Contacts of the helix formed by residues 465 - 483 (chain A) in PDB entry 1QI9
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 PHE 465 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LEU* 3.6 26.5 - - + +
294A LEU* 4.0 26.0 - - + -
295A ASP 5.8 0.4 - - - -
296A ALA* 4.0 24.7 - - + -
433A ILE* 5.3 1.3 - - + -
437A ARG* 3.5 20.6 - - + +
438A GLY* 3.4 8.2 + - - +
440A ASP* 3.0 33.5 + - + -
441A CYS 4.2 5.8 - - - -
442A TYR* 3.7 28.3 - + - -
443A PRO* 3.8 20.2 - - + -
463A LEU 3.7 1.0 + - - -
464A THR* 1.3 70.3 - - - +
466A GLU* 1.3 58.7 + - - +
468A GLU* 3.2 6.3 + - + +
469A ILE* 3.0 37.3 + - + +
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Residues in contact with GLU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 4.2 10.6 - - + +
430A LYS* 4.0 19.5 - - + +
435A LEU* 4.3 10.2 - - - +
438A GLY* 2.9 36.8 + - - +
439A GLY* 4.1 5.6 + - - -
464A THR* 3.4 9.0 + - - +
465A PHE* 1.3 76.0 - - - +
467A GLY* 1.3 59.8 + - - +
469A ILE* 3.4 12.1 + - - +
470A ASN* 2.9 36.6 + - - +
522A ARG* 2.7 50.5 + - + +
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Residues in contact with GLY 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 3.6 20.8 - - - +
201A GLY* 3.9 14.1 - - - -
464A THR* 2.9 21.3 + - - -
466A GLU* 1.3 75.8 - - - +
468A GLU* 1.3 65.6 + - - +
470A ASN* 3.3 1.7 + - - +
471A LYS* 2.7 30.3 + - - +
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Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLY 4.5 1.7 - - - +
204A THR 4.5 0.2 - - - +
208A ILE 4.4 0.2 - - - +
209A SER* 2.8 32.7 + - - +
210A GLN* 2.8 42.5 + - + +
211A LEU* 3.9 6.0 - - + +
442A TYR* 4.3 18.2 - - + -
463A LEU* 3.6 33.5 - - + +
464A THR 2.8 18.0 + - - +
465A PHE 3.2 3.6 + - - +
467A GLY* 1.3 80.3 - - - +
469A ILE* 1.3 54.2 + - - +
471A LYS* 2.8 32.8 + - - -
472A LEU* 3.0 14.7 + - - +
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Residues in contact with ILE 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LEU* 4.0 11.2 - - + -
291A LEU* 3.8 33.0 - - + -
426A ALA* 3.7 37.7 - - + +
429A LEU* 4.1 14.8 - - + -
430A LYS* 4.1 18.6 - - + -
433A ILE* 3.9 19.5 - - + -
438A GLY* 6.4 0.2 - - - -
465A PHE* 3.0 27.0 + - + +
466A GLU* 3.6 4.5 - - - +
468A GLU* 1.3 72.5 - - - +
470A ASN* 1.4 69.8 + - - +
472A LEU* 3.2 3.9 + - - +
473A ALA* 3.1 20.4 + - - +
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Residues in contact with ASN 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 5.1 1.3 - - + -
200A VAL* 2.9 47.9 + - - +
202A VAL* 4.3 7.4 - - + -
430A LYS* 2.9 35.8 + - - +
466A GLU* 2.9 22.2 + - - +
467A GLY 3.6 0.2 - - - +
469A ILE* 1.4 78.4 - - - +
471A LYS* 1.3 62.6 + - - +
473A ALA* 3.1 4.4 + - - +
474A VAL* 3.0 25.5 + - - +
522A ARG* 5.3 0.6 + - - +
523A LEU 4.9 1.0 + - - -
524A PHE* 3.3 29.7 - - + +
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Residues in contact with LYS 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLY 3.4 19.1 - - - -
