Contacts of the helix formed by residues 392 - 409 (chain A) in PDB entry 1QF6
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 GLN 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A TYR 5.2 1.4 + - - -
351A LEU* 3.4 13.2 + - - +
352A PRO* 3.3 29.5 - - + +
388A CYS* 3.4 14.5 - - + +
389A THR* 2.6 58.5 + - - +
391A GLU* 1.3 73.7 - - + +
393A ILE* 1.3 67.3 + - - +
394A ARG 3.5 0.4 - - - -
395A ASP* 3.4 10.3 + - + +
396A GLU* 3.0 26.6 + - - +
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Residues in contact with ILE 393 (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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388A CYS* 4.4 4.2 - - - -
389A THR 3.3 2.5 + - - +
390A GLU* 3.1 24.0 + - - +
392A GLN* 1.3 73.6 - - - +
394A ARG* 1.3 69.9 + - - +
396A GLU* 2.7 18.3 + - - -
397A VAL* 2.8 34.3 + - + -
436A ARG* 3.5 28.3 - - - +
440A ASP* 4.3 14.4 - - + +
485A LEU* 3.9 16.2 - - + -
487A PHE* 3.6 28.7 - - + -
508A VAL* 3.9 17.7 - - + -
510A ILE* 4.7 1.3 - - + -
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Residues in contact with ARG 394 (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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390A GLU 4.7 0.2 + - - -
391A GLU 4.3 7.4 + - - +
392A GLN 3.4 0.8 + - - -
393A ILE* 1.3 81.0 - - - +
395A ASP* 1.3 78.0 + - - +
397A VAL* 3.4 3.4 + - - +
398A ASN* 2.9 39.7 + - - +
440A ASP* 6.1 2.0 - - - -
443A VAL* 5.7 5.9 - - + +
444A ALA* 5.7 3.8 - - + -
447A GLU* 3.6 35.3 + - - +
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Residues in contact with ASP 395 (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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391A GLU 5.1 1.3 + - - +
392A GLN* 3.4 12.9 + - - +
393A ILE 3.2 0.2 - - - -
394A ARG* 1.3 92.0 + - - +
396A GLU* 1.3 64.9 + - - +
398A ASN* 3.6 6.7 - - - +
399A GLY* 3.1 22.2 + - - -
402A ARG* 4.8 2.9 + - - -
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Residues in contact with GLU 396 (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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352A PRO* 3.8 16.4 - - + +
354A ARG* 2.7 44.0 + - - -
386A ILE* 3.4 33.9 - - + +
388A CYS* 4.7 3.8 - - - -
392A GLN* 3.0 16.5 + - - +
393A ILE* 2.7 14.6 + - - +
395A ASP* 1.3 75.6 - - - +
397A VAL* 1.3 66.2 + - - +
399A GLY* 2.8 14.4 + - - -
400A CYS* 3.1 14.7 + - - -
510A ILE* 3.7 13.5 - - + -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ILE* 2.8 39.1 + - + +
394A ARG* 3.9 3.8 - - - +
396A GLU* 1.3 71.1 - - - +
398A ASN* 1.3 65.1 + - - +
400A CYS* 2.8 19.2 + - - +
401A ILE* 3.0 20.2 + - + +
440A ASP 5.7 1.8 - - - +
441A LEU* 4.3 16.2 - - + -
444A ALA* 3.5 25.6 - - + -
466A ILE* 4.5 6.5 - - + -
483A VAL* 4.7 9.0 - - + -
485A LEU* 4.0 14.6 - - + -
510A ILE* 3.9 15.5 - - + +
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Residues in contact with ASN 398 (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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394A ARG* 2.9 31.9 + - - +
395A ASP* 3.6 7.2 - - - +
397A VAL* 1.3 76.7 - - - +
399A GLY* 1.3 64.3 + - - +
401A ILE* 3.3 9.0 + - - +
402A ARG* 3.0 39.4 + - - +
444A ALA* 3.4 21.7 - - - +
447A GLU* 3.9 25.4 + - - +
448A ASN* 3.0 28.1 + - - +
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Residues in contact with GLY 399 (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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288A TYR* 3.9 10.1 - - - -
