Contacts of the helix formed by residues 413 - 432 (chain G) in PDB entry 6C3P
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 THR 413 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407G LEU* 3.6 4.7 - - - +
410G GLY 4.8 5.6 - - - +
411G GLU 4.8 3.4 - - - +
412G MET* 1.3 78.7 - - - +
414G ALA* 1.3 66.7 + - - +
415G GLY* 3.0 5.5 + - - -
416G GLN* 3.1 23.5 + - - +
417G ILE* 3.0 23.9 + - - +
497G LYS* 5.7 12.0 - - + +
1475G THR* 6.2 1.8 - - - -
1476G GLU* 4.3 26.2 - - + +
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Residues in contact with ALA 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407G LEU* 3.4 10.1 - - + +
413G THR* 1.3 72.4 - - - +
415G GLY* 1.3 63.4 + - - +
417G ILE* 3.7 10.4 - - - +
418G CYS* 2.9 26.9 + - - +
1204G ALA* 6.5 0.7 - - - -
1207G VAL* 3.6 29.8 - - + +
1208G GLU* 5.2 9.2 - - + +
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Residues in contact with GLY 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413G THR* 3.0 7.5 + - - -
414G ALA* 1.3 78.2 - - - +
416G GLN* 1.3 56.4 + - - +
418G CYS* 3.3 3.1 + - - +
419G ASN* 2.8 27.9 + - - +
500G ASN* 5.0 14.1 - - - -
504G ARG* 6.0 3.1 - - - -
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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
----------------------------------------------------------
411G GLU 2.7 29.9 + - - -
412G MET* 3.1 13.9 - - - +
413G THR* 3.1 24.8 + - - +
415G GLY* 1.3 72.1 - - - +
417G ILE* 1.3 62.8 + - + +
419G ASN* 3.7 10.0 - - + +
420G LEU* 2.9 33.4 + - + +
493G ASN* 5.3 17.4 + - + +
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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* 5.3 1.6 - - - +
399G ILE* 3.5 18.2 - - + -
402G LEU* 4.5 5.8 - - + -
407G LEU* 3.6 21.1 - - + -
412G MET* 3.5 37.9 - - + -
413G THR 3.0 18.3 + - - +
414G ALA* 3.7 7.0 - - - +
416G GLN* 1.3 78.0 - - + +
418G CYS* 1.3 58.8 + - - +
420G LEU* 3.0 28.7 - - + +
421G VAL* 3.9 4.3 + - - +
613G PHE* 3.5 31.2 - - + -
1207G VAL* 4.7 11.4 - - + -
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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
----------------------------------------------------------
414G ALA 2.9 15.8 + - - +
415G GLY* 4.0 2.5 - - - +
417G ILE* 1.3 75.5 - - - +
419G ASN* 1.3 61.2 + - - +
420G LEU 3.2 0.7 - - - -
421G VAL* 3.0 10.4 - - - +
422G ALA* 2.9 24.7 + - - +
1200G LEU* 3.7 32.8 - - - -
1203G PHE* 3.8 28.9 - - + -
1204G ALA* 4.8 7.2 - - + +
1207G VAL* 5.9 4.8 - - + +
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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 2.8 19.5 + - - +
416G GLN* 3.2 11.4 + - + +
418G CYS* 1.3 74.5 - - - +
420G LEU* 1.3 60.9 + - - +
422G ALA* 4.0 5.8 - - - +
423G ILE* 2.9 47.6 + - - +
493G ASN* 4.1 10.5 + - - -
496G LEU* 3.2 32.7 - - - +
1125G SER* 5.2 7.5 + - - -
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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
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395G ILE* 3.7 37.2 - - + -
416G GLN* 2.9 16.9 + - + +
417G ILE* 3.0 29.4 - - - +
419G ASN* 1.3 77.0 - - - +
421G VAL* 1.3 71.8 + - - +
424G ASP* 2.8 44.8 + - + +
609G LYS* 5.5 7.6 - - + +
610G LEU* 4.4 12.3 - - + -
613G PHE* 3.8 35.9 - - + -
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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* 3.8 25.5 + - + +
395G ILE* 4.7 11.4 - - + -
417G ILE 4.2 2.2 - - - +
418G CYS* 3.0 23.1 - - - +
420G LEU* 1.3 91.1 - - + +
422G ALA* 1.3 54.6 + - - +
425G THR* 2.4 44.1 + - + -
1200G LEU* 4.8 1.6 - - + -
1203G PHE* 3.4 45.8 - - + -
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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
----------------------------------------------------------
418G CYS* 2.9 18.2 + - - +
419G ASN* 3.6 10.8 - - - +
420G LEU 3.1 0.4 - - - -
421G VAL* 1.3 80.1 - - - +
423G ILE* 1.3 61.1 + - + +
425G THR* 3.8 0.6 + - - -
426G ASN* 2.4 36.0 + - - -
1196G GLN* 5.3 1.0 + - - -
1200G LEU* 3.7 27.8 - - + -
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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
----------------------------------------------------------
419G ASN* 2.9 32.3 + - - +
422G ALA* 1.3 88.5 - - + +
424G ASP* 1.3 67.4 + - - +
425G THR 3.1 1.1 - - - -
