + - - -
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Residues in contact with ASP 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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297A ALA* 3.5 7.3 - - + +
298A GLY* 3.4 33.6 - - - +
301A LYS* 3.3 27.0 + - - +
315A GLY* 1.3 71.7 - - - -
317A LYS* 1.3 57.9 + - - +
320A ALA* 2.8 32.7 + - - +
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Residues in contact with LYS 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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297A ALA* 4.4 14.4 - - + -
315A GLY 3.2 1.0 - - - -
316A ASP* 1.3 80.2 - - + +
318A GLU* 1.3 72.6 + - + +
320A ALA* 3.4 2.9 + - - +
321A GLU* 3.2 21.1 + - - +
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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
----------------------------------------------------------
314A LEU* 4.0 21.5 - - + +
315A GLY* 3.3 18.5 + - - +
317A LYS* 1.3 87.0 + - + +
319A GLY* 1.3 66.4 + - - +
321A GLU* 3.4 6.7 + - - +
322A ALA* 3.1 24.9 + - - +
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LYS* 4.1 11.2 - - - -
311A ILE* 3.4 19.9 - - - +
314A LEU* 4.0 11.8 - - - +
315A GLY 2.8 17.9 + - - -
316A ASP 3.7 0.9 - - - -
318A GLU* 1.3 78.7 - - - +
320A ALA* 1.3 56.8 + - - +
322A ALA* 3.5 0.3 + - - +
323A THR* 2.9 32.1 + - - -
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Residues in contact with ALA 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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293A ALA* 4.6 7.2 - - + -
297A ALA* 3.6 26.0 - - + +
300A LEU* 3.8 25.3 - - + +
301A LYS* 4.4 1.7 - - - +
316A ASP 2.8 19.0 + - - +
317A LYS 3.7 4.9 - - - +
319A GLY* 1.3 75.2 - - - +
321A GLU* 1.3 58.9 + - - +
323A THR* 3.2 4.1 + - - -
324A ILE* 2.8 35.6 + - - +
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Residues in contact with GLU 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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317A LYS 3.2 10.8 + - - +
318A GLU* 3.7 9.9 - - - +
319A GLY 3.3 0.2 - - - -
320A ALA* 1.3 80.4 - - - +
322A ALA* 1.3 51.5 + - - +
324A ILE* 3.0 21.1 + - + +
325A GLN* 2.7 34.6 + - - +
328A ARG* 3.7 18.7 + - - -
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Residues in contact with ALA 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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309A LEU* 3.8 3.9 - - + +
311A ILE* 3.9 22.9 - - + -
314A LEU* 4.4 5.4 - - + -
318A GLU 3.1 17.3 + - - +
319A GLY 3.8 4.3 - - - +
321A GLU* 1.3 77.0 - - - +
323A THR* 1.3 56.8 + - - +
325A GLN* 3.3 8.2 + - - +
326A ALA* 2.9 29.1 + - - +
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Residues in contact with THR 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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200A PHE* 3.7 27.4 - - + -
300A LEU* 3.4 20.0 + - + +
304A GLY* 3.1 35.2 - - - +
307A MET* 4.5 4.7 - - - -
309A LEU* 3.6 8.5 - - - +
311A ILE* 3.4 5.5 - - - +
319A GLY 2.9 18.7 + - - -
320A ALA* 3.5 9.2 - - - -
321A GLU 3.2 0.2 - - - -
322A ALA* 1.3 74.2 - - - +
324A ILE* 1.3 67.2 + - + +
326A ALA* 3.2 2.8 + - - +
327A VAL* 3.0 23.2 + - - +
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Residues in contact with ILE 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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286A PRO* 3.8 16.8 - - + +
289A LEU* 3.6 24.2 - - + +
290A ALA* 3.5 35.9 - - + +
293A ALA* 4.4 8.1 - - + -
300A LEU* 4.5 5.4 - - + -
320A ALA 2.8 26.7 + - - +
321A GLU* 3.3 14.6 - - + +
323A THR* 1.3 78.3 - - - +
325A GLN* 1.3 60.6 + - - +
327A VAL* 3.3 8.8 + - - +
328A ARG* 3.1 54.2 + - - +
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Residues in contact with GLN 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 GLU* 2.7 26.5 + - - +
322A ALA* 3.6 9.4 - - - +
323A THR 3.2 0.2 - - - -
324A ILE* 1.3 74.2 - - - +
326A ALA* 1.3 56.5 + - - +
328A ARG* 3.0 38.1 + - - +
329A ASP* 2.7 60.6 + - - +
