Contacts of the helix formed by residues 372 - 381 (chain B) in PDB entry 3C0M
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 372 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ALA* 2.7 20.8 + - - +
330B TYR* 4.2 10.4 - - + +
332B HIS* 3.2 25.8 + - - +
368B VAL* 4.3 13.8 - - - +
370B TRP 3.8 1.6 + - - -
371B TRP* 1.3 70.1 - - - +
373B TRP* 1.3 59.8 + - - +
374B ASN* 3.2 10.7 + - - +
375B TRP* 2.9 38.7 + - + +
376B THR* 3.6 8.0 + - - +
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Residues in contact with TRP 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 4.4 8.7 - - + -
123B LEU* 3.8 28.3 - - + -
343B PHE* 4.3 17.0 - + - -
355B ILE* 4.1 25.6 - - + -
358B GLN* 3.1 57.6 + - + +
359B TRP* 3.7 33.0 - + + -
362B ARG* 4.2 16.2 - - + +
368B VAL* 5.5 0.6 - - - +
371B TRP* 3.1 26.1 + - + -
372B ASP* 1.3 70.2 + - - +
374B ASN* 1.3 67.3 + - - +
376B THR* 2.7 29.9 + - + -
377B ILE* 3.2 9.7 + - - +
385B MET* 4.3 6.5 - - + -
389B LEU* 3.9 19.1 - - + -
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Residues in contact with ASN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ARG* 3.1 41.2 - - - +
363B TYR* 3.2 37.0 + - - -
372B ASP* 3.2 8.5 + - - +
373B TRP* 1.3 77.4 - - - +
375B TRP* 1.3 65.0 + - - +
377B ILE* 3.1 26.4 + - - +
378B GLN* 3.2 11.8 + - - +
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Residues in contact with TRP 375 (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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122B TYR 3.8 15.3 - - - -
123B LEU 5.1 0.9 - - - -
124B GLY 5.4 0.4 - - - -
325B GLY 5.2 1.6 - - - -
326B GLY* 3.7 11.7 - - - -
327B ASN* 3.1 46.4 - - - -
328B ALA* 3.4 17.0 - - + -
332B HIS* 3.4 21.9 + + - -
372B ASP* 2.9 32.5 + - + +
374B ASN* 1.3 76.0 - - - +
376B THR* 1.3 76.4 + - - +
378B GLN* 2.9 25.1 + - - +
379B GLN* 2.9 54.4 + - + +
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Residues in contact with THR 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR 3.7 21.5 - - - +
123B LEU* 4.4 10.3 - - + -
328B ALA* 4.1 7.9 - - + -
359B TRP* 4.5 0.7 - - - -
372B ASP 4.1 8.7 - - - +
373B TRP* 2.7 26.7 + - + -
375B TRP* 1.3 90.1 - - + +
377B ILE* 1.3 57.5 + - - +
379B GLN* 4.0 4.3 - - - -
380B ASN* 2.9 32.8 + - - +
385B MET* 3.4 39.6 - - + +
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Residues in contact with ILE 377 (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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282A ARG* 5.3 0.2 + - - -
359B TRP* 4.1 17.0 - - + -
362B ARG* 3.8 26.5 - - - +
363B TYR* 4.8 1.6 - - - +
373B TRP 3.5 8.5 - - - +
374B ASN* 3.1 32.7 + - - +
375B TRP 3.0 1.0 - - - -
376B THR* 1.3 82.4 + - - +
378B GLN* 1.3 58.1 + - - +
381B GLY* 2.6 32.4 + - - +
382B LEU* 3.7 39.5 - - + +
385B MET* 4.2 5.8 - - + -
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Residues in contact with GLN 378 (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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282A ARG* 3.6 15.1 + - - -
374B ASN 3.2 7.0 + - - +
375B TRP* 2.9 17.6 + - - +
377B ILE* 1.3 80.4 - - - +
379B GLN* 1.3 87.3 + - - +
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Residues in contact with GLN 379 (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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282A ARG* 4.1 8.7 + - - +
284A THR* 5.1 6.2 + - - -
375B TRP* 2.9 59.3 + - + +
376B THR* 3.6 4.7 - - - +
378B GLN* 1.3 106.3 + - - +
380B ASN* 1.3 77.4 + - - +
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Residues in contact with ASN 380 (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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282A ARG* 4.3 19.3 + - - +
121B HIS* 5.5 1.2 + - - -
122B TYR* 3.3 44.7 + - + +
376B THR* 2.9 20.4 + - - +
379B GLN* 1.3 93.4 - - - +
381B GLY* 1.3 61.1 + - - +
384B THR* 3.3 34.8 + - + +
385B MET* 4.1 9.1 - - - -
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Residues in contact with GLY 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 3.9 17.3 - - - +
377B ILE* 2.6 23.9 + - - -
379B GLN 3.9 0.2 - - - -
380B ASN* 1.3 75.3 - - - +
382B LEU* 1.3 66.3 + - - -
383B SER 3.3 2.9 - - - -
384B THR* 3.3 2.4 + - - -
385B MET* 3.2 22.3 + - - +
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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