Contacts of the helix formed by residues 372 - 381 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ALA 2.9 18.4 + - - +
330A TYR* 4.4 11.3 - - - +
332A HIS* 4.0 17.8 + - - +
368A VAL* 4.1 16.8 - - + +
370A TRP 4.0 1.4 + - - -
371A TRP* 1.3 70.2 - - - +
373A TRP* 1.3 55.5 + - - +
374A ASN* 3.2 12.6 + - - +
375A TRP* 2.8 50.9 + - + +
376A THR* 3.4 8.3 + - - +
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Residues in contact with TRP 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.2 12.1 - - + -
123A LEU* 3.8 25.4 - - + -
343A PHE* 4.1 19.5 - + - -
355A ILE* 4.1 21.1 - - + -
358A GLN* 2.8 55.0 + - + +
359A TRP* 3.7 34.3 - + + -
362A ARG* 4.3 16.4 - - + +
368A VAL* 5.4 0.2 - - - +
371A TRP* 3.0 37.5 + - + +
372A ASP* 1.3 71.0 - - - +
374A ASN* 1.3 61.5 + - - +
376A THR* 2.9 34.0 + - + -
377A ILE* 3.0 13.9 - - - +
385A MET* 4.4 5.8 - - + -
389A LEU* 4.0 18.4 - - + -
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Residues in contact with ASN 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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362A ARG* 2.6 51.2 + - - +
363A TYR* 3.1 35.3 + - - -
372A ASP* 3.0 9.5 + - - +
373A TRP* 1.3 78.5 - - - +
375A TRP* 1.3 61.1 + - - +
377A ILE* 3.3 12.7 + - - +
378A GLN* 3.2 24.4 + - - +
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Residues in contact with TRP 375 (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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122A TYR 3.8 15.0 - - - -
123A LEU 3.9 1.1 - - - -
124A GLY* 5.6 0.7 - - - -
323A ARG* 5.8 2.5 - - - -
326A GLY* 3.7 9.4 - - - -
327A ASN 2.9 49.1 - - - -
328A ALA* 3.1 25.8 - - + -
332A HIS* 3.8 18.1 - + + -
372A ASP* 2.8 33.1 + - + +
374A ASN* 1.3 75.2 - - - +
376A THR* 1.3 77.2 + - + +
378A GLN* 3.0 47.2 + - - +
379A GLN* 3.0 48.5 + - + +
380A ASN* 6.2 0.2 - - - -
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Residues in contact with THR 376 (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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122A TYR 4.1 12.6 - - - +
123A LEU* 4.3 14.4 - - + -
328A ALA* 3.8 26.5 - - + -
359A TRP* 4.5 0.2 - - - -
371A TRP* 6.3 0.4 - - + -
372A ASP 3.9 7.9 - - - +
373A TRP* 2.9 25.2 + - + +
375A TRP* 1.3 83.7 - - + +
377A ILE* 1.3 56.5 + - - +
379A GLN* 3.4 4.0 + - - -
380A ASN* 3.0 35.2 + - - +
385A MET* 3.6 30.4 - - + +
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Residues in contact with ILE 377 (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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359A TRP* 3.8 24.9 - - + -
362A ARG* 3.7 43.5 - - - +
363A TYR* 5.3 0.7 - - - +
373A TRP 3.0 13.9 - - - +
374A ASN* 3.5 13.0 - - - +
375A TRP 3.0 0.8 - - - -
376A THR* 1.3 84.7 + - - +
378A GLN* 1.3 58.2 + - - +
381A GLY* 2.7 26.6 + - - +
382A LEU* 3.6 33.9 - - + +
385A MET* 4.1 7.9 - - + -
282B ARG* 4.1 2.1 + - - -
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Residues in contact with GLN 378 (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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374A ASN* 3.2 11.1 + - - +
375A TRP* 3.0 48.4 + - + +
377A ILE* 1.3 79.2 - - - +
379A GLN* 1.3 68.9 + - + +
282B ARG* 3.6 19.0 + - - +
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Residues in contact with GLN 379 (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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326A GLY* 5.0 5.5 - - - -
375A TRP* 3.0 68.5 + - + +
376A THR* 3.7 5.8 - - - +
378A GLN* 1.3 89.0 + - + +
380A ASN* 1.3 74.7 + - - +
282B ARG* 3.7 21.4 - - - +
284B THR* 4.7 12.5 + - - +
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Residues in contact with ASN 380 (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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122A TYR* 3.3 40.4 - - + +
376A THR* 3.0 18.9 + - - +
379A GLN* 1.3 91.5 + - - +
381A GLY* 1.3 61.8 + - - +
384A THR* 3.7 32.9 + - + -
385A MET* 4.1 6.7 - - - +
281B VAL* 5.1 2.1 - - + +
282B ARG* 3.9 26.7 + - - +
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Residues in contact with GLY 381 (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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377A ILE* 2.7 24.9 + - - -
379A GLN 3.8 0.4 - - - -
380A ASN* 1.3 75.0 - - - +
382A LEU* 1.3 68.1 + - - -
383A SER* 3.1 4.8 + - - -
384A THR 3.3 3.4 + - - -
385A MET* 3.3 20.3 + - - +
282B ARG* 3.9 18.4 - - - +
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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