Contacts of the helix formed by residues 318 - 331 (chain A) in PDB entry 4OG6
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 ILE 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A GLU* 2.9 12.1 + - - +
220A TRP* 3.6 25.4 - - + +
316A GLU 5.1 0.4 - - - +
317A HIS* 1.3 70.5 - - - +
319A TYR* 1.3 65.2 + - - +
320A PRO* 3.3 3.6 - - - -
321A TYR* 3.2 11.9 + - - +
322A MET* 3.2 32.6 + - + +
344A THR* 3.6 22.2 - - - +
347A VAL* 3.4 33.2 - - + -
348A ILE* 3.7 24.0 - - + +
351A TYR* 5.0 0.4 - - + -
360A ILE* 3.9 24.7 - - + -
364A PHE* 4.3 2.7 - - + -
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Residues in contact with TYR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 2.9 62.8 + - + +
180A ASP* 5.5 1.4 + - - -
220A TRP* 3.9 13.8 - + - -
278A MET* 4.8 7.2 - - + -
318A ILE* 1.3 72.7 - - + +
320A PRO* 1.4 64.5 - - + +
322A MET* 4.0 10.1 - - + -
323A TYR* 2.8 41.1 + - + -
359A GLU* 4.9 5.5 + - - +
360A ILE* 4.0 13.5 - - + +
363A GLU* 3.0 37.7 + - + +
602A 2S9 3.5 54.2 - + - +
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Residues in contact with PRO 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 3.6 2.7 - - - +
277A PRO* 4.0 18.6 - - + +
278A MET* 5.7 0.4 - - - +
302A TYR* 4.7 4.0 - - - +
305A GLY* 4.1 2.5 - - - +
306A ILE* 3.7 40.4 - - + +
309A ALA* 3.9 16.2 - - + -
317A HIS* 3.5 29.4 - - + +
318A ILE 3.3 5.4 - - - -
319A TYR* 1.4 90.3 - - + +
321A TYR* 1.3 63.2 + - + +
323A TYR* 3.7 9.2 + - + +
324A LEU* 3.4 16.3 + - - +
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Residues in contact with TYR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 3.5 33.0 - - + +
309A ALA* 6.0 1.3 - - + -
310A LYS* 3.2 24.9 + - - -
315A ASP* 2.7 31.0 + - - -
317A HIS 3.8 16.6 - - - -
318A ILE 3.2 3.4 + - - +
319A TYR 3.1 0.4 - - - -
320A PRO* 1.3 77.6 - - + +
322A MET* 1.3 61.0 + - - +
324A LEU* 3.3 9.2 + - + +
325A ALA* 2.9 28.9 + - - +
340A ALA* 3.7 9.6 - - - +
343A ASP* 3.5 35.2 - - + -
344A THR* 3.3 22.2 - - + -
347A VAL* 3.7 21.1 - - + -
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Residues in contact with MET 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 3.2 24.8 + - + +
319A TYR* 3.1 22.3 + - + +
321A TYR* 1.3 73.6 - - - +
323A TYR* 1.3 60.7 + - - +
325A ALA* 3.2 2.4 + - - -
326A GLY 2.8 26.7 + - - -
341A TRP* 4.0 19.7 - - + -
344A THR* 3.9 23.3 - - + +
360A ILE* 5.0 0.2 - - + -
363A GLU* 4.1 22.9 - - + -
364A PHE* 4.1 20.0 - - + -
367A VAL* 4.5 11.9 - - + -
602A 2S9 3.1 39.8 - - + -
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Residues in contact with TYR 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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277A PRO 5.4 0.9 - - - -
278A MET* 3.3 48.3 + - + +
281A GLY* 3.8 22.4 - - - -
282A ASN* 4.0 8.0 + - - +
285A ASP* 3.4 30.9 - - - +
302A TYR* 3.6 24.7 + - + -
319A TYR* 2.8 40.6 + - + +
320A PRO* 3.9 7.9 - - + +
322A MET* 1.3 72.5 - - - +
324A LEU* 1.3 64.1 + - - +
326A GLY* 3.4 1.4 + - - -
327A TYR* 3.2 17.0 + - - +
330A ARG* 4.8 1.4 + - - -
602A 2S9 3.3 48.3 - + + +
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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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299A LEU* 3.5 32.1 - - + -
302A TYR* 3.9 24.8 - - + -
303A HIS* 3.7 21.1 - - + +
306A ILE* 3.7 22.2 - - + -
