Contacts of the helix formed by residues 362 - 374 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349D ALA* 3.9 22.0 - - - +
350D ARG* 5.0 4.5 - - + +
353D CYS* 4.2 10.8 - - + +
356D LEU* 4.0 28.9 - - + +
357D THR 3.7 15.7 - - - +
358D GLN* 3.7 12.3 - - - +
360D GLN 3.7 1.0 - - - -
361D PHE* 1.3 86.5 - - - +
363D ALA* 1.3 53.5 + - - +
365D SER* 3.3 1.7 + - - -
366D LEU* 2.8 36.4 + - - +
401D GLU* 3.0 31.4 - - + +
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Residues in contact with ALA 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ALA* 3.5 19.2 - - + +
362D PRO* 1.3 78.5 - - - +
364D GLN* 1.3 58.7 + - - +
366D LEU 3.1 1.0 + - - -
367D ALA* 2.9 27.5 + - - +
380D GLU* 3.8 14.6 - - + +
382D GLY* 4.6 0.7 - - - -
401D GLU* 3.2 21.8 + - + +
402D THR 3.5 26.0 - - - +
403D VAL* 3.2 11.7 - - + +
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Residues in contact with GLN 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TYR 4.1 2.3 + - - +
34D ASN* 3.5 31.1 + - - +
35D THR* 4.3 7.9 + - - +
361D PHE* 3.7 20.7 + - + -
362D PRO 3.4 0.4 - - - -
363D ALA* 1.3 79.6 - - - +
365D SER* 1.3 61.3 + - - +
367D ALA* 3.6 5.3 + - - +
368D ALA* 3.2 20.4 + - - +
380D GLU* 3.5 28.9 + - + +
384D VAL* 3.2 33.2 - - + +
437D LEU* 4.0 11.2 - - + +
448D PHE* 5.4 2.3 + - - +
453D PHE* 3.8 26.1 - - + -
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Residues in contact with SER 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D LEU* 4.9 1.1 - - - -
361D PHE 3.2 18.6 + - - -
362D PRO* 3.8 4.7 - - - -
363D ALA 3.2 0.2 - - - -
364D GLN* 1.3 73.6 - - - +
366D LEU* 1.3 65.9 + - - +
368D ALA* 3.3 4.8 + - - +
369D SER* 3.0 25.5 + - - -
434D ILE* 3.5 13.1 - - - +
435D ARG 2.6 29.6 + - - -
437D LEU* 3.7 21.0 - - - +
455D PHE* 4.3 7.6 - - - -
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D LEU* 4.0 14.6 - - + -
349D ALA* 4.4 8.3 - - - -
352D PHE* 3.8 57.7 - - + -
353D CYS* 4.4 7.0 - - - -
362D PRO 2.8 18.4 + - - +
363D ALA 3.4 4.7 - - - +
365D SER* 1.3 77.3 - - - +
367D ALA* 1.3 57.4 + - - +
369D SER* 3.1 4.3 + - - -
370D ILE* 2.9 42.7 + - + +
403D VAL* 3.7 19.1 - - + -
427D LEU* 4.4 6.5 - - + -
434D ILE* 4.2 12.5 - - + +
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Residues in contact with ALA 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D THR* 3.8 19.4 - - + +
363D ALA 2.9 15.7 + - - +
364D GLN* 3.7 10.3 - - - +
366D LEU* 1.3 77.7 - - - +
368D ALA* 1.3 61.0 + - - +
370D ILE* 3.4 6.7 + - - +
371D TYR* 3.2 17.7 + - - +
376D VAL 5.0 0.3 - - - +
378D SER* 3.7 33.4 + - - +
380D GLU* 5.0 8.5 - - + +
403D VAL* 4.2 7.1 - - + +
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Residues in contact with ALA 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D MET* 3.2 27.1 - - + +
33D TYR* 3.6 30.7 - - + +
35D THR* 4.4 1.1 - - - +
364D GLN 3.2 7.0 + - - +
365D SER* 3.6 11.4 - - - +
366D LEU 3.2 0.4 - - - -
