Contacts of the helix formed by residues 415 - 434 (chain G) in PDB entry 6BAA
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 GLY 415 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414G ALA* 1.3 77.3 - - - +
416G GLN* 1.3 52.3 + - - +
418G CYS* 3.3 11.5 + - - +
419G ASN* 2.7 42.7 + - - +
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Residues in contact with GLN 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G ALA* 3.1 5.7 - - - +
415G GLY* 1.3 75.9 - - - +
417G ILE* 1.3 62.2 + - + +
419G ASN* 3.3 19.3 + - - +
420G LEU* 2.8 28.1 + - - +
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Residues in contact with ILE 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G ILE* 5.1 2.7 - - + -
399G ILE* 4.2 13.0 - - + -
414G ALA* 2.9 25.4 + - + +
416G GLN* 1.3 76.8 - - + +
418G CYS* 1.3 65.0 + - - +
420G LEU* 3.2 11.8 + - + +
421G VAL* 3.0 24.7 + - + +
613G PHE* 4.6 28.0 - - + -
1204G PHE* 3.6 26.9 - - + -
1208G VAL* 4.1 18.2 - - + -
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Residues in contact with CYS 418 (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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414G ALA* 3.0 20.3 + - - -
415G GLY* 3.5 11.7 - - - +
417G ILE* 1.3 78.0 - - - +
419G ASN* 1.3 57.8 + - - +
421G VAL* 3.5 1.0 + - - +
422G ALA* 2.8 34.4 + - + +
1201G VAL* 4.8 7.4 - - + +
1204G PHE* 3.9 18.2 - - + -
1205G ALA* 3.5 38.8 - - - -
1208G VAL* 5.4 1.8 - - - -
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Residues in contact with ASN 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G GLY* 2.7 30.0 + - - +
416G GLN* 3.5 26.6 + - - +
417G ILE 3.2 0.2 - - - -
418G CYS* 1.3 74.4 - - - +
420G LEU* 1.3 58.3 + - - +
422G ALA* 4.5 2.4 - - - +
423G ILE* 2.9 46.5 + - + +
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Residues in contact with LEU 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G ILE* 4.8 13.7 - - + -
416G GLN 2.8 13.6 + - - +
417G ILE* 3.3 16.6 - - + +
419G ASN* 1.3 74.5 - - - +
421G VAL* 1.3 61.8 + - + +
424G ASP* 2.9 61.6 + - + +
425G THR* 3.7 2.4 + - - -
609G LYS* 3.9 23.6 - - + +
610G LEU* 4.6 8.1 - - + +
613G PHE* 3.9 40.4 - - + -
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Residues in contact with VAL 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392G GLN* 4.3 30.5 + - + +
395G ILE* 3.8 28.7 - - + -
417G ILE 3.0 9.3 + - - +
418G CYS 4.1 2.2 - - - +
420G LEU* 1.3 78.3 - - + +
422G ALA* 1.3 65.1 + - - +
423G ILE 3.2 1.0 + - - -
425G THR* 3.3 27.1 + - - +
426G ASN* 4.2 1.4 + - - +
1200G LEU* 4.8 11.2 - - + -
1201G VAL* 5.3 4.9 - - + -
1204G PHE* 3.5 40.4 - - + -
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Residues in contact with ALA 422 (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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418G CYS* 2.8 21.6 + - + +
419G ASN* 4.3 3.4 - - - +
421G VAL* 1.3 79.3 - - - +
423G ILE* 1.3 68.7 + - + +
426G ASN* 4.0 14.3 + - - +
1201G VAL* 4.5 20.2 - - + -
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Residues in contact with ILE 423 (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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419G ASN* 2.9 29.0 + - + +
422G ALA* 1.3 88.0 - - + +
424G ASP* 1.3 74.2 + - - +
425G THR 3.3 1.3 - - - -
426G ASN* 3.1 8.4 + - - +
427G GLN* 2.9 43.6 + - + +
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Residues in contact with ASP 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420G LEU* 2.9 43.5 + - + +
423G ILE* 1.3 86.8 - - - +
425G THR* 1.3 62.0 + - - +
427G GLN* 3.2 5.4 + - - +
428G LEU* 2.9 29.8 + - + +
602G LYS 5.3 0.5 - - - +
605G VAL* 5.0 6.5 - - - +
606G SER* 3.0 37.8 + - - +
609G LYS* 3.8 16.5 - - - +
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Residues in contact with THR 425 (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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388G ARG* 3.4 44.5 - - + +
391G ILE* 4.3 13.0 - - + +
392G GLN* 4.3 10.7 - - + +
395G ILE* 4.3 13.9 - - - +
420G LEU 4.1 0.9 + - - -
421G VAL* 3.3 28.3 + - - +
424G ASP* 1.3 74.1 - - - +
426G ASN* 1.3 60.9 + - - +
428G LEU* 3.1 14.1 + - + +
429G MET* 2.9 27.5 + - - +
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Residues in contact with ASN 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388G ARG* 5.7 1.5 - - - +
