Contacts of the helix formed by residues 357 - 371 (chain A) in PDB entry 4O14
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 ASP 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A GLN* 4.1 8.1 - - - +
355A GLY 3.3 2.8 + - - -
356A VAL* 1.3 75.8 - - - +
358A ILE* 1.3 61.9 + - + +
359A ASN* 3.4 11.8 + - - +
360A THR* 2.7 44.4 + - - +
361A LEU* 2.8 27.9 + - - +
386A LEU* 4.8 18.4 - - + +
389A LYS* 6.2 0.2 - - - +
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Residues in contact with ILE 358 (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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54A TYR* 3.8 26.0 - - + +
164A ASN* 4.1 8.0 - - - +
167A GLU* 3.5 35.9 - - + +
168A GLN* 3.8 24.4 - - + +
171A ILE* 3.6 24.3 - - + +
357A ASP* 1.3 78.2 - - + +
359A ASN* 1.3 76.2 + - - +
361A LEU* 3.5 3.1 - - - +
362A GLN* 3.2 22.9 + - - +
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Residues in contact with ASN 359 (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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357A ASP* 3.2 12.7 + - - +
358A ILE* 1.3 91.6 - - - +
360A THR* 1.3 63.0 + - + +
362A GLN* 3.4 6.7 + - - +
363A GLU* 3.1 21.9 + - - +
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Residues in contact with THR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PRO* 5.2 10.1 - - + -
355A GLY 2.6 28.3 + - - +
356A VAL* 3.1 4.2 - - - -
357A ASP* 2.7 37.3 + - - +
359A ASN* 1.3 75.9 - - + +
361A LEU* 1.3 66.3 + - - +
363A GLU* 3.2 15.7 + - - +
364A ILE* 2.9 37.6 + - - +
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Residues in contact with LEU 361 (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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168A GLN* 3.5 52.0 - - + +
171A ILE* 4.4 13.5 - - + -
172A LEU* 3.9 15.5 - - + -
190A LEU* 5.0 1.1 - - + -
356A VAL* 4.1 11.9 - - + +
357A ASP 2.8 17.0 + - - +
358A ILE 3.5 4.0 - - - +
360A THR* 1.3 78.5 + - - +
362A GLN* 1.3 62.4 + - - +
364A ILE* 3.2 5.3 + - - +
365A VAL* 3.0 27.4 + - + +
380A PHE* 3.4 47.8 - - + -
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Residues in contact with GLN 362 (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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171A ILE* 3.6 31.8 - - + +
175A TYR* 2.9 34.3 + - - -
358A ILE 3.2 10.0 + - - +
359A ASN* 3.5 12.1 - - - +
361A LEU* 1.3 80.7 - - - +
363A GLU* 1.3 63.3 + - - +
365A VAL* 3.4 7.3 - - - +
366A GLU* 3.0 31.5 + - + +
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Residues in contact with GLU 363 (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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316A ASN* 4.5 9.2 + - - +
317A PRO* 6.1 0.3 - - - +
318A LEU* 3.6 38.0 + - + +
359A ASN 3.1 12.7 + - - +
360A THR* 3.2 21.1 + - - +
362A GLN* 1.3 78.0 - - - +
364A ILE* 1.3 60.1 + - + +
366A GLU* 3.8 3.7 - - - +
367A GLY* 2.8 27.2 + - - -
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Residues in contact with ILE 364 (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 PRO* 3.9 26.7 - - + +
318A LEU* 3.9 25.6 - - + +
321A VAL* 4.1 26.2 - - + -
352A GLN* 4.1 12.8 - - + -
356A VAL* 4.5 6.1 - - + -
360A THR* 2.9 24.2 + - - +
361A LEU* 3.2 3.8 + - - +
363A GLU* 1.3 75.9 - - + +
365A VAL* 1.3 60.5 + - - +
367A GLY* 3.1 0.7 + - - -
368A MET* 2.7 34.0 + - - +
378A ILE* 4.3 0.4 - - + -
380A PHE* 3.6 36.8 - - + -
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Residues in contact with VAL 365 (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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171A ILE* 3.8 11.9 - - + -
172A LEU* 4.3 13.5 - - + -
175A TYR* 3.5 37.5 - - + -
361A LEU* 3.0 20.3 + - + +
362A GLN 3.4 6.1 - - - +
364A ILE* 1.3 75.1 - - - +
366A GLU* 1.3 61.3 + - - +
368A MET* 3.7 1.9 - - - +
369A LYS* 2.9 29.6 + - - +
375A ILE* 3.8 27.4 - - + +
378A ILE* 5.3 0.2 - - + -
380A PHE* 3.8 27.6 - - + -
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Residues in contact with GLU 366 (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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175A TYR* 2.7 41.4 + - - +
362A GLN* 3.0 24.0 + - - +
363A GLU* 4.0 4.5 - - - +
365A VAL* 1.3 78.0 - - - +
367A GLY* 1.3 57.0 + - - +
369A LYS* 3.3 12.8 + - - +
370A GLN* 2.9 67.5 + - + +
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Residues in contact with GLY 367 (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 LEU* 3.9 13.9 - - - -
322A LEU* 4.0 8.8 - - - +
363A GLU 2.8 20.0 + - - -
364A ILE 3.5 0.9 - - - -
366A GLU* 1.3 78.9 - - - +
368A MET* 1.3 61.9 + - - +
370A GLN* 3.3 9.4 + - - +
371A LYS* 3.1 26.3 + - - +
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Residues in contact with MET 368 (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 VAL* 4.1 9.0 - - + -
322A LEU* 3.9 20.9 - - + -
325A LEU* 3.8 22.2 - - + -
364A ILE* 2.7 26.4 + - - +
365A VAL* 3.7 4.5 - - - +
367A GLY* 1.3 70.5 - - - +
369A LYS* 1.3 65.4 + - - +
371A LYS* 3.0 3.1 + - - -
372A MET 3.0 5.5 + - - -
373A TRP* 2.9 35.1 + - + +
374A SER 3.3 26.5 - - - +
375A ILE* 3.9 11.4 - - + -
377A ASN* 4.6 2.7 - - + -
378A ILE* 3.5 47.3 - - + -
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Residues in contact with LYS 369 (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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174A LYS* 5.7 1.4 - - - +
175A TYR* 3.9 25.4 - - + -
178A GLU* 2.5 40.9 + - + +
179A THR* 4.5 6.5 - - + -
341A TYR* 3.6 33.2 + - + +
365A VAL 2.9 17.8 + - - +
366A GLU* 3.6 16.0 + - - +
368A MET* 1.3 77.7 - - - +
370A GLN* 1.3 65.8 + - + +
372A MET* 3.0 18.5 + - - +
373A TRP 4.1 3.3 + - - -
375A ILE* 5.0 0.4 - - - +
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Residues in contact with GLN 370 (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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366A GLU* 2.9 49.9 + - + +
367A GLY* 3.5 11.2 - - - +
368A MET 3.2 0.2 - - - -
369A LYS* 1.3 80.3 - - - +
371A LYS* 1.3 64.3 + - + +
372A MET* 3.2 10.1 + - - +
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Residues in contact with LYS 371 (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 LEU* 4.2 23.3 - - + -
342A LYS* 2.9 20.8 + - - -
367A GLY 3.1 14.8 + - - +
368A MET 3.0 5.1 + - - +
370A GLN* 1.3 80.6 - - + +
372A MET* 1.3 62.8 + - - +
373A TRP* 3.3 20.2 + - + +
602A EDO 4.7 15.6 + - - +
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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