Contacts of the helix formed by residues 354 - 361 (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 SER 354 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 4.4 2.6 - - - -
344B VAL 5.3 1.8 - - - -
348B TYR* 3.8 18.3 - - - -
349B LYS 5.7 0.7 - - - -
350B ASP 3.3 17.7 - - - -
351B LYS 3.0 7.7 + - - -
352B ALA 3.3 1.4 + - - -
353B SER* 1.3 77.9 - - - +
355B ILE* 1.3 63.4 + - - +
356B ARG* 3.9 4.3 + - - +
357B TYR* 3.3 27.0 + - - +
358B GLN* 3.2 27.8 + - - +
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 4.2 6.5 - - + -
119B LEU* 4.2 24.2 - - + -
343B PHE* 3.7 33.2 - - + -
344B VAL 5.7 0.8 + - - -
345B ILE* 4.5 6.3 - - + -
353B SER 4.0 1.6 + - - -
354B SER* 1.3 71.1 - - - +
356B ARG* 1.3 65.2 + - - +
358B GLN* 3.5 2.1 + - - +
359B TRP* 2.9 26.4 + - + +
373B TRP* 4.1 15.6 + - + -
389B LEU* 3.8 35.9 - - + -
392B VAL* 4.3 9.2 - - + -
393B LEU* 4.1 28.2 - - + +
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Residues in contact with ARG 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLN* 3.3 37.9 + - - +
45A TRP* 3.9 10.3 - - + -
60A GLY* 6.2 0.7 - - - -
84B GLU* 5.7 2.8 - - - +
85B ILE* 3.4 43.5 + - + +
86B PRO 3.8 6.9 + - - -
87B THR* 3.0 29.1 + - - +
354B SER* 3.4 4.8 + - - +
355B ILE* 1.3 80.1 - - - +
357B TYR* 1.3 62.9 + - - +
359B TRP* 3.5 5.5 - - - +
360B ASP* 2.9 32.0 + - - +
393B LEU* 4.0 26.1 + - + +
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Residues in contact with TYR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.5 35.3 - + + -
61A TYR* 3.7 22.1 + + - -
348B TYR* 4.6 2.7 - + + -
351B LYS* 3.3 49.5 + - + -
354B SER* 3.3 24.5 + - - +
356B ARG* 1.3 78.5 - - - +
358B GLN* 1.3 72.2 + - + +
360B ASP* 2.9 13.9 + - - -
361B LYS* 3.0 51.0 + - + +
367B GLU* 2.4 35.5 + - + +
370B TRP* 5.1 4.0 - + - -
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Residues in contact with GLN 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PHE* 4.4 5.8 - - - -
351B LYS 2.9 18.6 + - - +
352B ALA* 2.5 34.1 + - - +
354B SER 3.2 16.4 + - - +
355B ILE 3.9 1.1 - - - +
357B TYR* 1.3 83.2 - - + +
359B TRP* 1.3 59.3 + - - +
361B LYS* 3.8 3.8 - - - +
362B ARG* 3.3 19.6 + - - +
367B GLU 5.6 2.7 - - - +
368B VAL* 6.0 0.2 - - - +
370B TRP* 4.0 25.7 - - + +
371B TRP* 3.6 25.5 + - - +
373B TRP* 3.1 38.3 + - + +
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Residues in contact with TRP 359 (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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83B GLY 2.9 28.5 + - - -
85B ILE* 3.6 29.3 - - + +
355B ILE* 2.9 20.0 + - + +
356B ARG 3.5 3.6 - - - +
358B GLN* 1.3 77.0 - - - +
360B ASP* 1.3 78.0 + - - +
361B LYS 3.4 0.9 + - - -
362B ARG* 2.9 45.9 + - - +
373B TRP* 3.7 37.7 - + + -
376B THR* 4.5 3.4 - - - -
377B ILE* 4.1 13.9 - - + -
382B LEU* 3.8 16.6 - - + -
385B MET* 3.6 31.6 - - + -
386B GLN* 4.2 6.7 - - + -
389B LEU* 3.2 31.0 - - + -
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Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLN* 3.6 14.9 + - - -
45A TRP* 3.1 35.4 + - + +
81B VAL* 3.4 41.2 - - + +
82B THR 5.6 0.2 - - - +
84B GLU* 4.4 21.8 - - - +
85B ILE 5.2 0.5 + - - -
356B ARG* 2.9 19.1 + - - +
357B TYR 2.9 4.6 + - - +
359B TRP* 1.3 91.2 - - - +
361B LYS* 1.3 63.3 + - + +
362B ARG* 3.5 1.0 + - - -
363B TYR* 5.2 0.9 + - - +
364B ILE* 5.1 1.6 - - - +
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Residues in contact with LYS 361 (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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45A TRP* 4.1 32.7 + - - +
61A TYR* 4.8 3.4 + - - -
357B TYR* 3.0 56.9 + - + +
358B GLN* 3.8 6.1 - - - +
359B TRP 3.2 0.2 - - - -
360B ASP* 1.3 84.6 - - + +
362B ARG* 1.3 58.5 + - - +
363B TYR 3.1 7.5 + - - +
364B ILE* 3.2 35.3 + - + +
367B GLU* 3.7 23.9 - - + +
368B VAL* 4.4 1.6 - - - +
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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
------------------------------------------------------------
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