Contacts of the helix formed by residues 367 - 382 (chain Z) in PDB entry 5GJQ
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 367 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364Z GLN 4.5 1.6 + - - -
365Z VAL* 3.8 1.0 - - - +
366Z ASP* 1.3 84.0 - - - +
368Z ALA* 1.3 52.5 - - - +
369Z ARG* 4.2 7.6 - - - -
370Z MET* 2.8 16.9 + - - +
371Z ASN* 2.1 41.8 + - - +
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Residues in contact with ALA 368 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367Z SER* 1.3 69.7 - - - +
369Z ARG* 1.3 58.1 + - - +
371Z ASN* 3.7 9.6 - - - -
372Z LEU* 2.5 35.0 + - - +
401Z LYS* 3.5 33.0 - - + +
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Residues in contact with ARG 369 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367Z SER* 3.3 6.7 - - - -
368Z ALA* 1.3 79.1 - - - +
370Z MET* 1.3 60.4 + - - +
372Z LEU* 3.4 14.8 - - - +
373Z ALA 4.3 1.7 + - - -
756Z PRO* 5.8 7.6 - - + -
760Z PHE* 4.5 14.0 - - - +
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Residues in contact with MET 370 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365Z VAL* 3.6 25.6 - - + +
366Z ASP* 4.3 2.0 - - + +
367Z SER* 2.8 23.1 + - - +
369Z ARG* 1.3 76.1 - - - +
371Z ASN* 1.3 60.7 + - - -
372Z LEU 3.1 2.0 + - - -
373Z ALA* 3.7 4.5 + - - +
374Z SER* 3.3 21.1 + - - -
756Z PRO* 5.7 3.1 - - + +
759Z LEU* 6.5 0.9 - - + -
760Z PHE* 5.7 6.6 - - - +
763Z ARG* 5.4 2.9 - - - +
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Residues in contact with ASN 371 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364Z GLN 4.8 11.4 - - - +
365Z VAL* 4.7 0.2 - - - +
367Z SER 2.1 30.4 + - - +
368Z ALA* 3.7 10.5 - - - -
370Z MET 1.3 66.6 - - - +
372Z LEU* 1.3 70.6 + - - +
373Z ALA 3.5 0.2 - - - -
374Z SER* 3.7 9.0 - - - -
375Z SER* 3.0 23.0 + - - -
397Z LYS 5.0 1.8 - - - +
398Z TRP* 4.1 10.3 - - - +
401Z LYS* 4.3 15.7 - - + -
402Z ASN* 4.5 1.3 - - - +
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Residues in contact with LEU 372 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368Z ALA 2.5 21.2 + - - +
369Z ARG* 3.4 14.6 - - - +
370Z MET 3.1 0.2 - - - -
371Z ASN* 1.3 77.0 - - - +
373Z ALA* 1.3 64.1 + - - +
375Z SER* 3.5 6.8 + - - -
376Z PHE* 3.6 8.3 + - - +
402Z ASN* 4.1 22.8 - - + +
403Z LYS 5.8 2.0 - - - +
406Z GLY* 4.9 8.1 - - - +
409Z SER* 6.0 0.7 - - - -
410Z ALA* 4.7 1.7 - - - +
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Residues in contact with ALA 373 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369Z ARG 4.3 1.2 + - - -
370Z MET 3.7 4.2 + - - +
372Z LEU* 1.3 79.0 - - - +
374Z SER* 1.3 55.8 + - - +
376Z PHE* 2.7 37.1 + - + +
377Z VAL* 3.0 6.8 + - - +
760Z PHE* 3.4 36.6 - - + +
763Z ARG* 4.2 5.6 - - + -
764Z LEU* 3.9 16.9 + - + +
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Residues in contact with SER 374 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362Z GLY* 5.5 3.4 - - - -
363Z SER 3.4 28.5 - - - -
364Z GLN* 5.3 1.1 - - - -
365Z VAL* 4.9 3.1 - - - -
370Z MET 3.3 18.3 + - - -
371Z ASN* 4.0 7.9 - - - -
372Z LEU 3.3 0.4 - - - -
373Z ALA* 1.3 77.8 - - - +
375Z SER* 1.3 62.6 + - - +
377Z VAL* 3.1 22.8 + - - +
378Z ASN* 3.5 5.9 + - - +
763Z ARG* 4.8 9.4 - - - +
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Residues in contact with SER 375 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371Z ASN 3.0 12.7 + - - -