202A VAL* 3.7 29.7 - - + +
204A THR 2.7 25.0 + - - -
205A GLY 4.1 1.6 - - - -
206A PRO* 2.9 30.2 + - - +
207A PHE 3.5 17.3 - - - +
208A ILE 3.7 0.6 + - - -
209A SER* 3.5 22.7 - - - +
210A GLN* 5.9 0.2 - - - +
463A LEU* 4.6 0.6 - - - +
467A GLY 2.7 19.8 + - - +
468A GLU* 2.8 29.0 + - - +
469A ILE 3.3 0.2 - - - -
470A ASN* 1.3 71.6 - - - +
472A LEU* 1.3 57.4 + - - +
474A VAL* 3.2 1.7 + - - +
475A ASN* 2.7 36.7 + - - +
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A SER* 3.5 19.2 - - - +
211A LEU* 4.0 25.1 - - + -
212A LEU* 3.4 38.8 - - + -
283A GLU* 3.7 35.9 - - + +
284A ALA* 4.1 10.8 - - + +
287A GLY* 4.5 2.0 - - - -
422A ASN* 5.2 2.5 - - - +
429A LEU* 5.8 3.8 - - + -
468A GLU 3.0 9.9 + - - +
469A ILE* 3.6 8.1 - - - +
470A ASN 3.2 0.2 - - - -
471A LYS* 1.3 74.2 - - - +
473A ALA* 1.3 65.8 + - - +
475A ASN* 3.2 1.9 + - - +
476A VAL* 3.1 25.4 + - + +
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A ASN* 3.6 34.9 - - + +
426A ALA* 4.1 9.6 - - + -
469A ILE 3.1 13.2 + - - +
470A ASN 3.6 7.0 - - - +
472A LEU* 1.3 80.8 - - - +
474A VAL* 1.3 57.5 + - + +
476A VAL* 3.5 2.4 + - - +
477A ALA* 3.1 26.2 + - - +
495A LEU* 3.8 19.6 - - + +
524A PHE* 4.4 4.3 - - + -
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Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ARG* 5.8 0.2 - - - -
197A ALA* 4.5 5.6 - - + -
199A PHE* 4.1 15.5 - - + -
202A VAL* 3.8 35.9 - - + -
470A ASN 3.0 16.2 + - - +
471A LYS 4.0 2.7 - - - +
473A ALA* 1.3 73.8 - - + +
475A ASN* 1.3 62.5 + - - +
477A ALA* 4.4 0.7 - - - -
478A PHE* 2.9 63.6 + - + +
492A ILE* 5.3 0.4 - - + -
495A LEU* 3.8 22.7 - - + -
524A PHE* 5.4 1.3 - - + -
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Residues in contact with ASN 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL* 6.1 1.2 - - - +
207A PHE* 3.1 37.6 + - - -
208A ILE* 3.4 9.3 - - - -
209A SER* 2.7 34.1 + - - -
212A LEU* 3.6 17.1 - - + +
271A LEU* 3.5 17.5 - - + +
471A LYS* 2.7 28.7 + - - +
472A LEU 3.2 5.6 + - - +
474A VAL* 1.3 73.6 - - - +
476A VAL* 1.3 57.1 + - - +
478A PHE* 3.6 2.0 - - - -
479A GLY* 2.7 29.6 + - - -
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LEU* 5.5 1.6 - - + -
271A LEU* 5.1 1.6 - - + -
274A VAL* 5.8 1.1 - - + -
275A THR* 3.3 21.9 - - + +
278A ASP* 3.9 0.4 - - - +
283A GLU* 3.8 39.7 - - + +
418A HIS* 3.8 25.4 - - + +
422A ASN* 3.5 40.8 - - - +
472A LEU* 3.1 18.5 + - + +
473A ALA 3.9 2.2 - - - +
474A VAL 3.3 0.2 - - - -
475A ASN* 1.3 75.5 - - + +
477A ALA* 1.3 67.1 + - - +
479A GLY 3.3 1.9 + - - -
480A ARG* 3.4 6.8 + - - +
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Residues in contact with ALA 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A SER* 5.2 2.2 + - - -
419A ALA* 3.8 35.4 - - + +
473A ALA 3.1 15.5 + - - +
474A VAL 3.3 3.8 + - - +
476A VAL* 1.3 80.0 - - - +
478A PHE* 1.3 64.7 + - + +
480A ARG* 3.2 18.2 + - - +
481A GLN* 3.5 14.9 + - - +
486A HIS* 5.5 0.7 - - - +
491A GLY* 4.1 12.8 - - - -
