Contacts of the helix formed by residues 357 - 374 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C THR 4.4 4.0 - - - +
100C ARG* 3.7 20.3 + - - +
103C LEU* 4.2 2.6 - - - +
333C THR* 4.5 3.8 + - - -
356C GLY* 1.3 75.7 - - - +
358C PRO* 1.3 74.6 - - - +
359C SER* 2.9 27.0 + - - -
360C LYS* 2.9 41.2 + - + +
361C ASN* 3.3 14.3 + - - +
360D LYS* 2.8 34.9 + - - -
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Residues in contact with PRO 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C THR* 3.7 18.7 - - + +
99C ASN 5.6 0.2 - - - +
100C ARG* 4.9 0.9 - - + -
101C PRO* 3.7 39.3 - - + +
103C LEU* 4.0 20.1 - - + -
108C PRO* 4.3 14.8 - - + -
110C ASN* 5.7 2.9 - - - +
111C PHE* 5.4 2.2 - - + -
114C LYS* 5.3 1.0 - - - +
357C ASP* 1.3 91.6 - - - +
359C SER* 1.3 54.7 + - - +
361C ASN* 3.1 15.7 + - + +
362C LEU* 2.9 28.9 + - - +
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Residues in contact with SER 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C THR* 3.6 21.7 - - - +
97C PHE* 3.6 33.8 - - - -
357C ASP* 2.9 32.1 + - - -
358C PRO* 1.3 77.0 - - - +
360C LYS* 1.3 72.6 + - - +
362C LEU* 3.4 4.6 + - - +
363C LEU* 3.2 28.1 + - - +
360D LYS* 4.4 4.0 + - - -
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Residues in contact with LYS 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C MET* 3.8 32.2 - - + +
333C THR* 4.0 14.1 - - - -
357C ASP* 2.9 29.0 + - + +
359C SER* 1.3 85.5 + - - +
361C ASN* 1.3 58.6 + - - +
363C LEU* 3.4 14.6 + - + +
364C LEU* 2.8 30.1 + - - +
97D PHE 4.6 12.7 + - - -
100D ARG* 3.7 29.3 - - - +
357D ASP* 2.8 29.8 + - - -
359D SER* 4.3 4.4 + - - -
360D LYS* 5.9 1.0 - - - +
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Residues in contact with ASN 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 5.2 1.6 - - - +
111C PHE* 3.8 28.3 + - - -
114C LYS* 3.8 19.6 - - + +
115C LEU* 4.0 17.9 - - + +
118C SER* 4.4 8.6 - - - +
119C LEU* 5.6 0.9 - - - -
132C THR* 4.8 6.4 + - - +
333C THR* 3.5 26.6 + - - +
357C ASP 3.3 14.0 + - - +
358C PRO* 3.1 14.9 + - + +
360C LYS* 1.3 73.1 - - - +
362C LEU* 1.3 65.9 + - - +
364C LEU* 3.7 6.9 - - - +
365C ALA* 3.0 25.6 + - - +
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Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.6 28.0 - - + +
93C ASN* 3.7 45.5 - - + +
96C THR* 4.2 15.9 - - + +
97C PHE* 4.0 22.7 - - + -
114C LYS* 3.8 32.4 - - + +
358C PRO 2.9 13.2 + - - +
359C SER* 3.4 8.7 - - - +
361C ASN* 1.3 77.3 - - - +
363C LEU* 1.3 63.0 + - + +
365C ALA* 3.5 9.0 + - - +
366C GLU 3.6 4.7 + - - -
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 3.9 12.8 - - + +
87C LEU* 4.1 22.7 - - + -
97C PHE* 4.5 18.6 - - + -
332C MET* 3.9 26.0 - - + -
359C SER* 3.2 16.9 + - - +
360C LYS* 3.7 20.0 - - + +
362C LEU* 1.3 80.4 - - + +
364C LEU* 1.3 62.8 + - - +
366C GLU* 3.1 6.8 + - - +
367C VAL* 3.0 25.0 + - - +
97D PHE 3.4 24.0 - - - +
98D ILE* 4.2 22.0 - - + -
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Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C SER* 4.0 8.1 - - - +
119C LEU* 3.8 36.8 - - + -
310C PHE* 5.8 0.2 - - + -
331C MET* 3.3 47.8 - - + +
332C MET* 4.1 7.2 - - + +
333C THR* 4.3 7.0 - - + -
360C LYS 2.8 21.8 + - - +
361C ASN* 3.7 7.0 - - - +
363C LEU* 1.3 74.8 - - - +
365C ALA* 1.3 63.9 + - - +
367C VAL* 3.1 14.2 + - + -
368C ILE* 2.9 41.9 + - + +
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Residues in contact with ALA 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LYS* 3.7 22.2 - - + +
117C GLU* 3.8 31.3 - - + +
118C SER* 3.8 13.2 - - - +
361C ASN 3.0 17.4 + - - +
362C LEU 3.7 4.0 - - - +
