Contacts of the helix formed by residues 357 - 374 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A LYS* 2.8 35.0 + - - -
96B THR 4.4 4.5 - - - +
100B ARG* 3.7 21.2 + - - +
103B LEU* 4.2 2.6 - - - +
333B THR* 4.5 4.4 + - - -
356B GLY* 1.3 76.1 - - - +
358B PRO* 1.3 74.8 - - - +
359B SER* 2.8 27.3 + - - -
360B LYS* 2.9 39.1 + - + +
361B ASN* 3.3 14.4 + - - +
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Residues in contact with PRO 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B THR* 3.6 18.7 - - + +
99B ASN 5.6 0.2 - - - +
100B ARG* 4.9 0.7 - - + -
101B PRO* 3.7 38.4 - - + +
103B LEU* 4.0 21.3 - - + -
108B PRO* 4.3 14.4 - - + -
110B ASN* 5.7 2.7 - - - +
111B PHE* 5.4 2.5 - - + -
114B LYS* 5.3 0.9 - - - +
356B GLY 4.8 0.2 - - - +
357B ASP* 1.3 91.3 - - - +
359B SER* 1.3 55.3 + - - +
361B ASN* 3.2 15.0 + - + +
362B LEU* 2.9 29.5 + - - +
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Residues in contact with SER 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LYS* 4.2 5.2 + - - -
96B THR* 3.5 21.1 + - - +
97B PHE* 3.6 34.2 - - - -
357B ASP* 2.8 31.9 + - - -
358B PRO* 1.3 77.4 - - - +
360B LYS* 1.3 70.6 + - - +
362B LEU* 3.4 4.3 - - - +
363B LEU* 3.1 28.1 + - - +
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Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 4.7 12.9 + - - +
100A ARG* 3.7 30.4 - - - +
357A ASP* 2.8 29.6 + - - -
359A SER* 4.3 4.8 + - - -
360A LYS* 5.8 1.2 - - - +
97B PHE* 6.4 0.4 - - - -
332B MET* 3.8 27.6 - - + +
333B THR* 3.9 20.4 - - - -
357B ASP* 2.9 27.7 + - + +
359B SER* 1.3 85.9 + - - +
361B ASN* 1.3 59.6 + - - +
363B LEU* 3.3 13.9 + - + +
364B LEU* 2.8 30.2 + - - +
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Residues in contact with ASN 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 5.3 2.0 - - - +
111B PHE* 3.8 28.7 + - - -
114B LYS* 3.8 19.8 - - + +
115B LEU* 4.0 17.8 - - + +
118B SER* 4.4 8.2 - - - +
119B LEU* 5.6 1.3 - - - -
132B THR* 4.8 6.2 - - - +
333B THR* 3.5 25.4 + - - +
357B ASP 3.5 13.2 + - - +
358B PRO* 3.2 14.9 + - + +
360B LYS* 1.3 72.6 - - - +
362B LEU* 1.3 66.1 + - - +
364B LEU* 3.7 7.4 - - - +
365B ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 3.5 27.3 - - + +
93B ASN* 3.6 47.3 - - + +
96B THR* 4.2 15.9 - - + +
97B PHE* 4.1 22.0 - - + -
114B LYS* 3.8 33.1 - - + +
358B PRO 2.9 12.8 + - - +
359B SER* 3.4 9.0 - - - +
361B ASN* 1.3 77.9 - - - +
363B LEU* 1.3 62.5 + - + +
365B ALA* 3.6 8.5 + - - +
366B GLU* 3.7 4.7 + - - +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE 3.4 23.6 - - - +
98A ILE* 4.3 18.6 - - + -
84B LEU* 3.8 13.9 - - + +
87B LEU* 4.1 22.7 - - + -
88B VAL* 4.8 0.2 - - + -
97B PHE* 4.5 20.0 - - + -
332B MET* 3.6 27.4 - - + -
359B SER 3.1 16.2 + - - +
360B LYS* 3.7 20.6 - - + +
362B LEU* 1.3 78.1 - - + +
364B LEU* 1.3 62.3 - - - +
366B GLU* 3.1 6.4 + - - +
367B VAL* 3.0 24.5 + - - +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B SER* 4.1 8.1 - - - +
119B LEU* 3.8 36.8 - - + -
330B LYS 4.6 0.4 - - - +
331B MET* 3.3 52.7 - - + +
332B MET* 4.1 6.9 - - + +
333B THR* 4.2 7.2 - - + -
360B LYS 2.8 21.7 + - - +
361B ASN* 3.2 7.2 + - - +
363B LEU* 1.3 72.4 - - - +
365B ALA* 1.3 59.3 + - - +
367B VAL* 3.0 14.3 + - + -
368B ILE* 2.8 43.7 + - + +
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LYS* 3.7 22.0 - - + +
117B GLU* 3.7 32.2 - - + +
118B SER* 3.8 14.1 - - - +