426G ASN* 3.2 11.2 + - + +
427G GLN* 2.9 47.9 + - + +
1125G SER 6.1 0.2 - - - +
1126G SER* 4.3 22.4 - - - +
1129G ASN* 4.5 22.7 - - - +
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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
----------------------------------------------------------
391G ILE* 4.4 1.9 - - - +
395G ILE* 5.0 0.2 - - - +
419G ASN 4.0 0.2 + - - -
420G LEU* 2.8 31.5 + - + +
423G ILE* 1.3 74.7 - - - +
425G THR* 1.3 63.3 + - - +
427G GLN* 3.2 5.7 + - - +
428G LEU* 2.9 37.5 + - - +
606G SER* 2.0 46.3 + - - +
610G LEU* 3.1 40.3 - - + +
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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
----------------------------------------------------------
388G ARG* 4.4 11.6 - - - +
391G ILE* 3.6 33.4 - - + +
392G GLN* 4.3 14.7 + - + -
395G ILE* 4.9 3.6 - - + -
420G LEU 3.5 0.2 + - - -
421G VAL* 2.4 55.8 + - + +
422G ALA 3.8 4.0 + - - -
424G ASP* 1.3 80.8 - - - +
426G ASN* 1.3 67.5 + - - +
428G LEU* 3.3 2.5 + - - +
429G MET* 2.8 29.7 + - - +
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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* 5.2 6.2 + - - -
422G ALA 2.4 28.8 + - - -
423G ILE* 3.2 16.2 + - + +
425G THR* 1.3 85.1 + - - +
427G GLN* 1.3 58.8 + - + +
429G MET* 3.3 25.6 - - + +
430G TRP* 2.9 46.9 + - + -
1196G GLN* 4.3 20.7 + - - +
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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
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423G ILE* 2.9 41.5 + - + +
424G ASP* 3.6 4.3 - - - +
426G ASN* 1.3 75.9 - - + +
428G LEU* 1.3 61.7 + - - +
430G TRP* 3.3 16.4 + - + +
431G PHE* 2.8 27.9 + - - +
489G LEU* 5.7 7.5 - - - +
599G SER* 4.3 2.9 + - - +
602G LYS* 3.4 49.1 - - + +
603G ALA* 4.8 1.5 - - - +
606G SER* 3.7 25.2 + - - +
1133G GLN* 4.7 6.3 - - - +
1134G HIS* 5.9 0.2 - - - -
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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* 6.4 0.9 - - + -
387G LEU* 4.9 11.2 - - + -
391G ILE* 4.2 17.0 - - + -
424G ASP* 2.9 42.0 + - - +
425G THR* 3.8 4.0 - - - +
427G GLN* 1.3 71.7 - - - +
429G MET* 1.3 61.2 + - - +
431G PHE* 3.2 2.8 + - + +
432G PHE* 2.9 53.5 + - + -
603G ALA* 3.9 23.6 - - + +
606G SER* 4.5 1.8 - - - +
607G VAL* 3.6 24.7 - - + -
610G LEU* 3.5 18.4 - - + -
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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* 4.7 21.7 - - - +
385G ILE* 4.5 6.3 - - + -
388G ARG* 3.4 38.6 - - + +
425G THR 2.8 17.9 + - - +
426G ASN* 3.3 21.8 - - + +
428G LEU* 1.3 77.1 - - - +
430G TRP* 1.3 82.8 + - + +
432G PHE* 3.3 2.1 + - - +
433G PHE* 2.9 58.7 + - + -
1237G SER* 5.2 1.3 - - - -
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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 30.3 + - + +
427G GLN* 3.3 15.5 + - + +
429G MET* 1.3 92.2 - - + +
431G PHE* 1.3 64.8 + - - +
433G PHE* 3.0 32.8 + + + +
434G LEU* 3.0 27.3 + - + +
599G SER* 3.9 8.3 - - - +
602G LYS* 5.9 0.4 - - - -
1134G HIS* 3.3 41.3 - + - -
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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 2.8 17.0 + - - +
428G LEU* 3.2 6.7 + - + +
430G TRP* 1.3 77.8 - - - +
432G PHE* 1.3 92.9 + + - +
434G LEU* 3.2 7.6 - - + -
435G CYS* 2.8 30.2 + - + -
438G LEU* 5.6 7.0 - - + -
439G TRP* 5.6 9.9 - + - -
596G VAL 5.5 0.2 - - - -
599G SER* 3.4 19.5 + - - +
600G THR* 3.6 34.3 - - + -
603G ALA* 3.4 29.6 - - + -
604G LEU* 5.5 5.6 - - + -
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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
----------------------------------------------------------
288G TRP* 6.6 0.2 - + - -
291G LEU* 4.1 21.5 - - + -
295G PHE* 4.9 4.5 - + - -
299G LEU* 4.0 24.2 - - + -
380G ALA* 3.4 26.7 - - - +
383G THR* 3.8 10.7 + - - +
384G GLY* 4.4 9.9 - - - +
387G LEU* 3.4 32.3 - - + -
428G LEU* 2.9 40.4 + - + +
429G MET* 3.5 4.5 - - - +
431G PHE* 1.3 98.4 - + - +
433G PHE* 1.3 62.6 + - - +
435G CYS* 3.5 26.9 - - + +
439G TRP* 6.3 0.7 - + - -
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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
------------------------------------------------------------
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