Contacts of the helix formed by residues 381 - 393 (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 GLY 381 (chain A).
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Specific contacts
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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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Residues in contact with LEU 382 (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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82A THR* 4.3 21.8 - - + +
83A GLY* 4.0 21.3 - - - +
359A TRP* 4.0 25.6 - - + -
362A ARG* 5.0 1.3 - - - +
377A ILE* 3.6 30.3 - - + +
381A GLY* 1.3 71.8 - - - +
383A SER* 1.3 61.4 + - - +
385A MET* 3.5 1.8 + - - +
386A GLN* 3.1 40.8 + - + +
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Residues in contact with SER 383 (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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381A GLY 3.1 1.8 + - - -
382A LEU* 1.3 74.5 - - - +
384A THR* 1.3 67.6 + - - +
385A MET 3.0 2.3 + - - -
386A GLN* 3.0 11.5 + - - -
387A ASN* 2.9 38.8 + - - +
280B SER* 5.2 9.4 - - - -
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Residues in contact with THR 384 (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* 3.2 38.4 - - + +
380A ASN* 3.7 31.5 + - + -
381A GLY 3.3 2.2 + - - -
383A SER* 1.3 78.7 - - - +
385A MET* 1.3 59.7 + - - +
387A ASN* 4.2 5.0 - - - +
388A ASN* 3.0 26.9 + - - +
280B SER 3.6 20.4 + - - -
281B VAL* 4.5 8.9 - - + +
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Residues in contact with MET 385 (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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119A LEU* 5.3 0.9 - - + -
122A TYR* 4.0 29.2 - - + -
123A LEU* 5.8 0.2 - - + -
359A TRP* 3.6 21.3 - - + -
373A TRP* 4.4 12.6 - - + -
376A THR* 3.6 46.7 - - - +
377A ILE* 4.1 4.3 - - + -
380A ASN* 4.1 10.5 - - + +
381A GLY 3.3 15.1 + - - +
382A LEU 3.9 1.8 - - - +
383A SER 3.0 0.8 - - - -
384A THR* 1.3 77.6 - - - +
386A GLN* 1.3 67.2 + - - +
388A ASN* 3.3 16.0 + - - +
389A LEU* 2.9 38.9 + - + +
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Residues in contact with GLN 386 (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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5A TYR* 5.1 1.4 + - - -
83A GLY* 2.9 35.3 - - - +
84A GLU 2.6 26.7 + - - +
85A ILE* 4.6 3.3 - - - +
86A PRO* 4.3 14.5 - - + +
359A TRP* 4.2 6.9 - - + -
382A LEU* 3.1 26.4 + - + +
383A SER* 3.0 14.5 + - - +
385A MET* 1.3 76.2 - - - +
387A ASN* 1.3 61.3 + - - +
389A LEU* 3.0 3.9 + - - +
390A ALA* 2.6 38.2 + - - +
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Residues in contact with ASN 387 (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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86A PRO* 5.4 5.9 - - - +
383A SER* 2.9 25.1 + - - +
384A THR* 4.2 3.8 - - - +
386A GLN* 1.3 83.8 + - - +
388A ASN* 1.3 65.6 + - - +
390A ALA* 3.3 7.8 + - - +
391A ARG* 3.2 27.2 + - + +
279B GLN* 5.3 2.6 - - - +
413B ASN* 5.1 14.1 + - - +
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Residues in contact with ASN 388 (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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115A PRO* 3.1 30.7 + - - +
118A TYR* 3.9 11.9 - - - +
119A LEU* 3.7 21.5 - - - +
122A TYR* 3.5 30.0 - - + -
384A THR 3.0 21.4 + - - +
385A MET* 3.7 7.1 - - - +
386A GLN 3.2 0.2 - - - -
387A ASN* 1.3 79.0 - - - +
389A LEU* 1.3 65.2 + - - +
391A ARG* 3.2 6.0 + - - +
392A VAL* 2.9 23.9 + - - +
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Residues in contact with LEU 389 (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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85A ILE* 3.6 27.6 - - + -
119A LEU* 3.7 29.8 - - + -
355A ILE* 3.9 25.6 - - + -
359A TRP* 3.4 38.4 - - + -
373A TRP* 4.0 8.5 - - + -
385A MET* 2.9 18.6 + - + +
386A GLN 3.7 2.2 - - - +
388A ASN* 1.3 74.6 - - - +
390A ALA* 1.3 60.5 + - - +
391A ARG 3.1 2.5 - - - -
392A VAL* 3.2 11.5 - - + +
393A LEU* 2.9 35.7 + - + +
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Residues in contact with ALA 390 (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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85A ILE* 3.9 10.5 - - - +
86A PRO* 3.9 32.1 - - + +
88A LEU* 3.4 30.6 + - + +
386A GLN 2.6 20.5 + - - +
387A ASN* 3.7 9.9 - - - +
389A LEU* 1.3 73.6 - - - +
391A ARG* 1.3 59.6 + - - +
393A LEU* 4.1 1.2 - - - -
394A ARG* 3.3 16.1 + - - +
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Residues in contact with ARG 391 (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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88A LEU* 3.6 25.6 - - + +
110A ALA 5.5 5.8 - - - +
111A ASN* 4.5 19.0 + - - +
115A PRO* 3.8 22.9 - - + -
387A ASN* 3.2 14.9 + - + +
388A ASN* 3.4 9.0 - - - +
389A LEU 3.1 0.6 - - - -
390A ALA* 1.3 75.6 - - - +
392A VAL* 1.3 65.5 + - - +
394A ARG* 3.1 46.4 - - - +
249B LEU* 4.5 9.5 - - - +
252B GLU* 5.5 4.2 + - - +
254B GLU* 2.9 34.2 + - - +
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Residues in contact with VAL 392 (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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111A ASN 5.9 0.4 - - - -
115A PRO* 4.5 12.7 - - - +
116A THR* 4.9 10.5 - - + +
119A LEU* 4.1 22.9 - - + -
314A TYR* 4.3 8.0 + - - -
316A LEU* 4.3 9.6 - - + -
345A ILE* 4.1 24.7 - - + +
355A ILE* 4.2 14.1 - - + -
388A ASN* 2.9 25.1 - - - +
389A LEU* 3.2 31.2 - - + +
391A ARG* 1.3 76.2 - - - +
393A LEU* 1.3 55.4 + - + +
394A ARG 3.1 6.1 + - - +
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Residues in contact with LEU 393 (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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85A ILE* 4.1 22.9 - - + -
87A THR* 6.1 0.2 - - - +
344A VAL 5.6 1.8 - - - +
345A ILE* 4.1 31.5 - - + +
346A GLY 6.1 0.2 - - - +
355A ILE* 4.2 29.8 - - + +
356A ARG* 3.8 47.1 + - + +
389A LEU* 2.9 23.1 + - + +
390A ALA* 4.1 2.5 - - - +
392A VAL* 1.3 72.3 - - + +
394A ARG* 1.3 64.9 + - - +
395A PRO* 3.4 8.0 - - - +
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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