421G VAL 4.2 1.4 + - - -
422G ALA 4.0 15.5 + - - +
423G ILE* 3.1 11.3 + - - +
425G THR* 1.3 79.2 - - - +
427G GLN* 1.3 60.2 + - + +
429G MET* 3.2 16.9 + - - +
430G TRP* 2.9 53.0 + - - +
2001G GBM 5.4 2.8 - - - +
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Residues in contact with GLN 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G ILE* 2.9 38.3 + - + +
424G ASP* 3.3 13.0 - - - +
426G ASN* 1.3 81.0 - - - +
428G LEU* 1.3 52.8 + - - +
430G TRP* 3.4 9.6 + - - +
431G PHE* 2.6 37.1 + - - +
599G SER* 5.3 2.8 - - - +
602G LYS* 3.3 48.1 + - + +
603G ALA* 6.0 2.0 - - - -
606G SER* 3.8 11.2 - - - +
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Residues in contact with LEU 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G LEU* 6.2 4.3 - - + -
384G GLY* 5.8 0.2 - - - -
387G LEU* 6.0 5.2 - - + -
391G ILE* 3.7 35.7 - - + -
424G ASP* 2.9 20.5 + - + +
425G THR* 3.1 18.1 + - + +
427G GLN* 1.3 74.6 - - - +
429G MET* 1.3 57.5 + - - +
431G PHE* 3.8 11.3 - - + +
432G PHE* 2.8 46.9 + - + +
603G ALA* 5.4 7.0 - - + +
606G SER* 4.3 19.7 - - - +
607G VAL* 5.5 4.7 - - + +
610G LEU* 5.6 6.5 - - + -
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Residues in contact with MET 429 (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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384G GLY* 3.9 18.8 - - - +
385G ILE* 3.4 43.1 - - + -
387G LEU* 6.3 0.2 - - - -
388G ARG* 3.4 50.5 - - + +
425G THR 2.9 11.8 + - - +
426G ASN* 3.4 19.3 - - - +
428G LEU* 1.3 76.7 - - - +
430G TRP* 1.3 64.2 + - + +
432G PHE* 3.4 1.9 + - - +
433G PHE* 3.2 43.9 + - + -
1238G SER* 4.7 0.4 - - - -
2001G GBM 3.9 20.9 - - + -
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Residues in contact with TRP 430 (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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426G ASN* 2.9 52.0 + - - +
427G GLN* 3.8 9.9 - - - +
429G MET* 1.3 75.1 - - + +
431G PHE* 1.3 66.4 + - - +
433G PHE* 3.0 31.2 + + - +
434G LEU* 3.2 31.9 + - + +
599G SER* 5.9 2.2 - - - +
2001G GBM 3.8 63.9 - + + +
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Residues in contact with PHE 431 (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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427G GLN 2.6 23.1 + - - +
428G LEU* 3.2 9.6 + - + +
430G TRP* 1.3 72.2 - - - +
432G PHE* 1.3 88.0 + + - +
434G LEU* 3.1 9.6 + - + +
435G CYS* 2.9 42.9 + - + -
438G LEU* 5.8 8.3 - - + -
596G VAL* 6.4 0.2 - - + -
599G SER* 4.0 25.7 - - - +
600G THR* 3.4 31.2 - - + -
603G ALA* 3.7 27.8 - - + -
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Residues in contact with PHE 432 (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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291G LEU* 5.5 14.8 - - + -
292G CYS* 5.9 7.4 - - - -
295G PHE* 5.0 6.5 - - + -
299G LEU* 3.9 26.0 - - + +
380G ALA* 4.1 7.0 - - - +
383G THR* 3.4 32.3 - - + -
384G GLY* 4.4 13.9 - - - +
387G LEU* 3.8 20.0 - - + -
428G LEU* 2.8 30.8 + - + +
429G MET 3.9 4.3 - - - +
431G PHE* 1.3 100.2 - + - +
433G PHE* 1.3 65.9 + - - +
435G CYS* 3.2 14.6 + - + +
436G PRO* 3.3 9.9 - - - +
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Residues in contact with PHE 433 (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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306G ARG* 4.4 3.8 + - - -
380G ALA* 3.6 22.6 - - - +
381G ILE* 3.4 47.8 - - + -
384G GLY* 4.0 5.6 - - - -
429G MET* 3.2 41.7 - - + -
430G TRP* 3.0 32.5 + + - +
432G PHE* 1.3 75.8 - - - +
434G LEU* 1.3 60.2 + - + +
436G PRO* 3.2 19.2 - - - +
2001G GBM 3.4 64.2 + + + +
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Residues in contact with LEU 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G TRP* 3.2 29.2 - - + +
431G PHE* 3.1 15.0 + - + +
433G PHE* 1.3 77.1 - - + +
435G CYS* 1.3 58.9 + - - +
436G PRO 3.5 2.0 - - - -
437G ASN* 3.9 20.9 + - + +
438G LEU* 4.3 1.6 + - - +
592G LEU* 5.7 5.4 - - + -
595G SER* 4.2 13.2 - - - +
596G VAL* 3.7 40.4 - - + +
599G SER* 4.1 19.5 - - - +
2001G GBM 3.3 34.1 - - - +
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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
------------------------------------------------------------
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