Contacts of the helix formed by residues 362 - 376 (chain G) in PDB entry 4DVQ
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 362 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343G GLU* 3.5 30.5 - - + +
344G SER* 3.8 22.4 - - - +
347G ALA* 4.2 0.7 - - + -
351G ILE* 3.6 21.5 - - + -
358G ALA* 3.5 23.8 + - + +
360G THR 3.7 0.4 - - - -
361G GLU* 1.3 87.5 - - - +
363G PRO* 1.4 59.5 - - - +
364G LEU 3.3 2.5 - - - -
365G LEU* 3.3 15.3 + - + -
366G ARG* 3.0 31.7 + - - +
461G LEU* 4.7 6.7 - - + -
465G HIS* 3.4 32.8 - - + +
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Residues in contact with PRO 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G GLU* 3.3 10.1 - - - +
359G THR 5.5 0.4 - - - +
360G THR 4.3 7.2 - - - +
361G GLU* 3.3 10.3 - - - +
362G LEU* 1.4 88.9 - - - +
364G LEU* 1.3 67.4 + - + +
366G ARG* 3.6 10.7 - - + +
367G ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G ILE* 3.6 27.8 - - + -
340G LEU* 3.3 23.4 - - + +
343G GLU* 2.9 28.6 + - + +
363G PRO* 1.3 84.3 - - + +
365G LEU* 1.3 56.8 + - - +
367G ALA* 3.4 9.3 + - + +
368G ALA* 2.9 22.5 + - - +
425G PRO* 4.2 8.1 - - + +
426G GLN* 6.0 5.8 - - + -
429G LEU* 4.4 23.1 - - + -
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Residues in contact with LEU 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G THR* 5.6 0.2 - - + -
330G LEU* 5.1 2.5 - - + -
340G LEU* 3.6 19.2 - - + +
343G GLU* 3.1 14.7 + - - +
344G SER* 4.4 6.7 - - - +
362G LEU* 3.6 18.8 - - + +
363G PRO 3.3 0.4 - - - -
364G LEU* 1.3 74.5 - - - +
366G ARG* 1.3 66.0 + - - +
368G ALA* 3.0 17.1 + - + +
369G LEU* 3.0 13.2 + - + +
461G LEU* 3.6 26.2 - - + +
464G LEU* 4.0 28.3 - - + -
465G HIS* 3.8 31.2 - - - +
468G LEU* 4.2 14.6 - - + -
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Residues in contact with ARG 366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359G THR* 3.2 48.3 + - - +
362G LEU 3.0 17.7 + - - +
363G PRO* 3.6 10.8 - - + +
365G LEU* 1.3 76.7 - - - +
367G ALA* 1.3 62.6 + - - +
369G LEU* 3.1 11.8 + - + +
370G LYS* 3.1 44.0 + - - +
457G GLU* 4.0 21.6 + - - +
461G LEU* 3.7 24.5 - - + +
603G SO4 2.6 42.9 + - - -
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Residues in contact with ALA 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363G PRO 2.8 17.9 + - - +
364G LEU* 3.5 10.5 - - + +
366G ARG* 1.3 72.5 - - - +
368G ALA* 1.3 60.2 + - - +
370G LYS* 3.2 13.7 + - - +
371G GLU* 2.9 29.6 + - - +
425G PRO* 3.6 25.6 - - + +
428G TRP* 3.6 19.3 - - + +
429G LEU* 6.3 2.7 - - + -
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Residues in contact with ALA 368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G THR* 5.1 3.8 - - + -
330G LEU* 5.0 1.1 - - + -
340G LEU* 3.8 25.4 - - + -
364G LEU 2.9 14.0 + - - +
365G LEU* 3.2 15.9 - - + +
367G ALA* 1.3 76.3 - - - +
369G LEU* 1.3 55.6 + - - +
371G GLU* 3.1 3.6 + - - +
372G THR* 2.8 17.7 + - - -
423G TYR* 2.6 30.6 + - + +
425G PRO* 4.0 15.8 - - + +
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Residues in contact with LEU 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G THR* 3.9 9.6 - - + +
365G LEU 3.0 14.0 + - - +
366G ARG* 3.1 10.9 + - + +
368G ALA* 1.3 72.5 - - - +
370G LYS* 1.3 61.0 + - - +
372G THR* 3.1 6.9 + - - +
373G LEU* 2.9 37.4 + - + +
457G GLU* 4.4 14.8 - - + +
460G MET* 3.5 48.0 - - + +
461G LEU* 4.0 29.8 - - + +
464G LEU* 3.8 26.5 - - + -