361B ASN 3.0 16.9 + - - +
362B LEU 3.8 3.6 - - - +
363B LEU 3.3 0.2 - - - -
364B LEU* 1.3 75.9 - - - +
366B GLU* 1.3 58.4 + - - +
368B ILE* 3.6 2.3 + - - +
369B ASN* 3.1 26.5 + - - +
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA* 3.8 37.8 - - + +
84B LEU* 4.0 10.3 - - + -
87B LEU* 3.6 27.9 - - + +
362B LEU 3.7 1.4 + - - -
363B LEU 3.1 9.2 + - - +
365B ALA* 1.3 79.8 - - - +
367B VAL* 1.3 64.2 + - - +
369B ASN* 3.3 25.2 + - - +
370B ILE* 3.0 29.6 + - + +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PRO* 3.7 38.4 - - + -
77B ILE* 3.9 26.2 - - + -
84B LEU* 4.2 12.3 - - + -
330B LYS 4.9 0.2 - - - +
332B MET* 4.3 6.3 - - + -
363B LEU 3.0 21.9 + - - +
364B LEU* 3.0 21.5 + - + +
366B GLU* 1.3 77.5 - - - +
368B ILE* 1.3 57.3 + - - +
370B ILE* 3.2 3.8 + - - +
371B ILE* 2.9 41.0 + - + +
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU 4.3 7.0 - - - +
118B SER* 3.5 34.8 - - - +
119B LEU 4.2 0.4 - - - +
121B SER* 3.8 5.6 - - - +
122B VAL* 4.1 17.9 - - + -
310B PHE* 4.2 17.7 - - + -
331B MET* 4.4 2.9 - - + -
364B LEU* 2.8 39.5 + - + +
365B ALA 3.9 2.9 - - - +
367B VAL* 1.3 71.1 - - - +
369B ASN* 1.3 68.3 + - - +
371B ILE* 3.3 9.0 + - + +
372B LYS* 3.0 54.7 + - + +
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Residues in contact with ASN 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B ALA 3.1 14.5 + - - +
366B GLU* 3.3 29.6 + - - +
368B ILE* 1.3 78.8 - - - +
370B ILE* 1.3 57.9 + - - +
372B LYS* 3.4 5.7 + - - +
373B ARG* 3.0 36.1 + - - +
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ILE* 4.1 21.1 - - + -
81B HIS* 3.9 32.5 - - + +
83B ALA* 4.0 8.1 - - + -
366B GLU* 3.0 34.0 + - - +
367B VAL 3.5 7.4 - - - +
369B ASN* 1.3 77.1 - - - +
371B ILE* 1.3 64.8 + - - +
373B ARG* 4.8 3.4 - - + -
374B GLU* 2.9 41.5 + - + +
376B LEU* 4.0 17.0 - - + -
451B VAL* 5.7 0.9 - - + -
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Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PRO* 5.1 1.1 - - + -
77B ILE* 4.2 3.8 - - + -
304B GLY* 4.3 2.5 - - - +
310B PHE* 4.1 29.2 - - + -
330B LYS* 6.3 0.2 - - + -
331B MET* 6.4 0.2 - - - -
364B LEU* 6.4 0.2 - - + -
367B VAL* 2.9 37.9 + - + +
368B ILE* 3.3 8.9 + - + +
370B ILE* 1.3 74.7 - - - +
372B LYS* 1.3 64.0 + - + +
375B ASP* 3.3 1.9 + - - -
376B LEU* 3.0 44.7 + - + -
377B LEU* 4.1 31.7 + - + +
450B LEU* 3.5 31.2 - - + -
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Residues in contact with LYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU 5.4 0.2 + - - -
121B SER* 3.0 41.6 + - - -
122B VAL* 4.1 11.1 - - - +
310B PHE* 6.3 1.3 - - + -
368B ILE* 3.0 33.1 + - + +
369B ASN* 3.8 6.7 - - - +
371B ILE* 1.3 80.7 - - + +
373B ARG* 1.3 63.6 + - - +
375B ASP* 3.3 12.5 + - - +
377B LEU* 6.4 1.3 - - + -
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Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ASN* 3.0 28.2 + - - +
370B ILE* 4.4 3.6 - - + +
372B LYS* 1.3 77.8 - - - +
374B GLU* 1.3 65.1 + - + +
375B ASP* 3.3 2.4 + - - +
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Residues in contact with GLU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B ILE* 2.9 36.0 + - + +
373B ARG* 1.3 80.4 - - + +
375B ASP* 1.3 71.6 + - - +
376B LEU* 3.2 23.7 + - + +
379B ASN* 5.2 0.3 - - - +
453B ARG* 4.2 20.5 + - - +
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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