Contacts of the helix formed by residues 376 - 388 (chain B) in PDB entry 3QG2
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 LEU 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B PHE* 4.0 16.6 - - + -
368B LEU* 3.9 22.2 - - + -
374B LEU* 4.2 1.5 + - + +
375B PHE* 1.3 83.7 - - - +
377B ARG* 1.3 68.1 + - - +
378B GLY 3.1 3.5 + - - -
379B ILE* 3.2 22.7 + - + +
380B ILE* 2.9 35.8 + - + +
520B PHE* 4.8 5.6 - - + -
523B ALA* 3.7 19.3 - - + -
527B ILE* 4.1 10.8 - - + -
593B ILE* 3.9 34.5 - - + -
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Residues in contact with ARG 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B PHE* 3.9 2.5 - - + +
376B LEU* 1.3 75.6 - - - +
378B GLY* 1.3 66.4 + - - +
380B ILE* 3.2 3.4 + - - +
381B GLU* 3.0 40.9 + - + +
399B LYS* 2.8 34.3 + - - +
400B ASN* 3.4 20.8 + - - +
401B VAL* 3.9 15.1 - - - +
588B ILE* 4.0 27.8 - - + +
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Residues in contact with GLY 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B PHE* 5.2 2.6 + - - +
376B LEU 3.1 1.4 - - - -
377B ARG* 1.3 83.9 - - - +
379B ILE* 1.3 61.8 + - - +
381B GLU* 3.3 3.6 + - - +
382B GLU* 3.1 19.4 + - - +
401B VAL* 3.7 27.8 - - - +
403B ILE* 4.2 7.6 - - - -
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Residues in contact with ILE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B PHE 4.6 1.7 + - - +
376B LEU* 3.4 40.1 - - + +
378B GLY* 1.3 73.3 - - - +
380B ILE* 1.3 67.4 + - + +
382B GLU* 3.7 18.1 - - - +
383B LEU* 3.2 21.8 + - + +
403B ILE* 4.1 15.7 - - + -
520B PHE* 4.0 35.9 - - + +
524B SER* 4.0 25.3 + - - +
527B ILE* 3.8 23.3 - - + -
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Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU* 2.9 32.0 + - + +
377B ARG* 3.8 4.3 - - - +
378B GLY 3.2 0.2 - - - -
379B ILE* 1.3 86.2 - - + +
381B GLU* 1.3 67.4 + - - +
383B LEU* 3.0 10.5 + - + +
384B LEU* 2.9 27.0 + - + +
527B ILE* 3.9 17.9 - - + -
574B LEU* 5.9 1.1 - - + -
588B ILE* 3.8 18.4 - - + -
591B PHE* 3.7 61.5 - - + -
593B ILE* 6.1 2.2 - - + -
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ARG* 3.0 39.8 + - + +
378B GLY 3.6 4.5 - - - +
380B ILE* 1.3 77.0 - - - +
382B GLU* 1.3 55.7 + - - +
384B LEU* 3.3 16.3 + - - +
385B TRP* 2.9 29.5 + - - +
388B ARG* 4.8 5.0 + - - -
396B LEU* 4.0 7.9 - - + +
399B LYS* 3.8 31.9 + - + +
401B VAL* 3.9 15.0 - - + -
588B ILE* 3.5 34.9 - - + +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLY 3.1 12.6 + - - +
379B ILE* 3.7 18.7 - - - +
380B ILE 3.2 0.2 - - - -
381B GLU* 1.3 76.0 - - - +
383B LEU* 1.3 57.5 + - - +
385B TRP* 3.1 11.2 + - + +
386B PHE* 2.8 59.3 + - + -
396B LEU* 4.3 10.0 - - + +
403B ILE* 3.9 24.9 - - + +
404B TRP* 2.8 32.9 + - + +
430B TYR* 5.6 0.2 - - - -
491B HIS* 6.0 1.8 - - - -
