Contacts of the helix formed by residues 357 - 371 (chain Q) 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 357 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351Q SER* 4.3 0.4 - - - -
356Q LEU* 1.3 78.7 - - - +
358Q LYS* 1.3 70.0 + - - +
359Q ALA* 3.4 14.9 + - - +
360Q ASP* 3.6 13.8 + - - -
361Q VAL* 3.2 18.2 + - - +
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Residues in contact with LYS 358 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347Q ILE* 5.4 5.8 - - + -
348Q GLU* 3.7 26.2 - - - +
351Q SER* 3.8 11.4 + - - -
356Q LEU 3.6 2.6 + - - -
357Q SER* 1.3 73.6 + - - +
359Q ALA* 1.3 75.0 + - + +
361Q VAL* 2.4 34.4 + - - -
362Q GLU* 2.9 30.8 + - - +
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Residues in contact with ALA 359 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357Q SER* 3.3 10.6 + - - +
358Q LYS* 1.3 86.8 - - + +
360Q ASP* 1.3 57.4 + - - +
362Q GLU* 3.5 15.5 - - - +
363Q ARG* 3.0 24.8 + - - +
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Residues in contact with ASP 360 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356Q LEU* 3.8 27.6 - - - -
357Q SER* 3.6 17.6 + - - -
359Q ALA* 1.3 76.1 - - - +
361Q VAL* 1.3 72.7 + - - +
363Q ARG* 3.2 12.0 - - + +
364Q LYS* 2.9 17.5 + - - +
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Residues in contact with VAL 361 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331Q LEU* 6.4 0.7 - - - -
335Q LEU* 4.5 9.6 - - + -
347Q ILE* 4.4 9.4 - - + -
350Q ILE* 4.0 16.6 - - + -
351Q SER* 4.5 6.7 - - - +
354Q ILE* 4.2 22.9 - - + -
356Q LEU* 4.3 12.6 - - + -
357Q SER 3.2 19.8 + - - +
358Q LYS* 2.4 21.7 + - - +
360Q ASP* 1.3 69.3 - - - +
362Q GLU* 1.3 56.7 + - - +
364Q LYS* 2.4 31.6 + - - +
365Q LEU* 2.8 34.3 + - + -
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Residues in contact with GLU 362 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347Q ILE* 3.5 33.9 - - + +
348Q GLU* 5.2 0.5 - - - +
358Q LYS* 2.9 27.0 + - - +
359Q ALA* 3.5 20.0 - - - +
361Q VAL* 1.3 74.2 - - - +
363Q ARG* 1.3 58.5 + - - +
365Q LEU* 3.8 9.0 - - - -
366Q SER* 2.9 29.8 + - - -
378Q LEU* 4.1 13.3 - - + +
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Residues in contact with ARG 363 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359Q ALA 3.0 24.0 + - - +
360Q ASP* 3.2 17.7 - - + +
362Q GLU* 1.3 77.6 - - - +
364Q LYS* 1.3 55.7 + - - +
366Q SER* 2.3 24.4 + - - -
367Q GLN* 3.7 5.0 + - - +
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Residues in contact with LYS 364 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328Q ASP* 4.2 23.4 + - - -
331Q LEU* 3.2 30.7 - - + -
332Q GLU* 2.3 40.1 + - - +
335Q LEU* 4.0 5.6 - - + -
360Q ASP 2.9 10.7 + - - +
361Q VAL* 2.4 22.6 + - - +
363Q ARG* 1.3 66.7 - - - +
365Q LEU* 1.3 58.0 + - - +
366Q SER 2.9 1.8 - - - -
367Q GLN* 2.4 45.5 + - + +
368Q MET* 2.8 21.6 + - + +
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Residues in contact with LEU 365 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335Q LEU* 4.4 12.8 - - + -
