Contacts of the helix formed by residues 357 - 374 (chain A) in PDB entry 1OHV
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR 4.4 4.5 - - - +
100A ARG* 3.7 21.3 + - - +
103A LEU* 4.2 3.0 - - - +
333A THR* 4.7 3.6 + - - -
356A GLY* 1.3 76.2 - - - +
358A PRO* 1.3 73.4 - - - +
359A SER* 2.8 31.5 + - - -
360A LYS* 2.9 40.6 + - + +
361A ASN* 3.3 14.6 + - - +
360B LYS* 2.8 30.1 + - - -
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Residues in contact with PRO 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 3.7 18.9 - - + +
100A ARG* 4.9 1.1 - - + -
101A PRO* 3.7 37.9 - - + +
103A LEU* 4.0 21.5 - - + -
108A PRO* 4.3 14.6 - - + -
110A ASN* 5.7 2.7 - - - +
111A PHE* 5.4 2.0 - - + -
114A LYS* 5.2 1.0 - - - +
356A GLY 4.8 0.2 - - - +
357A ASP* 1.3 91.6 - - - +
359A SER* 1.3 55.7 + - - +
361A ASN* 3.1 16.0 + - + +
362A LEU* 2.9 29.1 + - - +
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Residues in contact with SER 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A THR* 3.6 21.0 + - - +
97A PHE* 3.7 34.1 - - - -
357A ASP* 2.8 33.7 + - - -
358A PRO* 1.3 78.9 - - - +
360A LYS* 1.3 68.0 + - - +
362A LEU* 3.4 4.1 - - - +
363A LEU* 3.1 32.1 + - - +
360B LYS* 4.3 3.8 + - - -
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Residues in contact with LYS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 6.4 0.2 - - - -
332A MET* 3.8 38.0 - - + +
333A THR* 4.1 9.6 - - - -
357A ASP* 2.9 28.9 + - + +
359A SER* 1.3 85.3 + - - +
361A ASN* 1.3 59.9 + - - +
363A LEU* 3.3 12.8 + - + +
364A LEU* 2.8 31.2 + - - +
97B PHE* 4.6 13.9 + - - -
100B ARG* 3.8 29.5 - - - +
357B ASP* 2.8 30.1 + - - -
359B SER* 4.2 5.3 + - - -
360B LYS* 5.8 0.8 - - - +
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Residues in contact with ASN 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 5.2 2.0 - - - +
111A PHE* 3.8 28.9 + - - -
114A LYS* 3.8 19.3 - - + +
115A LEU* 4.0 17.5 - - + +
118A SER* 4.4 8.7 - - - +
119A LEU* 5.5 0.9 - - - -
132A THR* 4.9 6.0 - - - +
333A THR* 3.4 25.8 + - - +
357A ASP 3.3 12.4 + - - +
358A PRO* 3.1 16.0 + - + +
360A LYS* 1.3 72.1 - - - +
362A LEU* 1.3 66.5 + - - +
364A LEU* 3.7 7.1 - - - +
365A ALA* 3.0 25.6 + - - +
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Residues in contact with LEU 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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87A LEU* 3.6 24.8 - - + +
93A ASN* 3.7 46.9 - - + +
96A THR* 4.2 15.9 - - + +
97A PHE* 4.1 22.0 - - + -
114A LYS* 3.8 31.3 + - + +
358A PRO 2.9 12.3 + - - +
359A SER* 3.4 9.4 - - - +
361A ASN* 1.3 79.2 - - - +
363A LEU* 1.3 64.5 + - + +
365A ALA* 3.5 9.0 + - - +
366A GLU* 3.6 6.2 + - - +
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Residues in contact with LEU 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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84A LEU* 3.8 11.2 - - + +
87A LEU* 4.1 22.4 - - + -
97A PHE* 4.5 19.3 - - + -
332A MET* 3.8 26.7 - - + -
359A SER 3.1 16.8 + - - +
360A LYS* 3.7 19.5 - - + +
362A LEU* 1.3 80.4 - - + +
364A LEU* 1.3 62.4 + - - +
366A GLU* 3.1 7.4 + - - +
367A VAL* 3.0 23.7 + - - +
97B PHE 3.4 23.6 - - - +
98B ILE* 4.2 22.4 - - + -
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 4.0 9.0 - - - -
119A LEU* 3.7 36.8 - - + -
331A MET* 3.2 46.9 - - + +
332A MET* 4.0 9.1 - - + +
333A THR* 4.2 7.2 - - + -
360A LYS 2.8 21.3 + - - +
361A ASN* 3.3 6.3 + - - +
363A LEU* 1.3 71.3 - - - +
365A ALA* 1.3 59.6 + - - +
367A VAL* 3.1 12.9 + - + -
368A ILE* 2.9 47.7 + - + +
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Residues in contact with ALA 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS* 3.7 22.2 - - + +
117A GLU* 3.7 32.4 - - + +
118A SER* 3.8 13.2 - - - +
361A ASN 3.0 16.1 + - - +
362A LEU 3.7 4.0 - - - +
363A LEU 3.3 0.2 - - - -
364A LEU* 1.3 76.7 - - - +
366A GLU* 1.3 59.2 + - - +
368A ILE* 3.6 2.3 + - - +
369A ASN* 3.1 26.0 + - - +
