Contacts of the helix formed by residues 362 - 374 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349C ALA* 3.9 21.8 - - - +
350C ARG* 5.0 5.2 - - + +
353C CYS* 4.2 18.0 - - + +
356C LEU* 4.1 20.2 - - + +
357C THR 3.6 6.1 - - - +
358C GLN* 3.5 23.3 - - - +
360C GLN 3.6 0.8 - - - -
361C PHE* 1.3 87.9 - - - +
363C ALA* 1.3 54.9 + - - +
365C SER* 3.2 2.1 + - - -
366C LEU* 2.8 30.8 + - - +
401C GLU* 3.1 29.8 - - + +
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Residues in contact with ALA 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ALA* 3.4 19.8 - - + +
362C PRO* 1.3 77.3 - - - +
364C GLN* 1.3 63.1 + - - +
367C ALA* 3.0 22.0 + - - +
380C GLU* 4.0 13.4 - - + +
382C GLY* 4.8 0.4 - - - -
401C GLU* 3.1 22.1 + - - +
402C THR 3.2 28.5 - - - +
403C VAL* 3.2 12.0 - - - +
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Residues in contact with GLN 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TYR 4.1 3.5 + - - +
34C ASN* 3.6 32.6 + - - +
35C THR* 4.3 8.3 + - - +
361C PHE* 3.5 20.9 + - + +
362C PRO 3.3 0.4 - - - -
363C ALA* 1.3 78.9 - - - +
365C SER* 1.3 63.5 + - - +
367C ALA* 3.5 5.5 + - - +
368C ALA* 3.2 21.0 + - - +
380C GLU* 3.1 33.5 + - - +
384C VAL* 3.3 24.6 - - + +
401C GLU* 4.7 0.2 + - - -
437C LEU* 3.8 9.8 - - + +
448C PHE 5.5 1.6 + - - +
453C PHE* 3.7 28.0 - - + -
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Residues in contact with SER 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C LEU* 4.8 1.3 - - - -
361C PHE 3.1 17.0 + - - -
362C PRO* 3.6 5.6 - - - -
364C GLN* 1.3 74.7 - - - +
366C LEU* 1.3 65.7 + - - +
368C ALA* 3.2 5.7 + - - +
369C SER* 3.0 25.5 + - - -
434C ILE* 3.5 12.6 - - - +
435C ARG 2.5 30.3 + - - -
437C LEU* 3.7 19.9 - - - +
455C PHE* 4.4 7.3 - - - -
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Residues in contact with LEU 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C LEU* 3.7 24.9 - - + -
349C ALA* 4.5 6.5 - - - -
352C PHE* 3.8 48.2 - - + -
353C CYS* 4.5 7.4 - - - -
362C PRO 2.8 20.7 + - - +
363C ALA* 3.7 4.7 - - - +
365C SER* 1.3 72.4 - - - +
367C ALA* 1.3 58.3 + - - +
369C SER* 3.2 5.4 + - - -
370C ILE* 2.9 42.3 + - + +
403C VAL* 3.5 21.5 - - + -
427C LEU* 4.7 5.4 - - + -
434C ILE* 4.3 12.3 - - + +
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Residues in contact with ALA 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C THR* 3.8 23.8 - - + +
363C ALA 3.0 17.8 + - - +
364C GLN* 3.5 9.2 - - - +
366C LEU* 1.3 77.3 - - - +
368C ALA* 1.3 62.7 + - - +
370C ILE* 3.4 7.4 + - - +
371C TYR* 3.3 16.3 + - - +
376C VAL 5.0 0.3 - - - +
378C SER* 3.6 27.0 + - - +
380C GLU* 4.9 8.3 - - + +
403C VAL* 4.2 7.4 - - + +
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Residues in contact with ALA 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C MET* 3.1 36.4 - - + +
33C TYR* 3.8 23.3 - - + +
