Contacts of the helix formed by residues 381 - 394 (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 GLY 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with LEU 382 (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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82B THR* 5.3 7.0 - - + -
83B GLY* 4.1 21.1 - - - +
359B TRP* 3.8 19.3 - - + -
362B ARG* 5.0 2.7 - - - +
377B ILE* 3.7 34.5 - - + +
381B GLY* 1.3 70.4 - - - -
383B SER* 1.3 58.4 + - - +
385B MET* 3.3 2.3 + - - +
386B GLN* 2.9 60.2 + - + +
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Residues in contact with SER 383 (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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381B GLY 3.3 0.6 - - - -
382B LEU* 1.3 79.0 - - - +
384B THR* 1.3 63.8 + - - +
386B GLN* 3.3 12.3 + - - +
387B ASN* 3.1 38.2 + - - +
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER 5.6 1.4 + - - -
281A VAL* 5.8 5.9 - - - +
282A ARG 5.8 0.7 + - - -
122B TYR* 3.5 31.9 - - + +
380B ASN* 3.3 31.4 + - + +
381B GLY 3.3 2.6 + - - -
382B LEU 3.3 0.4 - - - -
383B SER* 1.3 78.7 - - - +
385B MET* 1.3 64.9 + - - +
387B ASN* 4.1 4.3 - - - +
388B ASN* 3.2 21.5 + - - +
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Residues in contact with MET 385 (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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119B LEU* 5.4 1.6 - - + -
122B TYR* 4.0 34.8 - - + -
123B LEU* 5.5 0.2 - - + -
359B TRP* 3.6 22.2 - - + -
373B TRP* 4.3 18.8 - - + -
376B THR* 3.4 52.3 - - + +
377B ILE* 4.2 2.5 - - - +
380B ASN* 4.1 9.9 - - + -
381B GLY 3.2 12.7 + - - +
382B LEU* 3.7 6.5 - - - +
384B THR* 1.3 78.9 - - - +
386B GLN* 1.3 62.4 + - - +
388B ASN* 3.4 4.2 + - - +
389B LEU* 3.0 36.0 + - + +
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Residues in contact with GLN 386 (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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5B TYR* 5.0 1.6 + - - -
83B GLY* 3.1 24.8 - - - +
84B GLU 2.8 26.4 + - - +
85B ILE* 4.2 2.2 - - - +
86B PRO* 3.8 20.5 - - + +
359B TRP* 4.2 7.0 - - + -
382B LEU* 2.9 48.0 + - + +
383B SER* 3.7 12.4 - - - +
384B THR 3.3 0.2 - - - -
385B MET* 1.3 77.5 - - - +
387B ASN* 1.3 60.3 + - - +
389B LEU* 3.5 3.4 + - - +
390B ALA* 2.9 29.5 + - - +
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Residues in contact with ASN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 4.7 12.9 - - - +
88B LEU* 6.2 1.2 - - - +
383B SER* 3.1 28.7 + - - +
384B THR* 4.1 4.6 - - - +
386B GLN* 1.3 76.5 - - - +
388B ASN* 1.3 67.8 + - - +
390B ALA* 3.3 6.1 + - - +
391B ARG* 3.2 28.4 + - + +
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Residues in contact with ASN 388 (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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115B PRO* 3.1 29.9 + - - +
118B TYR* 3.6 13.5 - - - +
119B LEU* 3.4 33.1 - - - +
122B TYR* 3.6 23.7 - - + -
384B THR 3.2 17.8 + - - +
385B MET* 3.7 5.6 - - - +
386B GLN 3.3 0.2 - - - -
387B ASN* 1.3 76.7 - - - +
389B LEU* 1.3 66.5 + - + +
390B ALA 3.0 1.2 + - - -
391B ARG* 3.1 16.1 + - - +
392B VAL* 3.1 16.0 + - - +
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Residues in contact with LEU 389 (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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85B ILE* 3.6 31.4 - - + -
119B LEU* 3.6 32.3 - - + -
355B ILE* 3.8 27.1 - - + -
359B TRP* 3.2 40.8 - - + -
373B TRP* 3.9 9.0 - - + -
385B MET* 3.0 19.4 + - + +
386B GLN 4.1 0.4 - - - +
388B ASN* 1.3 81.3 - - - +
390B ALA* 1.3 56.7 + - - +
392B VAL* 3.8 4.9 - - + -
393B LEU* 3.0 34.1 + - - +
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Residues in contact with ALA 390 (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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85B ILE* 3.8 7.8 - - - +
86B PRO* 3.6 30.6 - - + +
88B LEU* 3.7 24.7 + - + +
386B GLN 2.9 18.6 + - - +
387B ASN* 3.6 9.4 - - - +
389B LEU* 1.3 74.6 - - - +
391B ARG* 1.3 60.8 + - - +
393B LEU* 3.4 2.1 + - - -
394B ARG* 2.9 29.3 + - - +
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Residues in contact with ARG 391 (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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254A GLU* 5.9 1.2 + - - -
88B LEU* 3.9 25.8 - - + +
110B ALA 5.1 4.7 + - - -
111B ASN* 4.4 27.2 + - - +
115B PRO* 3.8 29.6 - - + -
387B ASN* 3.2 17.1 + - + +
388B ASN* 3.1 8.2 + - - +
390B ALA* 1.3 77.1 - - - +
392B VAL* 1.3 62.9 + - - +
394B ARG* 3.2 34.4 - - - +
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASN 6.0 0.2 - - - -
115B PRO* 3.7 31.4 - - + +
116B THR* 4.3 9.1 - - + +
119B LEU* 4.2 25.1 - - + -
314B TYR* 4.5 6.2 + - - -
316B LEU* 4.5 15.0 - - + -
345B ILE* 4.1 17.3 - - + +
355B ILE* 4.3 15.5 - - + -
388B ASN* 3.1 22.6 + - - +
389B LEU* 3.8 9.0 - - + +
391B ARG* 1.3 77.4 - - - +
393B LEU* 1.3 62.4 + - + +
394B ARG 3.3 2.3 + - - +
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 4.0 28.3 - - + -
345B ILE* 4.0 33.3 - - + +
346B GLY 6.1 0.2 - - - +
355B ILE* 4.1 28.9 - - + +
356B ARG* 4.0 35.1 + - + +
389B LEU 3.0 21.7 + - - +
390B ALA* 3.7 2.9 - - - +
392B VAL* 1.3 76.1 - - + +
394B ARG* 1.3 66.0 + - - +
395B PRO* 3.3 7.8 - - - +
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Residues in contact with ARG 394 (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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249A LEU* 4.3 22.4 - - - +
88B LEU* 3.1 39.0 - - + +
89B SER* 2.6 37.0 + - - +
90B ALA 3.4 9.5 + - - -
91B LEU* 3.5 34.8 - - - +
111B ASN* 5.1 10.5 + - - -
314B TYR* 5.5 0.5 + - - -
345B ILE* 5.4 4.5 - - - +
390B ALA 2.9 12.5 + - - +
391B ARG* 3.2 35.6 + - - +
392B VAL 3.3 2.8 - - - +
393B LEU* 1.3 77.6 - - - +
395B PRO* 1.3 75.7 - - + +
396B VAL* 3.4 14.3 + - + +
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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