364C LEU* 1.3 76.8 - - - +
366C GLU* 1.3 57.4 + - - +
368C ILE* 3.5 2.8 + - - +
369C ASN* 3.1 26.0 + - - +
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Residues in contact with GLU 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ALA* 3.8 37.1 - - + +
84C LEU* 4.0 10.3 - - + -
87C LEU* 3.6 29.7 - - + +
362C LEU 3.6 1.2 + - - -
363C LEU 3.1 9.4 + - - +
365C ALA* 1.3 79.5 - - - +
367C VAL* 1.3 63.6 + - - +
369C ASN* 3.3 25.2 + - - +
370C ILE* 3.0 36.4 + - + +
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Residues in contact with VAL 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PRO* 3.7 38.6 - - + -
77C ILE* 3.9 27.3 - - + +
84C LEU* 4.2 12.6 - - + -
330C LYS 4.9 0.2 - - - +
332C MET* 4.3 6.7 - - + -
363C LEU 3.0 21.0 + - - +
364C LEU* 3.1 21.3 + - + +
366C GLU* 1.3 77.6 - - - +
368C ILE* 1.3 56.0 + - - +
370C ILE* 3.2 3.6 + - - +
371C ILE* 2.9 42.0 + - + +
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Residues in contact with ILE 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLU 4.3 7.0 - - - +
118C SER* 3.5 35.7 - - - +
119C LEU 4.2 0.2 - - - +
121C SER* 3.8 5.6 - - - +
122C VAL* 4.2 17.3 - - + -
310C PHE* 4.2 16.4 - - + -
331C MET* 4.4 3.1 - - + -
364C LEU* 2.9 36.8 + - + +
365C ALA 3.8 3.6 - - - +
367C VAL* 1.3 74.6 - - - +
369C ASN* 1.3 66.8 + - - +
371C ILE* 3.2 10.0 + - + +
372C LYS* 3.1 53.6 + - + +
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Residues in contact with ASN 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C ALA 3.1 14.7 + - - +
366C GLU* 3.5 30.6 - - - +
368C ILE* 1.3 79.4 - - - +
370C ILE* 1.3 59.0 + - - +
372C LYS* 4.0 5.0 - - - +
373C ARG* 3.0 38.6 + - - +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ILE* 4.1 21.8 - - + -
81C HIS* 3.8 32.3 - - + +
83C ALA* 4.0 7.4 - - + -
366C GLU* 3.0 33.8 + - - +
367C VAL 3.5 7.0 - - - +
368C ILE 3.2 0.2 - - - -
369C ASN* 1.3 75.5 - - - +
371C ILE* 1.3 64.8 + - - +
373C ARG* 4.8 2.5 - - + -
374C GLU* 2.9 46.8 + - + +
376C LEU* 4.0 14.4 - - + -
451C VAL* 5.7 1.6 - - + -
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Residues in contact with ILE 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C PRO* 5.2 0.9 - - + -
77C ILE* 4.3 3.1 - - + -
304C GLY* 4.4 2.7 - - - +
310C PHE* 4.1 28.0 - - + -
330C LYS* 6.4 0.2 - - + -
367C VAL* 2.9 37.1 + - + +
368C ILE* 3.2 8.5 + - + +
370C ILE* 1.3 75.7 - - - +
372C LYS* 1.3 64.4 + - + +
375C ASP* 3.3 1.7 + - - -
376C LEU* 2.9 44.8 + - + -
377C LEU* 4.1 31.4 + - + +
450C LEU* 3.5 30.7 - - + -
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Residues in contact with LYS 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLU 5.6 0.2 + - - -
121C SER* 3.1 41.8 + - - -
122C VAL* 4.4 11.7 - - - -
310C PHE* 6.2 1.3 - - + -
368C ILE* 3.1 30.3 + - + +
369C ASN* 4.0 5.2 - - - +
371C ILE* 1.3 80.1 - - + +
373C ARG* 1.3 65.7 + - - +
375C ASP* 3.2 13.9 + - - +
377C LEU* 6.3 2.9 - - + -
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Residues in contact with ARG 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C ASN* 3.0 27.6 + - - +
370C ILE* 4.4 3.8 - - + +
372C LYS* 1.3 77.9 - - - +
374C GLU* 1.3 64.2 + - + +
375C ASP* 3.4 4.9 + - - +
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Residues in contact with GLU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ILE* 2.9 40.5 + - + +
373C ARG* 1.3 78.6 - - + +
375C ASP* 1.3 71.9 + - - +
376C LEU* 3.3 22.8 + - + +
379C ASN* 5.3 0.3 - - - +
453C ARG* 4.8 15.8 + - - +
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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