367D ALA* 1.3 79.2 - - - +
369D SER* 1.3 62.8 + - - +
371D TYR 3.3 0.3 + - - -
372D MET* 3.1 37.1 + - + +
437D LEU* 5.2 0.7 - - + -
455D PHE* 5.8 2.0 - - + -
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Residues in contact with SER 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D SER* 3.0 17.1 + - - -
366D LEU* 3.5 10.3 - - - -
368D ALA* 1.3 73.3 - - - +
370D ILE* 1.3 66.7 + - - +
372D MET* 3.4 13.9 + - - +
373D GLU* 3.0 30.3 + - - +
427D LEU* 3.8 24.5 - - - +
434D ILE* 4.2 18.1 - - - +
435D ARG 5.6 0.3 + - - -
455D PHE* 5.7 2.6 - - - -
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Residues in contact with ILE 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D LEU* 3.9 27.8 - - + -
366D LEU* 2.9 24.4 + - + +
367D ALA* 3.6 7.6 - - - +
368D ALA 3.3 0.2 - - - -
369D SER* 1.3 75.7 - - - +
371D TYR* 1.3 56.8 + - - +
373D GLU* 3.9 0.4 - - - -
374D THR* 2.7 43.6 + - + +
376D VAL* 3.6 31.6 - - + +
378D SER* 3.9 19.7 - - - +
403D VAL* 4.0 8.5 - - + -
405D LEU* 4.9 1.6 - - + -
420D VAL* 6.3 0.2 - - - -
424D ILE* 3.9 26.7 - - + -
427D LEU* 3.8 15.3 - - + -
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Residues in contact with TYR 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 3.9 12.3 - - - +
24D ARG* 3.4 35.8 + - + -
27D LYS* 4.0 5.5 - - - +
28D MET* 3.3 37.7 - - + -
35D THR* 4.7 2.2 - - + -
38D LEU* 3.7 34.1 - - + -
42D ASP* 2.6 39.4 + - - +
43D ILE* 4.1 6.5 - - + -
367D ALA 3.2 6.3 + - - +
369D SER 3.2 0.4 - - - -
370D ILE* 1.3 77.8 - - - +
372D MET* 1.3 65.5 + - - +
375D GLY* 2.8 49.5 + - - +
376D VAL 3.4 17.0 - - - +
377D ARG* 4.7 0.4 - - - -
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Residues in contact with MET 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 3.4 17.8 - - - +
24D ARG* 3.3 25.4 + - - +
25D VAL* 4.2 32.8 - - + -
28D MET* 3.6 28.3 - - + -
33D TYR* 3.8 29.2 - - + -
368D ALA* 3.1 29.5 + - + +
369D SER* 3.4 12.8 + - - +
371D TYR* 1.3 77.7 - - - +
373D GLU* 1.3 64.6 + - - +
455D PHE* 4.1 13.7 - - + -
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Residues in contact with GLU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 2.6 39.9 + - - +
24D ARG* 3.2 13.5 + - - +
369D SER* 3.0 20.0 + - - +
370D ILE 4.1 2.0 - - - +
372D MET* 1.3 83.0 - - - +
374D THR* 1.3 67.2 + - + +
423D GLY* 5.1 2.9 - - - +
426D LYS* 3.8 33.4 + - + +
427D LEU* 4.4 19.9 - - + +
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Residues in contact with THR 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ARG* 4.1 11.2 + - - +
44D TYR* 4.1 16.3 - - - -
370D ILE* 2.7 27.0 + - + +
373D GLU* 1.3 85.0 - - + +
375D GLY* 1.3 60.0 + - - +
376D VAL* 2.8 31.4 + - - +
419D VAL* 3.8 21.3 - - + +
420D VAL* 4.9 2.4 - - - +
423D GLY* 3.4 35.4 - - - -
424D ILE* 4.8 0.7 - - + +
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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