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Residues in contact with ALA 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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307A MET* 4.8 9.5 - - + +
309A LEU* 3.6 31.6 - - + -
322A ALA 2.9 17.2 + - - +
323A THR 3.2 5.1 + - - +
325A GLN* 1.3 75.3 - - - +
327A VAL* 1.3 60.0 + - - +
329A ASP* 3.3 10.6 + - - +
330A LEU* 2.9 29.5 + - - +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A MET* 4.3 11.1 - - + +
196A LEU* 4.5 7.2 - - + -
200A PHE* 3.6 34.8 - - + -
285A LEU* 3.7 26.0 - - + -
286A PRO* 3.8 18.6 - - + -
289A LEU* 4.2 7.2 - - + -
307A MET* 4.6 7.6 - - + -
323A THR 3.0 17.4 + - - +
324A ILE* 3.6 8.5 - - - +
326A ALA* 1.3 75.2 - - - +
328A ARG* 1.3 65.1 + - - +
330A LEU* 3.2 7.6 + - - +
331A ALA* 3.0 22.9 + - + +
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Residues in contact with ARG 328 (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 PRO* 3.8 28.8 + - + +
287A HIS* 5.6 7.6 + - - +
290A ALA* 4.9 8.1 - - - +
321A GLU* 3.7 13.7 + - - -
324A ILE* 3.1 45.3 + - - +
325A GLN* 3.0 48.3 + - - +
327A VAL* 1.3 77.5 - - - +
329A ASP* 1.3 56.6 + - - +
331A ALA* 3.4 5.3 + - - +
332A ALA* 3.0 30.0 + - - +
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Residues in contact with ASP 329 (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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325A GLN* 2.7 51.3 + - - +
326A ALA* 3.7 8.7 - - - +
327A VAL 3.3 0.2 - - - -
328A ARG* 1.3 76.4 - - - +
330A LEU* 1.3 58.1 + - - +
332A ALA* 3.5 5.9 + - - +
333A SER* 2.9 29.9 + - - -
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Residues in contact with LEU 330 (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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193A MET* 3.9 14.4 - - - -
196A LEU* 3.8 28.5 - - + -
223A ILE* 4.8 9.2 - - + +
224A ALA* 5.4 8.5 - - - +
227A LEU* 4.3 17.9 - - + -
228A LYS* 4.8 12.3 - - + +
307A MET* 4.9 11.0 - - + -
326A ALA 2.9 17.4 + - - +
327A VAL* 3.2 5.1 + - - +
329A ASP* 1.3 73.5 - - - +
331A ALA* 1.3 66.2 + - - +
333A SER* 2.6 28.9 + - - +
334A ILE* 3.3 22.3 + - + +
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Residues in contact with ALA 331 (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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193A MET* 3.9 18.6 - - + +
282A ALA 5.0 3.8 - - - +
286A PRO* 5.6 2.7 - - + -
327A VAL* 3.0 17.2 + - + +
328A ARG* 3.7 6.7 - - - +
330A LEU* 1.3 75.2 - - - +
332A ALA* 1.3 62.9 + - - +
334A ILE* 3.2 11.4 + - - +
336A ILE* 3.1 50.3 + - + +
337A PRO 5.9 0.4 - - - +
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Residues in contact with ALA 332 (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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328A ARG 3.0 18.1 + - - +
329A ASP* 3.7 7.4 - - - +
331A ALA* 1.3 76.7 - - - +
333A SER* 1.3 62.4 + - - +
334A ILE 3.1 1.6 + - - -
335A GLY* 3.4 9.0 + - - -
336A ILE 4.8 6.7 - - - -
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Residues in contact with SER 333 (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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185A LYS* 4.6 3.8 + - - -
228A LYS* 2.7 43.3 + - - +
329A ASP 2.9 15.1 + - - -
330A LEU* 2.6 28.0 + - - +
332A ALA* 1.3 74.4 - - - +
334A ILE* 1.3 63.8 + - - +
335A GLY 3.7 0.2 - - - -
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Residues in contact with ILE 334 (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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185A LYS* 3.0 31.7 - - - +
189A ALA* 3.5 26.5 - - + +
193A MET* 3.9 19.7 - - + -
227A LEU* 3.8 29.4 - - + -
228A LYS* 4.0 21.5 - - + +
231A CYS* 3.8 18.2 - - + -
330A LEU* 3.3 17.5 - - + +
331A ALA 3.4 7.4 - - - +
332A ALA 3.1 0.2 - - - -
333A SER* 1.3 90.2 - - - +
335A GLY* 1.3 59.8 + - - +
336A ILE* 3.9 5.8 - - + -
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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
------------------------------------------------------------
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