339Q ILE* 4.4 9.9 - - + -
347Q ILE* 4.5 11.2 - - + -
350Q ILE* 4.7 11.2 - - + -
361Q VAL* 2.8 38.8 + - + +
362Q GLU* 4.1 6.7 - - - -
364Q LYS* 1.3 72.4 - - - +
366Q SER* 1.3 61.8 + - - +
368Q MET* 3.7 26.6 - - + +
369Q ILE* 2.9 32.8 + - + +
374Q PHE* 3.7 23.8 - - + -
378Q LEU* 4.5 11.0 - - + -
385Q LEU* 3.9 21.5 - - + -
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Residues in contact with SER 366 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362Q GLU 2.9 15.5 + - - -
363Q ARG* 2.3 33.3 + - - -
365Q LEU* 1.3 76.2 - - - +
367Q GLN* 1.3 58.7 + - - +
369Q ILE* 3.6 4.9 - - - +
370Q LEU* 2.9 36.6 + - - +
378Q LEU* 4.1 11.0 - - - +
310R SER* 5.3 9.2 - - - -
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Residues in contact with GLN 367 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363Q ARG 4.2 3.6 - - - +
364Q LYS* 2.4 44.8 + - + +
366Q SER* 1.3 74.6 + - - +
368Q MET* 1.3 55.3 + - + +
370Q LEU* 3.5 4.3 + - - -
371Q ASP* 2.9 59.3 + - - +
233R ARG* 2.4 32.8 + - - +
264R TYR* 5.1 8.3 + - - -
266R CYS* 6.3 0.6 - - - -
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Residues in contact with MET 368 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332Q GLU* 2.6 35.0 - - - +
335Q LEU* 4.1 10.1 - - + -
336Q ILE* 3.7 28.7 - - + +
339Q ILE* 4.9 0.7 - - + -
364Q LYS* 2.8 23.2 + - + +
365Q LEU* 3.7 23.1 - - + +
367Q GLN* 1.3 75.9 - - + +
369Q ILE* 1.3 67.4 + - - +
371Q ASP* 2.9 11.4 + - - -
372Q LYS 3.1 9.4 + - - -
373Q LYS* 3.3 27.8 + - + -
374Q PHE* 3.5 33.7 - - + -
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Residues in contact with ILE 369 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365Q LEU 2.9 28.5 + - - +
366Q SER* 3.6 5.8 - - - +
368Q MET* 1.3 75.5 - - - +
370Q LEU* 1.3 58.9 + - - +
372Q LYS* 3.1 19.7 + - - +
373Q LYS 5.3 0.2 - - - +
374Q PHE* 3.1 32.1 - - + -
375Q HIS* 5.2 3.8 + - - +
376Q GLY 3.2 45.3 - - - +
377Q ILE* 3.9 5.6 - - - +
378Q LEU* 5.1 9.2 - - + +
385Q LEU* 4.6 2.7 - - + -
309R GLU* 3.2 25.3 - - + +
310R SER* 4.2 24.0 - - - +
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Residues in contact with LEU 370 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366Q SER* 2.9 19.7 + - - +
367Q GLN* 3.8 4.5 - - - +
369Q ILE* 1.3 78.4 - - + +
371Q ASP* 1.3 59.0 + - - +
372Q LYS* 3.3 7.7 + - - +
233R ARG* 2.6 70.0 - - + +
234R PRO* 5.9 0.3 - - - +
266R CYS* 4.1 14.1 - - - -
306R GLN* 3.4 37.0 - - + +
309R GLU* 3.7 23.9 - - + +
310R SER* 6.3 2.5 - - - -
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Residues in contact with ASP 371 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367Q GLN* 2.9 50.8 + - - +
368Q MET* 2.9 4.1 + - - +
370Q LEU* 1.3 75.8 - - - +
372Q LYS* 1.3 68.9 + - - +
373Q LYS* 3.1 18.9 + - + +
233R ARG* 3.4 18.9 + - - +
234R PRO* 4.4 26.9 - - + +
237R ARG* 5.6 6.6 + - - +
264R TYR* 5.3 3.4 - - - -
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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