Contacts of the helix formed by residues 362 - 374 (chain B) in PDB entry 1C7G
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 PRO 362 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349B ALA* 3.9 22.4 - - + +
350B ARG* 5.0 4.9 - - + +
353B CYS* 4.3 16.4 - - + +
356B LEU* 4.3 21.5 - - + +
357B THR 3.7 5.2 - - - +
358B GLN* 3.6 23.3 - - - +
360B GLN 3.7 0.4 - - - -
361B PHE* 1.3 85.3 - - - +
363B ALA* 1.3 53.1 + - - +
365B SER* 3.2 2.3 + - - -
366B LEU* 2.7 36.9 + - - +
401B GLU* 3.1 34.3 - - + +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ALA* 3.4 19.4 - - + +
362B PRO* 1.3 78.7 - - - +
364B GLN* 1.3 63.1 + - - +
367B ALA* 3.0 21.5 + - - +
380B GLU* 3.9 12.1 - - + +
382B GLY 4.7 0.9 - - - +
401B GLU* 3.2 22.7 + - + +
402B THR 3.4 26.7 - - - +
403B VAL* 3.0 12.8 - - + +
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Residues in contact with GLN 364 (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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33B TYR 4.2 2.7 + - - +
34B ASN* 3.8 30.7 + - - +
35B THR* 4.4 8.7 + - - +
361B PHE* 3.6 21.6 + - + -
362B PRO 3.3 0.4 - - - -
363B ALA* 1.3 78.1 - - - +
365B SER* 1.3 61.5 + - - +
367B ALA* 3.4 6.7 + - - +
368B ALA* 3.2 20.8 + - - +
380B GLU* 3.3 24.6 + - - +
384B VAL* 2.9 39.5 - - + +
437B LEU* 3.8 13.0 - - + -
448B PHE* 5.3 1.6 + - - +
453B PHE* 3.8 25.1 - - + -
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Residues in contact with SER 365 (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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356B LEU* 4.8 1.3 - - - -
361B PHE 3.1 19.0 + - - -
362B PRO* 3.8 4.5 - - - -
364B GLN* 1.3 73.3 - - - +
366B LEU* 1.3 65.2 + - - +
368B ALA* 3.4 4.5 + - - +
369B SER* 3.0 25.6 + - - -
434B ILE* 3.7 12.2 - - - +
435B ARG 2.5 30.5 + - - -
437B LEU* 3.8 21.1 - - - +
455B PHE* 4.2 8.5 - - - -
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Residues in contact with LEU 366 (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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347B LEU* 3.8 24.5 - - + -
349B ALA* 4.5 5.6 - - - -
352B PHE* 3.9 49.8 - - + -
353B CYS* 4.3 7.9 - - - -
362B PRO 2.7 21.3 + - - +
363B ALA* 3.3 5.1 + - - +
365B SER* 1.3 73.5 - - - +
367B ALA* 1.3 57.6 + - - +
369B SER* 3.3 3.1 + - - -
370B ILE* 2.9 41.4 + - + +
403B VAL* 3.7 19.3 - - + -
427B LEU* 4.6 5.4 - - + -
434B ILE* 4.1 13.9 - - + +
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Residues in contact with ALA 367 (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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35B THR* 3.7 25.0 - - + +
363B ALA 3.0 17.3 + - - +
364B GLN* 3.6 9.6 - - - +
365B SER 3.2 0.2 - - - -
366B LEU* 1.3 78.1 - - - +
368B ALA* 1.3 60.8 + - - +
370B ILE* 3.4 6.3 + - - +
371B TYR* 3.3 16.6 + - - +
376B VAL 4.8 0.9 - - - +
378B SER* 3.4 29.6 + - - +
380B GLU* 4.8 7.9 - - + -
403B VAL* 4.1 6.7 - - + +
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Residues in contact with ALA 368 (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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28B MET* 3.2 28.2 - - + +
33B TYR* 3.7 30.3 - - + +
35B THR* 4.4 1.9 - - - +
364B GLN 3.2 7.0 + - - +
365B SER* 3.7 10.8 - - - +
