Contacts of the helix formed by residues 365 - 378 (chain C) in PDB entry 3H1J
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 365 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361C THR* 2.8 35.2 + - + +
363C LEU 3.6 0.2 - - - -
364C LEU* 1.3 84.6 - - + +
366C LEU* 1.3 73.5 + - + +
367C PHE 3.5 1.3 - - - -
368C PRO* 3.2 4.3 - - - +
369C THR* 2.5 40.9 + - - +
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Residues in contact with LEU 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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325C LEU* 3.5 35.7 - - + -
328C LEU* 5.7 2.9 - - + -
361C THR* 3.1 26.4 + - + +
362C ILE* 3.9 17.0 - - + +
365C ILE* 1.3 87.2 - - + +
367C PHE* 1.3 57.1 + - - +
369C THR* 3.0 6.7 + - + +
370C ILE* 2.6 42.5 + - + +
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Residues in contact with PHE 367 (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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103C LEU* 4.6 9.2 - - + -
308C LEU* 4.9 4.0 - - + +
316C MET* 3.3 32.3 - - + -
319C ARG* 5.6 3.0 + - - -
322C SER* 3.7 20.2 + - - -
325C LEU* 3.4 16.1 - - + +
326C PHE* 3.7 30.1 - + + -
329C LEU* 4.3 17.9 - - + -
362C ILE* 3.1 38.2 + - + +
363C LEU* 4.2 15.9 - - + +
366C LEU* 1.3 77.4 - - - +
368C PRO* 1.3 71.0 - - + +
370C ILE* 3.9 1.4 - - + +
371C GLY* 3.0 20.6 + - - -
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Residues in contact with PRO 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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308C LEU* 3.7 33.0 - - + +
310C LYS* 3.7 24.3 - - + +
363C LEU 4.0 9.0 - - - +
364C LEU 3.4 19.1 - - - +
365C ILE* 3.2 15.3 - - - +
367C PHE* 1.3 94.0 - - + +
369C THR* 1.3 68.2 + - - +
371C GLY* 3.1 2.4 + - - -
372C THR* 3.1 25.3 + - - -
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Residues in contact with THR 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 ILE* 2.5 34.5 + - + +
366C LEU* 3.0 7.1 + - + -
368C PRO* 1.3 77.3 - - - +
370C ILE* 1.3 72.0 + - + +
371C GLY 3.1 0.7 + - - -
372C THR* 3.1 8.6 + - - -
373C LEU* 2.9 24.9 + - + +
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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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321C LEU* 3.4 39.3 - - + -
322C SER* 4.1 9.2 - - - +
325C LEU* 3.7 20.6 - - + -
366C LEU* 2.6 28.7 + - + +
367C PHE* 4.0 2.9 - - - +
369C THR* 1.3 80.4 - - + +
371C GLY* 1.3 57.9 + - - +
373C LEU* 3.5 19.3 - - + +
374C GLU* 2.8 34.7 + - - +
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Residues in contact with GLY 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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310C LYS* 4.5 2.7 - - - -
311C SER* 4.3 10.0 - - - -
319C ARG* 4.5 13.2 - - - -
322C SER* 4.9 0.6 + - - -
367C PHE 3.0 14.3 + - - -
368C PRO 3.6 3.8 - - - -
369C THR 3.1 0.2 - - - -
370C ILE* 1.3 78.2 - - - +
372C THR* 1.3 55.6 + - - +
374C GLU* 3.3 14.7 + - - +
375C ASN* 3.0 36.0 + - - +
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Residues in contact with THR 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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310C LYS* 3.8 16.9 - - - +
368C PRO 3.1 11.3 + - - -
369C THR* 3.1 11.8 + - - +
371C GLY* 1.3 73.2 - - - +
373C LEU* 1.3 66.3 + - - +
375C ASN* 3.0 23.5 + - + +
376C LYS* 3.1 36.5 + - + +
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Residues in contact with LEU 373 (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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321C LEU* 4.6 11.9 - - + -
369C THR* 2.9 15.8 + - + +
370C ILE* 3.5 26.0 - - + +
372C THR* 1.3 78.3 - - - +
374C GLU* 1.3 63.3 + - - +
376C LYS* 3.0 19.7 + - + +
377C MET* 3.0 36.1 + - + +
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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
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319C ARG* 3.1 29.3 - - - +
321C LEU* 3.2 22.4 + - + +
322C SER* 2.7 45.1 + - - -
370C ILE* 2.8 22.6 + - - +
371C GLY* 3.5 8.0 - - - +
373C LEU* 1.3 73.0 - - - +
375C ASN* 1.3 65.6 + - - +
377C MET* 3.1 10.1 + - - +
378C LEU* 3.0 26.4 + - + +
20F TYR* 2.9 32.5 + - + +
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Residues in contact with ASN 375 (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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310C LYS* 2.8 27.9 + - - +
311C SER* 3.8 2.3 + - - -
312C LYS* 3.0 48.5 + - + +
313C GLN* 4.8 0.5 + - - +
371C GLY 3.0 17.8 + - - +
372C THR* 3.0 13.1 + - - +
374C GLU* 1.3 76.6 - - - +
376C LYS* 1.3 65.1 + - + +
378C LEU* 3.0 20.5 + - - +
380C TYR* 3.1 30.9 + - + +
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Residues in contact with LYS 376 (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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372C THR* 3.1 29.3 + - - +
373C LEU* 3.0 18.9 + - + +
375C ASN* 1.3 78.0 - - + +
377C MET* 1.3 60.5 + - + +
379C ASN* 2.9 20.4 + - - -
380C TYR 4.2 12.5 + - - +
17F ARG* 4.1 8.5 + - - -
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Residues in contact with MET 377 (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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321C LEU* 4.2 18.4 - - + -
373C LEU* 3.0 31.3 + - + +
374C GLU* 3.1 9.8 + - - +
376C LYS* 1.3 77.6 - - + +
378C LEU* 1.3 59.3 + - - +
379C ASN 3.1 0.7 - - - -
16F ILE* 3.8 24.0 - - + -
17F ARG* 3.4 30.3 - - - +
19F TRP* 3.3 37.2 - - + -
20F TYR* 3.3 37.3 - - + -
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C GLN* 3.7 36.1 - - + +
374C GLU* 3.0 10.3 + - + +
375C ASN* 3.0 17.3 + - - +
377C MET* 1.3 76.7 - - - +
379C ASN* 1.3 67.3 + - - +
380C TYR* 3.8 25.6 - - + -
17F ARG* 4.8 0.2 - - - -
20F TYR* 3.4 31.2 - - + +
21F TYR* 5.5 4.5 - - + -
24F ALA* 5.1 0.4 - - + -
26F PHE* 3.9 28.0 - - + -
33F ARG* 3.1 29.5 + - + -
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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