Contacts of the helix formed by residues 365 - 379 (chain B) in PDB entry 1GQF
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 GLU 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B LEU* 1.3 73.8 - - - +
366B ILE* 1.3 74.3 + - - +
367B MET* 2.4 40.0 + - - +
368B GLN* 2.6 48.6 + - + +
369B ILE* 2.9 9.7 + - - -
394B LEU* 5.1 0.7 - - - +
396B LYS 4.2 2.3 - - - +
397B GLU* 3.4 28.1 - - + +
398B LEU 2.7 37.5 + - - +
399B TYR* 3.4 20.0 - - + +
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Residues in contact with ILE 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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279B LEU* 5.0 1.8 - - + -
281B PHE* 4.4 15.0 - - + -
328B LEU* 4.9 7.6 - - + -
357B LEU* 5.5 1.6 - - + -
364B LEU 3.8 1.4 + - - -
365B GLU* 1.3 96.1 + - - +
367B MET* 1.3 66.2 + - + +
369B ILE* 3.1 15.0 + - + +
370B LEU* 2.7 65.6 + - + +
394B LEU* 4.0 15.7 - - + -
398B LEU* 2.9 38.3 + - + +
400B PHE* 4.0 28.4 - - + -
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Residues in contact with MET 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A MET* 3.9 46.0 - - + +
371A THR* 5.4 5.2 - - - +
392A SER* 5.5 3.4 - - - -
328B LEU* 3.2 36.8 - - + -
365B GLU* 2.4 29.9 + - - +
366B ILE* 1.3 79.1 - - + +
368B GLN* 1.3 57.0 + - + +
370B LEU* 3.7 12.0 - - + +
371B THR* 2.7 37.9 + - - -
389B VAL* 3.6 22.7 - - + -
392B SER* 4.1 12.1 - - - +
394B LEU* 4.9 1.3 - - + -
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Residues in contact with GLN 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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397A GLU* 3.2 39.8 + - + +
363B ASP 4.7 0.2 - - - +
364B LEU* 3.5 29.1 - - + +
365B GLU* 2.6 48.0 + - + +
367B MET* 1.3 72.3 - - + +
369B ILE* 1.3 67.0 + - - +
371B THR* 3.2 5.0 + - - -
372B ARG* 3.0 29.8 + - - +
399B TYR* 3.7 8.2 + - - -
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Residues in contact with ILE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 4.8 7.6 - - + +
356B ILE* 3.9 22.2 - - + -
357B LEU* 3.7 35.4 - - + -
360B HIS 4.0 15.5 - - - +
361B GLY* 4.1 6.7 - - - +
364B LEU* 3.5 40.8 - - + +
365B GLU 2.9 10.4 + - - +
366B ILE* 3.5 12.6 - - + +
368B GLN* 1.3 75.2 - - - +
370B LEU* 1.3 66.8 + - + +
372B ARG* 2.9 16.2 + - - +
373B VAL* 3.0 18.3 + - + +
400B PHE* 4.7 6.7 - - + -
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Residues in contact with LEU 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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281B PHE* 4.0 11.0 - - + -
328B LEU* 3.6 30.5 - - + -
330B ALA* 4.4 12.8 - - + -
349B PHE* 5.6 2.2 - - + -
353B LEU* 3.9 28.3 - - + -
366B ILE* 2.7 33.8 + - + +
367B MET* 3.7 22.9 - - + +
369B ILE* 1.3 72.3 - - + +
371B THR* 1.3 62.2 + - - +
373B VAL* 3.0 12.0 + - + +
374B ASN* 2.9 26.6 + - - +
389B VAL* 3.9 21.3 - - + -
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Residues in contact with THR 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A MET* 5.2 5.9 - - - +
392A SER* 4.9 7.3 + - - -
394A LEU* 3.5 11.3 + - + +
395A THR 3.5 2.7 - - - +
396A LYS* 3.3 44.4 + - - +
397A GLU* 5.3 4.7 - - + -
367B MET* 2.7 32.1 + - - +
368B GLN* 3.7 4.9 - - - -
370B LEU* 1.3 73.3 - - - +
372B ARG* 1.3 64.2 + - + +
374B ASN* 3.2 10.5 + - - +
375B ASP* 3.1 20.8 + - - +
389B VAL* 6.0 0.2 - - - -
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Residues in contact with ARG 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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149A PRO* 5.7 0.2 - - - +
151A TYR* 3.4 67.1 + - + +
