Contacts of the helix formed by residues 465 - 483 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LEU* 3.5 26.4 - - + +
294B LEU* 3.8 26.0 - - + -
295B ASP 5.9 0.2 - - - -
296B ALA* 3.9 22.4 - - + -
433B ILE* 5.4 2.2 - - + -
437B ARG 3.6 17.0 - - - +
438B GLY* 3.4 7.8 + - - +
440B ASP* 3.0 37.5 + - + -
441B CYS 4.2 4.0 - - - -
442B TYR* 3.6 31.4 - + - -
443B PRO* 3.7 20.4 - - + -
463B LEU 3.6 0.2 + - - -
464B THR* 1.3 72.1 - - - +
466B GLU* 1.3 57.8 + - - +
468B GLU* 3.1 5.7 + - + +
469B ILE* 2.8 39.2 + - + +
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Residues in contact with GLU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B VAL* 4.1 11.5 - - + +
430B LYS* 4.1 20.4 - - + +
435B LEU* 4.2 11.6 - - - +
438B GLY* 3.0 38.1 + - - +
439B GLY* 4.0 4.8 + - - -
464B THR* 3.5 9.5 + - - +
465B PHE* 1.3 75.8 - - - +
467B GLY* 1.3 60.5 + - - +
469B ILE* 3.6 12.4 - - - +
470B ASN* 2.9 36.9 + - - +
522B ARG* 2.8 50.4 + - + +
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Residues in contact with GLY 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL* 3.7 20.7 - - - +
201B GLY* 4.0 14.3 - - - -
464B THR* 3.1 22.1 + - - -
466B GLU* 1.3 79.3 - - - +
468B GLU* 1.3 61.5 + - - +
470B ASN* 3.4 2.6 + - - +
471B LYS* 2.8 28.8 + - - +
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Residues in contact with GLU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLY 4.7 1.6 - - - +
204B THR 4.5 0.3 - - - +
208B ILE 4.3 0.2 - - - +
209B SER* 2.7 33.7 + - - +
210B GLN* 2.9 46.0 + - + +
211B LEU* 3.7 9.8 - - + +
291B LEU* 6.5 0.7 - - + -
442B TYR* 4.7 7.9 - - + -
463B LEU* 3.5 33.0 - - + +
464B THR 2.9 19.4 + - - +
465B PHE* 3.1 5.8 + - + +
467B GLY* 1.3 75.3 - - - +
469B ILE* 1.3 63.9 + - - +
471B LYS* 3.0 30.7 + - - -
472B LEU* 3.1 10.4 + - - +
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Residues in contact with ILE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 4.1 11.7 - - + -
291B LEU* 3.9 31.9 - - + -
426B ALA* 3.7 37.3 - - + +
429B LEU* 4.1 15.7 - - + -
430B LYS* 4.1 18.6 - - + +
433B ILE* 4.0 19.1 - - + -
438B GLY* 6.4 0.2 - - - -
465B PHE* 2.8 26.9 + - + +
466B GLU* 3.6 5.2 - - - +
468B GLU* 1.3 74.7 - - - +
470B ASN* 1.3 64.0 + - - +
472B LEU* 3.3 5.5 + - + +
473B ALA* 3.2 20.4 + - - +
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Residues in contact with ASN 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 4.9 1.1 - - + -
200B VAL* 3.0 47.4 + - - +
202B VAL* 4.2 7.6 - - + -
430B LYS* 2.9 35.5 + - - +
466B GLU* 2.9 21.5 + - - +
467B GLY 3.6 0.7 - - - +
469B ILE* 1.3 74.6 - - - +
471B LYS* 1.4 65.9 + - - +
473B ALA* 3.2 3.8 + - - +
474B VAL* 3.0 25.5 + - - +
522B ARG 5.4 0.4 + - - -
523B LEU 5.0 0.6 + - - -
524B PHE* 3.2 29.6 - - + +
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Residues in contact with LYS 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B GLY 3.6 11.7 - - - -