320A PRO 3.4 10.9 + - - +
321A TYR* 3.3 9.3 + - + +
322A MET 3.2 0.4 - - - -
323A TYR* 1.3 76.6 - - - +
325A ALA* 1.3 65.8 + - - +
327A TYR* 3.2 4.4 + - + +
328A HIS* 3.0 40.7 + - + +
340A ALA* 4.1 15.3 - - + -
343A ASP* 5.9 1.3 - - - +
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Residues in contact with ALA 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 TYR 2.9 16.9 + - - +
322A MET 3.7 2.9 - - - +
324A LEU* 1.3 77.0 - - - +
326A GLY* 1.3 58.4 + - - +
328A HIS* 3.3 2.4 + - - +
329A CYS* 2.8 31.2 + - - +
337A ALA* 3.8 10.6 - - - +
340A ALA* 3.6 18.7 - - + +
341A TRP* 3.2 41.9 - - + +
602A 2S9 4.4 0.9 - - - -
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Residues in contact with GLY 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 MET 2.8 19.4 + - - -
323A TYR 3.4 2.2 + - - -
324A LEU 3.2 0.4 - - - -
325A ALA* 1.3 69.7 - - - +
327A TYR* 1.3 65.0 + - - +
329A CYS* 3.3 6.4 + - - +
330A ARG* 3.0 44.9 + - - +
602A 2S9 3.8 18.7 + - - -
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Residues in contact with TYR 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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288A GLU* 3.6 25.4 - - + -
297A ASP* 6.1 0.2 - - - +
298A PRO* 3.8 26.9 - - + +
299A LEU* 3.7 40.6 + - + +
302A TYR* 3.4 33.9 - + + +
323A TYR 3.2 6.4 + - - +
324A LEU 3.2 6.9 + - - +
326A GLY* 1.3 74.7 - - - +
328A HIS* 1.3 74.3 + + - +
330A ARG* 3.2 11.8 + - - +
331A ASN* 2.8 54.7 + - - -
333A ASN* 4.8 4.3 - - - -
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Residues in contact with HIS 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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299A LEU* 3.6 27.6 - - + +
303A HIS* 5.3 1.4 + - - -
324A LEU* 3.0 47.7 + - + +
325A ALA 3.8 4.9 - - - +
327A TYR* 1.3 79.5 - + - +
329A CYS* 1.3 57.4 + - - +
331A ASN 3.2 1.0 + - - -
332A ARG 2.9 8.1 + - - -
333A ASN* 2.8 58.1 + - - +
336A GLU* 3.4 42.5 - - + +
337A ALA* 3.6 19.5 - - - +
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Residues in contact with CYS 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 ALA 2.8 17.8 + - - +
326A GLY* 3.5 8.1 - - - +
328A HIS* 1.3 77.3 - - - +
330A ARG* 1.3 59.5 + - + +
332A ARG* 2.8 42.5 + - - +
333A ASN 5.6 0.2 - - - -
337A ALA* 3.9 5.8 - - - +
341A TRP* 3.9 12.3 - - + -
371A VAL* 3.7 29.6 - - - -
375A LEU* 3.9 23.1 - - - -
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Residues in contact with ARG 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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285A ASP* 3.7 20.4 + - - -
288A GLU* 2.7 41.4 + - - +
302A TYR* 3.7 1.2 + - - -
323A TYR 4.8 1.2 + - - -
326A GLY* 3.0 32.0 + - - +
327A TYR* 3.5 20.8 - - - +
329A CYS* 1.3 78.3 - - + +
331A ASN* 1.3 60.7 + - - +
332A ARG* 3.3 6.4 + - - +
601A SO4 4.0 22.6 + - - +
602A 2S9 5.8 2.8 - - - -
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Residues in contact with ASN 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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288A GLU* 3.5 14.3 + - - +
327A TYR* 2.8 57.9 + - - +
328A HIS 3.9 0.2 - - - +
329A CYS 3.1 0.4 - - - -
330A ARG* 1.3 77.6 - - - +
332A ARG* 1.3 69.4 + - - +
333A ASN* 3.2 26.4 + - - +
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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