524B SER* 4.9 6.6 + - - -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ILE* 3.2 12.1 + - + +
380B ILE* 3.0 13.1 + - + +
382B GLU* 1.3 79.4 - - - +
384B LEU* 1.3 57.6 + - + +
386B PHE* 3.1 23.4 + - + +
387B ILE* 3.0 34.6 + - + +
434B TRP* 4.3 7.6 - - + -
524B SER* 3.8 33.7 - - - +
525B TYR* 5.8 3.6 - - + -
527B ILE* 3.9 13.0 - - + -
528B PHE* 4.0 27.4 - - + +
531B MET* 3.7 28.5 - - - -
591B PHE* 5.6 0.9 - - + -
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ILE* 2.9 26.4 + - + +
381B GLU* 3.8 20.2 - - - +
383B LEU* 1.3 76.2 - - + +
385B TRP* 1.3 56.9 + - - +
387B ILE* 3.3 10.2 + - + +
388B ARG* 2.9 49.2 + - - +
531B MET* 4.0 15.7 - - + -
583B ILE 5.8 0.2 - - - +
586B PHE* 3.7 36.3 - - + +
587B THR* 3.9 7.0 - - - -
588B ILE* 3.7 30.7 - - - +
591B PHE* 4.2 5.4 - - + -
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Residues in contact with TRP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU 2.9 14.5 + - - +
382B GLU* 3.1 12.8 + - + +
384B LEU* 1.3 74.4 - - - +
386B PHE* 1.3 93.3 + + - +
388B ARG* 3.3 18.5 + - - +
389B GLY 3.3 2.6 + - - -
390B GLU* 3.2 68.2 + - + +
391B THR* 4.0 12.6 - - - -
392B ASN 3.3 25.4 + - - -
393B GLY* 4.3 0.4 - - - -
395B THR* 4.3 3.6 - - - -
396B LEU* 3.7 34.6 - - + +
404B TRP* 3.6 24.9 - + - -
426B LEU* 3.5 32.5 - - + -
429B ILE* 3.6 12.3 - - + -
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 2.8 48.8 + - + -
383B LEU* 3.3 25.8 - - + +
385B TRP* 1.3 104.4 - + - +
387B ILE* 1.3 55.2 + - - +
389B GLY* 2.7 26.5 + - - -
390B GLU 5.2 0.4 - - - -
404B TRP* 4.5 0.2 - + - -
430B TYR* 3.4 52.9 - + + -
431B GLY* 3.3 15.4 - - - +
434B TRP* 3.7 31.3 - + + -
435B ARG* 4.5 1.7 - - - +
491B HIS* 5.7 3.4 - + - -
524B SER* 5.6 2.9 - - - -
525B TYR* 4.9 9.4 - + - -
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Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU* 3.0 18.9 + - + +
384B LEU* 3.3 13.0 + - + +
386B PHE* 1.3 80.9 - - - +
388B ARG* 1.3 59.4 + - + +
389B GLY 3.2 0.5 + - - -
434B TRP* 4.3 14.8 - - + -
435B ARG* 2.8 30.3 + - - -
456B LEU* 3.9 23.6 - - + -
528B PHE* 4.4 7.9 - - + -
531B MET* 3.4 33.9 - - + -
583B ILE* 3.5 31.4 - - + +
584B GLU* 4.1 16.3 - - + +
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Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 4.8 5.3 + - - -
384B LEU* 2.9 38.9 + - - +
385B TRP* 3.7 21.0 - - - +
386B PHE 3.2 0.4 - - - -
387B ILE* 1.3 77.3 - - + +
389B GLY* 1.3 60.9 + - - +
390B GLU* 2.6 39.9 + - + +
395B THR* 3.9 14.5 - - - +
396B LEU* 5.6 1.0 - - - +
399B LYS* 4.5 12.7 - - - +
435B ARG* 4.6 5.8 + - - +
436B HIS* 5.8 0.9 + - - -
584B GLU* 5.6 4.3 - - - +
586B PHE 5.9 0.6 + - - -
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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