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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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83A ALA* 3.8 36.5 - - + +
84A LEU* 4.0 10.1 - - + -
87A LEU* 3.6 28.1 - - + +
362A LEU 3.6 1.2 + - - -
363A LEU 3.1 10.1 + - - +
365A ALA* 1.3 78.5 - - - +
367A VAL* 1.3 63.9 + - - +
369A ASN* 3.3 25.7 + - - +
370A ILE* 3.0 29.6 + - + +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO* 3.7 38.1 - - + -
77A ILE* 3.9 28.9 - - + +
84A LEU* 4.2 12.1 - - + -
330A LYS 4.9 0.4 - - - +
332A MET* 4.5 6.3 - - + -
363A LEU 3.0 22.1 + - - +
364A LEU* 3.1 21.1 + - + +
366A GLU* 1.3 76.4 - - - +
368A ILE* 1.3 57.9 + - - +
370A ILE* 3.1 4.0 + - - +
371A ILE* 2.9 42.8 + - + +
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Residues in contact with ILE 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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117A GLU 4.3 7.4 - - - +
118A SER* 3.5 35.2 - - - +
119A LEU 4.2 0.4 - - - +
121A SER* 3.8 6.1 - - - +
122A VAL* 4.2 17.7 - - + -
310A PHE* 4.2 17.5 - - + -
331A MET* 4.4 2.5 - - + -
364A LEU* 2.9 36.8 + - + +
365A ALA 3.9 3.4 - - - +
367A VAL* 1.3 73.8 - - - +
369A ASN* 1.3 66.8 + - - +
371A ILE* 3.2 11.0 + - + +
372A LYS* 3.1 52.5 + - + +
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Residues in contact with ASN 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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365A ALA 3.1 15.8 + - - +
366A GLU* 3.5 30.0 - - - +
367A VAL 3.3 0.2 - - - -
368A ILE* 1.3 79.9 - - - +
370A ILE* 1.3 58.5 + - - +
372A LYS* 3.4 6.9 + - - +
373A ARG* 3.0 31.8 + - - +
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Residues in contact with ILE 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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77A ILE* 4.0 21.5 - - + -
81A HIS* 3.8 32.5 - - + +
83A ALA* 4.0 7.9 - - + -
366A GLU* 3.0 33.4 + - - +
367A VAL 3.1 7.4 + - - +
369A ASN* 1.3 75.5 - - - +
371A ILE* 1.3 68.1 + - - +
372A LYS 3.1 1.3 - - - -
373A ARG* 4.5 5.2 - - + +
374A GLU* 3.0 40.0 + - + +
376A LEU* 4.0 15.9 - - + -
451A VAL* 5.7 1.6 - - + -
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Residues in contact with ILE 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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76A PRO* 5.3 1.1 - - + -
77A ILE* 4.3 3.4 - - + -
304A GLY* 4.2 2.9 - - - +
310A PHE* 3.9 28.7 - - + -
330A LYS* 6.4 0.2 - - + -
367A VAL* 2.9 35.7 + - + +
368A ILE* 3.2 10.3 + - + +
370A ILE* 1.3 74.3 - - - +
372A LYS* 1.3 60.7 + - + +
375A ASP* 3.2 4.3 + - - -
376A LEU* 2.8 47.0 + - + -
377A LEU* 4.0 32.7 + - + +
450A LEU* 3.5 30.3 - - + -
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Residues in contact with LYS 372 (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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121A SER* 3.1 40.5 + - - -
122A VAL* 4.1 10.8 - - - +
310A PHE* 6.2 1.8 - - - -
368A ILE* 3.1 31.2 + - + +
369A ASN* 3.8 7.0 - - - +
371A ILE* 1.3 80.9 - - + +
373A ARG* 1.3 65.5 + - - +
375A ASP* 3.1 13.2 + - - +
377A LEU* 6.4 1.8 - - + -
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Residues in contact with ARG 373 (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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369A ASN* 3.0 23.6 + - - +
370A ILE* 4.3 4.3 - - + +
372A LYS* 1.3 76.7 - - - +
374A GLU* 1.3 69.6 + - + +
375A ASP* 3.2 3.9 + - - +
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Residues in contact with GLU 374 (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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81A HIS* 6.2 0.4 - - - +
370A ILE* 3.0 33.1 + - + +
373A ARG* 1.3 82.6 - - + +
375A ASP* 1.3 72.5 + - - +
376A LEU* 3.1 25.0 + - + +
379A ASN* 5.1 0.9 - - - +
453A ARG* 4.7 17.7 + - - +
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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