372Z LEU 3.9 0.4 - - - -
374Z SER* 1.3 73.7 - - - +
376Z PHE* 1.3 66.8 + - - +
377Z VAL 3.2 0.7 + - - -
378Z ASN* 3.5 15.3 + - - +
379Z GLY 3.7 4.9 + - - -
398Z TRP* 3.4 37.7 - - - -
399Z LEU* 4.3 1.8 - - - -
410Z ALA* 3.4 26.0 - - - +
413Z SER* 3.8 6.6 - - - -
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Residues in contact with PHE 376 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372Z LEU 3.6 4.0 + - - +
373Z ALA* 2.7 26.6 + - - +
375Z SER* 1.3 74.9 - - - +
377Z VAL* 1.3 48.5 + - - +
379Z GLY* 2.9 6.9 + - - -
380Z PHE* 2.5 32.6 + - + +
409Z SER* 5.0 14.8 - - - -
410Z ALA* 4.4 3.6 - - - +
413Z SER* 3.6 13.5 - - - -
764Z LEU* 6.1 3.8 - - + -
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Residues in contact with VAL 377 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361Z SER* 6.0 1.6 - - - -
362Z GLY* 5.1 13.7 - - - +
373Z ALA 3.0 8.6 + - - +
374Z SER* 3.1 16.5 + - - +
376Z PHE* 1.3 73.5 - - - +
378Z ASN* 1.3 60.0 + - - +
379Z GLY 3.0 1.3 - - - -
380Z PHE* 2.7 11.8 + - - -
381Z VAL* 2.5 37.6 + - + +
763Z ARG* 4.3 8.3 - - + +
764Z LEU* 5.9 1.1 - - - +
767Z GLY* 4.2 18.8 - - - -
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Residues in contact with ASN 378 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362Z GLY* 6.1 0.6 - - - -
374Z SER 3.5 5.1 + - - +
375Z SER* 3.5 11.5 + - - +
376Z PHE 3.4 0.2 - - - -
377Z VAL* 1.3 77.2 - - - +
379Z GLY* 1.3 56.6 + - - +
381Z VAL* 4.9 2.5 - - - -
382Z ASN* 2.9 35.1 + - - +
387Z GLN* 4.8 8.4 - - + +
388Z ASP* 6.4 0.4 - - - -
390Z LEU* 4.9 18.4 - - + -
391Z LEU* 5.3 13.0 - - + +
417Z ILE* 4.7 4.9 - - - +
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Residues in contact with GLY 379 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375Z SER 3.7 2.6 + - - -
376Z PHE 2.9 10.5 + - - -
378Z ASN* 1.3 76.2 - - - +
380Z PHE* 1.3 56.9 + - - +
383Z ALA* 2.7 35.5 + - - +
413Z SER* 3.2 34.1 + - - -
416Z MET* 3.9 6.0 - - - +
417Z ILE 4.4 2.7 - - - -
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Residues in contact with PHE 380 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376Z PHE* 2.5 13.6 + - + +
377Z VAL* 2.7 18.9 + - - +
379Z GLY* 1.3 74.7 - - - +
381Z VAL* 1.3 64.0 + - - +
383Z ALA* 3.1 11.2 + - - +
764Z LEU* 4.9 1.8 - - - +
767Z GLY* 3.5 25.8 - - - -
768Z LEU* 3.9 3.8 - - - +
771Z LEU* 3.1 20.6 - - + +
772Z GLY 3.3 2.4 + - - -
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Residues in contact with VAL 381 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359Z GLY 5.7 1.6 - - - +
360Z GLY* 6.2 2.0 - - - -
361Z SER 6.2 2.2 - - - +
377Z VAL* 2.5 18.5 + - + +
378Z ASN* 4.6 2.7 - - - +
380Z PHE* 1.3 73.6 - - - +
382Z ASN* 1.3 59.5 + - + +
385Z PHE* 5.0 1.0 - - - +
767Z GLY* 3.8 3.5 + - - +
770Z HIS* 3.2 29.4 - - + +
771Z LEU* 3.5 1.1 - - - +
772Z GLY* 2.7 21.3 + - - -
773Z LYS* 2.9 13.6 + - - +
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Residues in contact with ASN 382 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378Z ASN* 2.9 20.2 + - - +
379Z GLY 3.6 1.8 - - - -
381Z VAL* 1.3 78.7 - - + +
383Z ALA* 1.3 56.3 + - - +
384Z ALA 3.2 0.5 + - - -
385Z PHE* 2.5 56.5 + - + +
387Z GLN* 3.5 29.8 - - + +
417Z ILE* 3.4 5.9 - - + -
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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