366B LEU 3.3 0.2 - - - -
367B ALA* 1.3 75.6 - - - +
369B SER* 1.3 65.0 + - - +
371B TYR 3.4 0.3 + - - -
372B MET* 3.2 36.0 + - + +
437B LEU* 5.3 1.1 - - + -
455B PHE* 5.7 1.8 - - + -
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Residues in contact with SER 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B SER* 3.0 18.8 + - - -
366B LEU* 3.6 7.9 - - - -
368B ALA* 1.3 76.0 - - - +
370B ILE* 1.3 64.3 + - - +
372B MET* 3.4 15.3 + - - +
373B GLU* 3.0 30.9 + - - +
427B LEU* 3.9 22.3 - - - +
434B ILE* 4.1 19.9 - - - +
435B ARG 5.5 0.3 + - - -
455B PHE* 5.8 2.4 - - - -
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Residues in contact with ILE 370 (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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347B LEU* 3.8 29.4 - - + -
366B LEU* 2.9 29.8 + - + +
367B ALA* 3.7 6.1 - - - +
368B ALA 3.3 0.2 - - - -
369B SER* 1.3 77.2 - - - +
371B TYR* 1.3 54.6 + - - +
373B GLU* 4.8 0.2 - - - -
374B THR* 2.5 42.4 + - + +
376B VAL* 3.5 30.7 - - + +
378B SER* 4.2 6.3 - - - +
403B VAL* 4.1 16.6 - - + -
405B LEU* 4.8 3.6 - - + -
420B VAL 5.9 0.2 - - - +
424B ILE* 4.2 21.3 - - + -
427B LEU* 3.8 19.5 - - + -
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Residues in contact with TYR 371 (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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19B ILE* 3.8 12.5 - - - +
24B ARG* 3.5 36.9 + - + -
27B LYS* 4.1 3.1 - - - +
28B MET* 3.2 35.0 - - + -
35B THR* 4.8 2.5 - - + -
38B LEU* 3.7 32.1 - - + -
42B ASP* 2.6 39.9 + - - +
43B ILE* 4.0 9.0 - - + -
367B ALA 3.3 6.9 + - - +
369B SER 3.2 0.4 - - - -
370B ILE* 1.3 77.8 - - - +
372B MET* 1.3 67.5 + - - +
375B GLY* 2.6 51.8 + - - +
376B VAL 3.3 17.7 + - - +
377B ARG* 5.0 0.2 - - - -
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Residues in contact with MET 372 (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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21B ARG* 3.4 15.0 - - - +
24B ARG* 3.0 28.7 + - - +
25B VAL* 4.2 32.5 - - + +
28B MET* 3.6 30.3 - - + -
33B TYR* 4.1 13.0 - - + -
368B ALA* 3.2 30.6 + - + +
369B SER* 3.9 12.8 - - - +
371B TYR* 1.3 79.3 - - - +
373B GLU* 1.3 62.6 + - - +
455B PHE* 4.1 26.7 - - + -
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Residues in contact with GLU 373 (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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21B ARG* 2.6 38.5 + - - +
24B ARG* 3.3 12.0 + - - +
369B SER* 3.0 19.9 + - - +
370B ILE 4.2 2.0 - - - +
372B MET* 1.3 83.1 - - - +
374B THR* 1.3 66.3 + - + +
423B GLY* 5.2 2.2 - - - +
426B LYS* 3.8 32.5 + - + +
427B LEU* 4.4 22.0 - - + +
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Residues in contact with THR 374 (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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24B ARG* 4.3 9.6 + - - +
44B TYR* 4.3 13.9 - - - -
370B ILE* 2.5 29.3 + - + +
373B GLU* 1.3 83.5 - - + +
375B GLY* 1.3 61.2 + - - +
376B VAL* 2.7 30.8 - - + +
419B VAL* 3.8 19.1 - - + +
420B VAL* 4.9 2.6 - - - +
423B GLY* 3.4 35.2 - - - -
424B ILE* 4.8 0.4 - - + +
427B LEU* 6.1 0.2 - - + -
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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