35C THR* 4.4 1.5 - - - +
364C GLN 3.2 11.2 + - - +
365C SER* 3.2 11.6 + - - +
367C ALA* 1.3 78.4 - - - +
369C SER* 1.3 63.7 + - - +
371C TYR 3.3 0.3 + - - -
372C MET* 3.1 31.5 + - + +
437C LEU* 5.4 0.4 - - + -
455C PHE* 5.9 2.5 - - + -
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Residues in contact with SER 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C SER* 3.0 14.6 + - - -
366C LEU* 3.4 11.9 - - - -
368C ALA* 1.3 75.9 - - - +
370C ILE* 1.3 64.9 + - - +
372C MET* 4.0 13.1 - - - +
373C GLU* 3.0 31.8 + - - +
427C LEU* 3.8 21.5 - - - +
434C ILE* 4.1 20.3 - - - +
435C ARG 5.6 0.2 + - - -
455C PHE* 6.0 1.4 - - - -
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C LEU* 3.9 27.8 - - + -
366C LEU* 2.9 28.0 + - + +
367C ALA 3.7 5.6 - - - +
368C ALA 3.3 0.2 - - - -
369C SER* 1.3 76.0 - - - +
371C TYR* 1.3 57.0 + - - +
373C GLU* 4.8 0.2 - - - -
374C THR* 2.5 42.8 + - + +
376C VAL* 3.6 30.3 - - + +
378C SER* 4.1 17.7 - - - +
403C VAL* 4.2 8.5 - - + -
405C LEU* 4.8 1.8 - - + -
420C VAL* 5.9 0.9 - - + +
424C ILE* 4.0 22.7 - - + -
427C LEU* 3.9 19.1 - - + -
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Residues in contact with TYR 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.7 15.9 - - - +
24C ARG* 3.3 38.9 + - + -
27C LYS* 3.9 5.4 - - - +
28C MET* 3.2 35.2 - - + -
35C THR* 4.8 2.7 - - + -
38C LEU* 3.7 33.4 - - + -
42C ASP* 2.8 36.4 + - - +
43C ILE* 4.1 9.0 - - + -
367C ALA 3.3 5.3 + - - +
368C ALA 3.3 0.8 + - - -
369C SER 3.2 0.4 - - - -
370C ILE* 1.3 78.4 - - - +
372C MET* 1.3 64.4 + - - +
375C GLY* 2.6 50.2 + - - +
376C VAL 3.3 17.7 + - - +
377C ARG 4.7 0.2 - - - -
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Residues in contact with MET 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG* 4.0 17.0 - - - +
24C ARG* 2.9 27.7 + - - +
25C VAL* 4.1 33.9 - - + -
28C MET* 3.6 33.0 - - + -
33C TYR* 4.1 18.6 - - + -
368C ALA* 3.1 33.7 + - + +
369C SER* 4.0 13.7 - - - +
371C TYR* 1.3 81.2 - - - +
373C GLU* 1.3 64.6 + - - +
455C PHE* 4.2 13.0 - - + -
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Residues in contact with GLU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ARG* 2.8 44.0 + - - -
24C ARG* 3.1 14.6 + - - +
369C SER* 3.0 20.7 + - - +
370C ILE 4.2 1.3 - - - +
372C MET* 1.3 81.6 - - - +
374C THR* 1.3 67.5 + - + +
423C GLY* 5.2 1.8 - - - +
426C LYS* 3.6 35.1 + - + +
427C LEU* 4.2 20.9 - - + +
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Residues in contact with THR 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ARG* 4.1 9.8 + - - +
44C TYR* 4.2 14.6 - - - +
370C ILE* 2.5 27.6 + - + +
373C GLU* 1.3 84.1 - - + +
375C GLY* 1.3 61.1 + - - +
376C VAL* 2.8 30.9 + - - +
419C VAL* 3.8 21.3 - - + +
420C VAL* 4.8 2.7 - - - +
423C GLY* 3.5 35.4 - - - -
427C 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