202B VAL* 3.6 28.9 - - + +
204B THR 2.7 29.0 + - - -
205B GLY* 4.1 2.4 - - - -
206B PRO* 2.8 21.0 + - - +
207B PHE 3.3 25.6 - - - +
208B ILE 4.8 0.6 + - - -
209B SER* 3.4 22.7 - - - +
467B GLY 2.8 19.5 + - - +
468B GLU* 3.0 30.4 + - - +
469B ILE 3.2 0.4 - - - -
470B ASN* 1.4 75.7 - - - +
472B LEU* 1.3 52.4 + - - +
474B VAL* 3.6 1.3 - - + +
475B ASN* 2.7 41.1 + - - +
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Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 3.7 12.7 - - - +
211B LEU* 4.0 24.2 - - + -
212B LEU* 3.2 39.3 - - + -
283B GLU* 3.7 36.1 - - + +
284B ALA* 4.0 10.5 - - + +
287B GLY* 4.6 1.3 - - - -
422B ASN* 5.1 2.7 - - - +
429B LEU* 5.8 3.6 - - + -
468B GLU 3.1 14.1 + - - +
469B ILE* 3.3 9.8 + - - +
471B LYS* 1.3 79.1 - - - +
473B ALA* 1.3 58.5 + - - +
475B ASN* 3.2 2.7 + - - +
476B VAL* 2.8 30.9 + - + +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ASN* 3.7 36.1 - - - +
426B ALA* 4.0 10.8 - - + -
469B ILE 3.2 8.1 + - - +
470B ASN 3.2 8.9 + - - +
472B LEU* 1.3 78.5 - - - +
474B VAL* 1.3 60.3 + - + +
476B VAL* 3.1 3.6 + - - +
477B ALA* 2.9 28.4 + - - +
495B LEU* 3.8 19.5 - - + +
524B PHE* 4.4 4.3 - - + -
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PHE 5.6 0.2 - - - +
196B ARG 5.4 0.2 - - - -
197B ALA* 4.4 5.2 - - + -
199B PHE* 3.9 20.4 - - + -
202B VAL* 3.9 30.5 - - + -
470B ASN* 3.0 16.3 + - - +
471B LYS 3.9 3.1 - - - +
473B ALA* 1.3 76.6 - - + +
475B ASN* 1.4 60.8 + - - +
478B PHE* 2.8 63.5 + - + +
492B ILE* 5.3 0.4 - - + -
495B LEU* 3.8 22.9 - - + -
524B PHE* 5.5 0.9 - - + -
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Residues in contact with ASN 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B VAL* 6.3 0.4 - - - +
207B PHE* 3.0 39.1 + - - -
208B ILE* 3.5 8.5 - - - -
209B SER* 2.7 34.2 + - - -
212B LEU* 3.7 9.8 - - + +
271B LEU* 3.4 28.4 - - + +
471B LYS* 2.7 30.7 + - - +
472B LEU 3.6 4.5 - - - +
474B VAL* 1.4 76.2 - - - +
476B VAL* 1.4 59.1 + - - +
478B PHE* 4.8 1.1 - - - -
479B GLY* 2.8 24.6 + - - -
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LEU* 5.2 1.6 - - + -
271B LEU* 5.3 1.1 - - + -
274B VAL* 5.6 1.1 - - + -
275B THR* 3.4 11.1 - - + +
278B ASP* 3.9 0.9 - - - +
283B GLU* 3.7 44.4 - - + +
418B HIS* 3.7 21.5 - - + +
422B ASN* 3.4 36.1 - - - +
472B LEU* 2.8 26.3 + - + +
473B ALA 3.1 3.3 + - - +
475B ASN* 1.4 82.1 - - + +
477B ALA* 1.3 63.6 + - - +
479B GLY 3.3 4.9 + - - -
480B ARG* 3.4 11.3 + - - +
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Residues in contact with ALA 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B SER* 5.0 1.9 + - - -
419B ALA* 3.4 38.5 - - + +
473B ALA 2.9 15.8 + - - +
474B VAL 3.9 2.7 - - - +
476B VAL* 1.3 74.2 - - - +
478B PHE* 1.3 65.8 + - + +
480B ARG* 3.1 24.1 + - - +
481B GLN* 3.5 12.1 + - - +
486B HIS* 5.4 0.2 - - - +
491B GLY* 4.1 11.8 - - - -
495B LEU* 4.1 11.9 - - + -