495A LEU* 4.2 11.9 - - + -
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Residues in contact with PHE 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A MET* 4.3 10.8 - - + -
195A PHE* 3.2 36.1 - - + -
196A ARG 3.9 7.0 - - - -
197A ALA* 4.1 11.2 - - + -
207A PHE* 5.2 3.1 - + + -
271A LEU* 5.3 0.9 - - + -
474A VAL* 2.9 35.5 + - + +
475A ASN* 4.2 2.7 - - - +
477A ALA* 1.3 75.1 - - + +
479A GLY* 1.3 58.7 + - - +
481A GLN* 3.1 35.6 + - - +
482A MET* 2.9 40.7 + - + +
488A ARG* 3.7 33.9 - - + -
492A ILE* 4.0 24.0 - - + -
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Residues in contact with GLY 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 3.8 18.1 - - - +
272A ALA* 3.3 14.0 - - - +
275A THR* 3.4 19.9 + - - -
475A ASN 2.7 22.3 + - - -
476A VAL 3.3 0.2 + - - -
477A ALA 3.2 0.4 - - - -
478A PHE* 1.3 73.2 - - - +
480A ARG* 1.3 59.0 + - - +
482A MET* 3.3 5.9 + - - -
483A LEU* 3.1 16.1 + - - +
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Residues in contact with ARG 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A THR* 3.0 38.0 + - - -
276A PHE* 4.2 8.5 - - - +
404A ILE* 5.8 0.2 - - - +
409A PRO* 3.6 15.2 - - - +
416A SER* 4.6 0.7 - - - +
418A HIS* 3.2 36.9 + - + -
476A VAL 3.4 14.6 + - - +
477A ALA 3.2 7.7 + - - +
479A GLY* 1.3 74.0 - - - +
481A GLN* 1.3 66.9 + - - +
483A LEU* 3.2 24.7 + - - +
485A ILE* 3.1 41.6 + - + +
486A HIS* 3.8 17.5 - - + -
600A VO4 3.1 39.8 + - - +
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Residues in contact with GLN 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 5.1 1.4 + - - -
141A VAL* 3.9 13.6 - - + +
144A MET* 3.7 25.3 - - - +
148A ARG* 5.1 0.2 + - - -
477A ALA 3.5 5.7 + - - +
478A PHE* 3.1 46.7 + - - +
480A ARG* 1.3 79.4 - - - +
482A MET* 1.3 54.3 + - - +
484A GLY* 3.0 21.0 + - - -
486A HIS* 3.3 36.2 - - + +
487A TYR* 3.3 17.9 - - - +
488A ARG* 3.4 18.7 - - - +
491A GLY* 3.5 17.8 + - - -
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Residues in contact with MET 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A MET* 3.8 36.8 - - + -
145A ALA* 5.1 0.2 - - - -
148A ARG* 2.9 30.9 + - + +
152A PHE* 4.5 3.8 - - + -
195A PHE* 4.4 8.7 - - + -
207A PHE* 3.6 34.5 - - + -
268A ALA* 3.4 45.5 - - + +
271A LEU* 3.8 20.4 - - + -
272A ALA* 3.8 5.5 - - - +
478A PHE* 2.9 23.1 + - + +
479A GLY* 3.6 7.0 - - - +
480A ARG 3.2 0.2 - - - -
481A GLN* 1.3 72.8 - - - +
483A LEU* 1.3 57.2 + - - +
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 3.2 3.6 + - - -
230A PHE* 4.2 6.3 - - + -
272A ALA* 3.5 31.4 - - + +
275A THR* 3.5 18.4 - - - +
276A PHE* 4.0 16.2 - - + -
402A GLN* 3.7 8.0 - - - +
403A ALA* 3.0 38.2 + - + -
404A ILE* 4.2 19.8 - - + +
479A GLY 3.1 9.4 + - - +
480A ARG* 3.2 31.1 + - - +
482A MET* 1.3 76.4 - - - +
484A GLY* 1.3 57.5 + - - +
485A ILE* 3.9 19.8 - - + +
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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