Contacts of the helix formed by residues 365 - 379 (chain G) in PDB entry 3V3K
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 ASP 365 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364G GLU* 1.3 76.5 - - - +
366G LEU* 1.3 63.0 + - - +
367G GLN* 2.9 36.0 - - - +
368G SER* 2.8 26.0 + - - -
369G LEU* 3.1 23.8 + - - +
397G LYS* 4.1 21.8 + - + +
398G LEU 3.6 18.6 - - - +
399G PHE* 3.5 31.1 - - + +
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Residues in contact with LEU 366 (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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279G LEU* 3.3 36.3 - - + -
281G PHE* 4.1 13.2 - - + -
328G PHE* 3.6 27.8 - - + -
357G PHE* 4.2 5.4 - - + -
365G ASP* 1.3 76.3 + - - +
367G GLN* 1.3 64.5 + - - +
369G LEU* 3.2 10.9 + - - +
370G LEU* 3.1 39.4 + - + +
394G LEU* 4.4 4.9 - - + -
398G LEU* 3.0 27.1 + - + +
400G PHE* 3.7 25.8 - - + -
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Residues in contact with GLN 367 (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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367E GLN* 4.1 29.8 + - + +
371E LEU* 3.0 39.1 - - + +
392E ASN* 5.5 2.0 + - - +
328G PHE* 4.9 7.9 - - + -
365G ASP* 2.9 24.3 - - - +
366G LEU* 1.3 85.1 + - - +
368G SER* 1.3 58.6 + - - +
369G LEU 3.4 0.2 - - - -
370G LEU* 3.9 6.3 - - - +
371G LEU* 3.1 34.3 + - + +
389G CYS* 5.9 1.1 - - - -
392G ASN* 3.7 23.9 - - - +
394G LEU* 4.9 7.0 - - - +
396G LYS 4.8 1.4 + - - -
397G LYS* 4.4 1.6 - - - -
398G LEU 4.3 9.2 + - - -
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Residues in contact with SER 368 (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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151E LEU* 5.9 0.2 - - - +
397E LYS* 3.5 25.5 + - - -
364G GLU* 3.7 24.7 - - - +
365G ASP* 2.8 30.0 + - - -
366G LEU 3.2 0.6 - - - -
367G GLN* 1.3 78.0 - - - +
369G LEU* 1.3 64.3 + - - +
371G LEU* 3.6 12.4 + - - +
372G ARG* 3.5 23.4 + - - +
397G LYS* 5.4 1.6 + - - -
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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
----------------------------------------------------------
356G ILE* 3.6 26.2 - - + +
357G PHE* 3.8 33.2 - - + -
360G TRP* 3.6 15.7 - - + +
361G ALA* 3.6 35.9 - - + +
364G GLU* 3.9 14.6 - - + +
365G ASP 3.1 25.2 + - - +
366G LEU* 3.2 9.2 + - - +
368G SER* 1.3 77.4 - - - +
370G LEU* 1.3 56.7 + - - +
372G ARG* 3.0 22.9 + - - +
373G VAL* 3.0 16.7 + - - +
400G PHE* 4.4 7.6 - - + -
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Residues in contact with LEU 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G PHE* 4.3 4.9 - - + -
328G PHE* 3.4 39.3 - - + -
330G SER* 3.3 21.3 - - - +
349G TYR* 3.9 18.6 - - + +
353G LEU* 4.4 12.6 - - + -
357G PHE* 5.0 4.5 - - + -
366G LEU* 3.1 27.2 + - + +
367G GLN* 3.9 4.9 - - - +
368G SER 3.4 0.2 - - - -
369G LEU* 1.3 76.0 - - - +
371G LEU* 1.3 59.1 + - - +
373G VAL* 3.8 13.9 - - + +
374G ALA* 3.0 26.9 + - - +
387G PRO* 5.8 1.4 - - + +
388G GLY* 6.1 0.3 - - - -
389G CYS* 3.7 17.4 - - - -
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Residues in contact with LEU 371 (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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365E ASP* 5.4 2.7 - - - +
367E GLN* 5.4 7.0 - - + -
392E ASN* 4.6 15.9 - - - +
394E LEU* 3.2 30.3 - - + +
395E ARG 3.0 21.2 - - - +
396E LYS* 3.2 24.2 - - - +
397E LYS* 3.9 29.2 - - + -
367G GLN* 3.1 24.1 + - + +
368G SER* 3.6 13.7 - - - +
370G LEU* 1.3 76.1 - - - +
372G ARG* 1.3 57.6 + - + +
374G ALA* 3.3 5.3 + - - +
375G ASN 2.9 23.7 + - - -