395A THR 5.4 0.7 - - - -
397A GLU* 5.2 7.8 + - - +
356B ILE* 3.6 24.0 - - + +
360B HIS* 3.2 36.4 + - - -
364B LEU* 3.6 29.0 - - - +
368B GLN* 3.0 15.2 + - - +
369B ILE 2.9 9.3 + - - +
371B THR* 1.3 77.6 - - + +
373B VAL* 1.3 57.3 + - - +
375B ASP* 3.4 6.2 + - - +
376B ARG* 2.8 30.0 + - - +
379B ARG* 4.8 1.6 + - - -
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Residues in contact with VAL 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PHE* 3.6 36.8 - - + -
352B ALA* 3.8 13.5 - - + +
353B LEU* 3.5 38.8 - - + +
356B ILE* 3.6 19.5 - - + -
369B ILE* 3.0 15.4 + - + +
370B LEU* 3.0 12.2 + - + +
372B ARG* 1.3 74.7 - - - +
374B ASN* 1.3 59.7 + - - +
376B ARG* 3.5 1.9 - - - +
377B VAL* 2.8 31.4 + - + +
387B PRO* 4.8 1.6 - - + -
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Residues in contact with ASN 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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392A SER* 3.4 23.4 + - - -
393A MET* 3.8 6.9 - - - +
394A LEU 3.0 23.3 + - - +
395A THR* 4.2 5.6 - - + -
349B PHE* 5.6 0.3 - - - -
370B LEU 2.9 15.7 + - - +
371B THR* 3.3 12.4 + - - +
373B VAL* 1.3 79.4 - - - +
375B ASP* 1.3 51.0 - - - +
377B VAL* 3.6 2.1 - - - +
378B ALA* 2.7 36.8 + - - +
386B ILE* 4.1 6.1 - - + +
387B PRO* 2.8 37.6 + - - +
389B VAL* 4.0 12.7 - - - +
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Residues in contact with ASP 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A THR* 3.2 43.4 + - - +
396A LYS* 3.9 18.7 - - - -
371B THR 3.1 4.0 + - - +
372B ARG* 3.7 8.5 - - - +
374B ASN* 1.3 79.0 - - - +
376B ARG* 1.3 54.6 + - - +
378B ALA* 3.0 3.3 + - - +
379B ARG* 2.8 68.2 + - - +
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Residues in contact with ARG 376 (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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352B ALA* 3.5 26.6 - - + +
355B SER* 2.5 32.5 + - - -
356B ILE* 3.3 29.8 - - + +
372B ARG 2.8 22.1 + - - +
373B VAL* 3.5 8.3 - - - +
375B ASP* 1.3 74.7 - - - +
377B VAL* 1.3 61.4 + - - +
379B ARG* 3.2 70.9 + - - +
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Residues in contact with VAL 377 (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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334B VAL* 4.3 20.6 - - + -
348B TRP* 4.1 9.4 - - + +
349B PHE* 3.6 35.0 - - + +
352B ALA* 4.1 9.2 - - + -
373B VAL* 2.8 28.5 + - + +
374B ASN 3.6 3.4 - - - +
376B ARG* 1.3 73.8 - - - +
378B ALA* 1.3 63.4 + - - +
379B HIS* 3.1 27.8 + - - +
380B PHE* 3.7 7.0 - - + -
385B GLN 4.5 6.5 - - - +
387B PRO* 3.6 23.3 - - + -
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Residues in contact with ALA 378 (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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325A ALA* 5.3 4.5 - - + -
395A THR* 4.2 12.8 - - + -
374B ASN 2.7 22.8 + - - +
375B ASP* 3.0 11.4 + - - +
377B VAL* 1.3 69.4 - - - +
379B ARG* 1.3 70.4 + - - +
380B PHE* 3.0 22.2 + - - +
381B GLU* 4.7 0.2 - - - +
385B GLN 4.4 11.7 - - - +
386B ILE* 4.4 11.4 - - + -
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Residues in contact with ARG 379 (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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372B ARG 4.8 1.2 + - - -
375B ASP* 2.8 50.2 + - - +
376B ARG* 3.2 58.0 - - - +
377B VAL 3.3 0.4 - - - -
378B ALA* 1.3 66.2 - - + +
379B HIS* 1.3 57.0 + - - +
380B PHE 2.8 11.2 + - - -
381B GLU* 3.1 41.9 + - - +
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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