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Residues in contact with LYS 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366G ARG* 3.1 42.5 + - - +
367G ALA* 3.4 10.1 - - - +
369G LEU* 1.3 74.9 - - - +
371G GLU* 1.3 57.0 + - - +
373G LEU* 3.2 2.6 + - - +
374G ARG* 2.9 29.6 + - - +
428G TRP* 3.8 46.0 - - + -
440G HIS* 3.6 45.9 + - + +
457G GLU* 5.3 4.8 + - - +
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Residues in contact with GLU 371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367G ALA 2.9 13.2 + - - +
368G ALA* 3.1 11.4 + - - +
370G LYS* 1.3 75.8 - - - +
372G THR* 1.3 63.2 + - - +
374G ARG* 2.7 46.4 + - - +
375G LEU* 3.4 22.7 + - - +
422G ARG 3.0 1.4 - - - +
423G TYR* 3.6 18.8 - - + -
424G ASN 2.8 42.6 + - - +
425G PRO* 4.6 1.1 - - + -
427G ARG* 2.9 11.4 + - - -
428G TRP* 2.9 21.7 + - + +
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Residues in contact with THR 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322G PRO* 3.5 24.0 - - + +
325G MET* 4.0 18.4 - - + -
326G THR* 2.8 32.7 + - - +
368G ALA 2.8 9.9 + - - -
369G LEU* 3.1 9.4 + - - -
371G GLU* 1.3 75.4 - - - +
373G LEU* 1.3 57.6 + - - +
375G LEU 3.3 1.2 + - - -
376G TYR* 2.8 37.5 + - + +
423G TYR* 2.9 30.4 + - - -
460G MET* 5.8 0.2 - - - -
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Residues in contact with LEU 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322G PRO* 4.0 26.2 - - + -
369G LEU* 2.9 23.8 + - + +
370G LYS 3.2 3.6 + - - +
372G THR* 1.3 74.5 - - - +
374G ARG* 1.3 64.4 + - - +
376G TYR 4.0 11.2 - - - +
377G PRO* 3.3 25.3 - - - +
378G VAL* 4.1 6.7 - - + +
440G HIS* 4.6 4.9 - - + -
442G PRO* 4.0 25.3 - - + +
443G PHE* 3.7 34.3 - - + -
457G GLU* 5.7 1.6 - - + +
460G MET* 5.2 7.6 - - + -
601G HEM 4.0 24.9 - - + -
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Residues in contact with ARG 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370G LYS 2.9 17.0 + - - +
371G GLU* 2.7 45.4 + - - +
372G THR 3.2 0.2 - - - -
373G LEU* 1.3 78.6 - - - +
375G LEU* 1.3 76.3 + - - +
377G PRO* 4.0 5.5 - - - +
407G LEU 4.5 4.7 - - - +
408G TYR 4.9 0.2 - - - +
411G GLY* 2.9 45.7 + - - +
412G ARG* 4.1 4.0 + - - +
417G PHE* 3.6 33.5 - - + +
420G PRO* 3.0 28.7 + - - +
422G ARG 3.0 15.8 + - - -
427G ARG* 3.3 16.4 - - - +
428G TRP* 4.1 10.5 - - + -
439G HIS 5.8 1.1 - - - +
440G HIS* 5.6 1.5 + - - +
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Residues in contact with LEU 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G GLU* 4.3 6.1 - - - +
371G GLU 3.4 7.7 + - - +
372G THR 3.3 2.7 + - - +
374G ARG* 1.3 100.2 - - - +
376G TYR* 1.3 89.6 + - + +
377G PRO* 3.4 6.1 - - - +
408G TYR* 4.2 3.1 - - - -
412G ARG* 2.7 49.0 + - + +
420G PRO 3.3 24.5 - - - +
421G GLU* 4.2 16.6 - - - +
423G TYR* 3.9 31.6 - - + -
483G MET* 5.7 0.2 - - - +
489G LEU* 5.6 0.2 - - - +
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Residues in contact with TYR 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322G PRO* 5.0 4.6 - - + +
325G MET* 4.1 32.5 - - + -
328G PHE* 4.6 5.2 - + - -
329G GLU* 2.3 44.7 + - + -
332G ARG* 3.8 8.3 + - - -
372G THR* 2.8 31.3 + - + +
373G LEU* 3.6 12.1 - - - +
375G LEU* 1.3 103.0 - - + +
377G PRO* 1.3 64.7 - - - +
378G VAL* 3.4 5.9 + - - +
412G ARG* 4.6 9.1 + - - -
480G ASP* 5.3 3.6 + - - +
481G ILE* 5.0 10.7 + - + -
483G MET* 3.8 46.1 - - + +
489G LEU* 5.1 1.7 - - - +
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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