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Residues in contact with PHE 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B MET* 4.4 7.2 - - + -
195B PHE 3.3 28.0 - - - -
196B ARG 3.9 8.7 - - - -
197B ALA* 4.2 1.8 - - + -
207B PHE* 5.3 2.5 - + + -
271B LEU* 5.4 0.4 - - + -
474B VAL* 2.8 39.2 + - + +
475B ASN* 4.4 2.7 - - - +
477B ALA* 1.3 74.1 - - + +
479B GLY* 1.3 60.4 + - - +
481B GLN* 3.1 37.0 + - - +
482B MET* 2.8 44.3 + - + +
488B ARG* 3.7 37.7 - - + -
491B GLY* 4.9 0.9 - - - -
492B ILE* 3.8 31.6 - - + -
495B LEU* 5.5 0.4 - - + -
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Residues in contact with GLY 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LEU* 4.0 17.9 - - - +
272B ALA* 3.4 8.4 - - - -
275B THR* 3.4 22.1 + - - -
475B ASN 2.8 19.1 + - - -
476B VAL 3.3 0.2 + - - -
477B ALA 3.3 0.4 - - - -
478B PHE* 1.3 78.1 - - - +
480B ARG* 1.3 60.5 + - - +
482B MET* 3.2 6.5 + - - -
483B LEU* 3.0 16.5 + - - +
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Residues in contact with ARG 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B THR* 2.9 43.6 + - - -
276B PHE* 4.1 7.5 - - - +
404B ILE* 6.0 0.2 - - - +
409B PRO* 3.5 13.9 - - - +
416B SER* 4.3 1.6 - - - +
418B HIS* 3.1 40.9 + - + -
476B VAL 3.4 14.5 + - - +
477B ALA 3.1 7.8 + - - +
479B GLY* 1.3 76.9 - - - +
481B GLN* 1.3 58.9 + - - +
483B LEU* 3.0 34.4 + - - +
485B ILE* 3.2 38.0 + - + +
486B HIS* 3.7 17.7 - - + -
600B VO4 3.2 34.0 + - - +
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Residues in contact with GLN 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLU* 5.1 0.8 + - - -
141B VAL* 4.0 12.5 - - + +
144B MET* 3.7 25.8 - - - +
477B ALA 3.5 5.8 + - - +
478B PHE* 3.1 46.1 + - - +
480B ARG* 1.3 75.8 - - - +
482B MET* 1.4 55.8 + - - +
484B GLY* 2.9 22.0 + - - -
486B HIS* 3.3 38.2 - - + +
487B TYR 3.4 15.2 - - - +
488B ARG* 3.4 21.3 - - - +
491B GLY* 3.5 17.2 + - - -
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Residues in contact with MET 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B MET* 3.8 34.1 - - + -
145B ALA* 5.2 0.3 - - - -
148B ARG* 3.0 29.6 + - + +
152B PHE* 4.8 1.3 - - + -
195B PHE* 4.4 10.1 - - + -
207B PHE* 3.6 34.8 - - + -
268B ALA* 3.6 48.9 - - + +
271B LEU* 3.8 19.1 - - + -
272B ALA* 3.9 6.7 - - + +
403B ALA* 4.4 0.2 - - - +
478B PHE* 2.8 28.3 + - + +
479B GLY* 3.2 9.4 + - - +
481B GLN* 1.4 73.2 - - - +
483B LEU* 1.4 56.3 + - - +
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ARG* 3.2 2.6 + - - -
230B PHE* 4.3 2.9 - - + -
272B ALA* 3.4 30.7 - - + +
275B THR* 3.5 12.3 - - - +
276B PHE* 4.2 9.0 - - + +
402B GLN* 3.7 7.3 - - - +
403B ALA* 3.0 34.4 + - + -
404B ILE* 4.1 34.9 + - + +
479B GLY 3.0 8.6 + - - +
480B ARG* 3.0 42.1 + - - +
482B MET* 1.4 75.7 - - - +
484B GLY* 1.3 57.1 + - - +
485B ILE* 3.9 20.6 - - + +
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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