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Residues in contact with ARG 372 (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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145E LEU* 5.4 1.0 - - - +
151E LEU* 3.3 47.8 - - + +
395E ARG 4.8 0.4 - - - -
356G ILE* 3.4 20.0 - - + -
360G TRP* 3.1 57.4 - - - +
364G GLU* 2.9 33.0 + - - -
368G SER 3.5 13.2 + - - +
369G LEU* 3.0 7.6 + - - +
371G LEU* 1.3 77.9 - - + +
373G VAL* 1.3 51.9 + - - +
375G ASN* 3.3 6.8 + - - +
376G ALA* 2.7 36.4 + - - +
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Residues in contact with VAL 373 (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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349G TYR* 4.1 37.5 - - + +
352G THR* 3.8 11.9 - - + +
353G LEU* 3.9 21.1 - - + +
356G ILE* 3.4 25.1 - - + -
357G PHE* 5.2 2.2 - - + -
369G LEU 3.0 12.9 + - - +
370G LEU* 3.8 20.2 - - + +
371G LEU 3.3 0.2 - - - -
372G ARG* 1.3 74.7 - - - +
374G ALA* 1.3 59.4 + - - +
376G ALA* 3.3 0.5 + - - +
377G VAL* 2.8 40.5 + - + +
387G PRO* 4.9 1.8 - - + -
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Residues in contact with ALA 374 (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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394E LEU 3.6 15.7 - - - +
370G LEU 3.0 20.0 + - - +
371G LEU 3.5 5.8 - - - +
373G VAL* 1.3 76.5 - - - +
375G ASN* 1.3 56.5 + - - +
378G SER* 3.1 30.5 + - - -
386G MET* 3.3 17.3 - - + +
387G PRO* 3.5 33.8 - - + +
388G GLY* 5.5 1.1 - - - -
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Residues in contact with ASN 375 (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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150E ASP* 3.4 31.7 + - - +
395E ARG* 3.3 46.5 + - + +
396E LYS* 4.6 3.6 - - - +
371G LEU 2.9 16.6 + - - +
372G ARG* 3.7 7.0 - - - +
374G ALA* 1.3 76.1 - - - +
376G ALA* 1.3 58.6 + - - +
378G SER* 2.8 17.9 + - - -
379G VAL* 3.6 16.3 - - - +
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Residues in contact with ALA 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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352G THR* 3.3 27.1 - - + -
356G ILE* 4.4 4.0 - - + -
372G ARG 2.7 21.4 + - - +
375G ASN* 1.3 72.9 - - - +
377G VAL* 1.3 61.4 + - - +
379G VAL* 3.1 26.9 - - - +
380G LYS* 3.8 9.7 - - - +
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Residues in contact with VAL 377 (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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348G TRP* 3.6 37.3 - - + +
349G TYR* 4.1 2.5 - - - -
352G THR* 3.6 13.5 - - - +
373G VAL* 2.8 29.8 + - + +
376G ALA* 1.3 70.9 - - - +
378G SER* 1.3 64.4 + - - +
380G LYS* 3.3 21.9 + - - +
385G GLN* 3.3 41.5 + - + +
387G PRO* 3.6 21.8 - - + -
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Residues in contact with SER 378 (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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320E SER* 2.9 21.0 + - - +
321E LEU* 4.5 3.0 - - - +
322E PRO* 3.8 28.4 - - - +
395E ARG* 3.5 21.5 - - - -
374G ALA 3.1 15.9 + - - -
375G ASN* 2.8 24.9 + - - -
377G VAL* 1.3 78.4 - - - +
379G VAL* 1.3 59.9 + - - +
380G LYS 3.4 2.4 + - - +
384G LYS* 4.4 4.3 - - - +
385G GLN 3.6 11.6 + - - -
386G MET* 4.4 3.4 - - - -
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Residues in contact with VAL 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E SER* 3.4 29.6 - - - +
321E LEU* 5.7 2.5 - - + -
395E ARG* 6.2 0.4 - - - +
375G ASN* 3.6 17.5 - - - +
376G ALA* 3.1 21.3 - - - +
378G SER* 1.3 77.9 + - - +
380G LYS* 1.3 65.4 + - + +
381G GLY 3.6 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