290A TYR* 5.9 1.1 - - - -
395A ASP 3.1 10.7 + - - -
396A GLU* 2.8 11.3 + - - -
398A ASN* 1.3 77.1 - - - +
400A CYS* 1.3 59.8 + - - +
402A ARG* 3.5 24.4 + - - +
403A LEU* 3.1 23.0 + - - +
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Residues in contact with CYS 400 (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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290A TYR* 4.6 2.7 - - - -
386A ILE* 3.9 22.2 - - - -
396A GLU 3.1 15.2 + - - -
397A VAL* 2.8 14.3 + - - +
399A GLY* 1.3 72.6 - - - +
401A ILE* 1.3 69.5 + - - +
403A LEU* 2.8 21.7 + - - +
404A VAL* 3.0 16.3 + - + +
483A VAL* 4.2 20.0 - - + -
510A ILE* 4.5 7.4 - - - -
512A ARG* 3.8 32.5 - - + -
514A ILE* 4.9 1.1 - - + +
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Residues in contact with ILE 401 (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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397A VAL* 3.4 21.1 - - + +
398A ASN* 3.6 9.0 - - - +
400A CYS* 1.3 76.1 - - - +
402A ARG* 1.3 63.9 + - + +
404A VAL* 3.3 12.8 + - - +
405A TYR* 3.4 36.2 + - + -
444A ALA* 4.9 2.0 - - + +
445A LEU* 3.8 15.3 - - + -
448A ASN* 3.9 33.7 - - + +
450A ILE* 4.3 5.2 - - + -
466A ILE* 3.7 29.6 - - + -
468A PHE* 3.9 16.2 - - + -
483A VAL* 5.0 3.3 - - + +
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Residues in contact with ARG 402 (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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288A TYR* 4.1 18.1 + - + +
395A ASP 4.8 2.2 + - - -
398A ASN* 3.0 36.8 + - - +
399A GLY* 3.6 21.8 + - - +
401A ILE* 1.3 78.2 - - - +
403A LEU* 1.3 59.2 + - - +
405A TYR* 3.5 4.3 + - - +
406A ASP* 2.9 29.7 + - - +
448A ASN* 4.3 13.9 + - - +
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Residues in contact with LEU 403 (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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284A LYS* 4.3 10.8 - - + +
285A LEU* 5.4 3.6 - - + -
288A TYR* 3.4 48.4 - - + +
290A TYR* 4.0 13.7 - - + +
399A GLY 3.1 10.3 + - - +
400A CYS* 2.8 14.9 + - - +
402A ARG* 1.3 73.2 - - - +
404A VAL* 1.3 66.8 + - - +
406A ASP* 3.3 2.3 - - + +
407A MET* 3.0 54.5 + - + +
512A ARG* 3.9 24.7 - - - +
514A ILE* 3.9 8.7 - - + -
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Residues in contact with VAL 404 (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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400A CYS 3.0 14.9 + - - +
401A ILE 3.5 8.5 - - - +
402A ARG 3.2 0.2 - - - -
403A LEU* 1.3 79.1 - - - +
405A TYR* 1.3 68.4 + - + +
407A MET* 3.0 2.3 + - - +
408A TYR* 2.9 51.9 + - + +
468A PHE* 3.8 43.1 - - + -
481A GLY* 5.0 0.7 - - - -
483A VAL* 5.5 3.8 - - + -
513A ALA 4.9 2.9 - - - +
514A ILE* 3.8 35.9 - - + +
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Residues in contact with TYR 405 (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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401A ILE* 3.4 25.2 + - + +
402A ARG* 4.2 4.7 - - - +
404A VAL* 1.3 81.0 - - + +
406A ASP* 1.3 65.1 + - - +
408A TYR* 4.4 4.0 - - - +
409A SER* 3.1 24.3 + - - -
416A ILE* 4.0 36.0 + - + +
418A VAL* 3.1 31.0 - - - +
450A ILE* 3.2 38.6 - - + +
468A PHE* 3.5 21.4 - + - -
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Residues in contact with ASP 406 (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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284A LYS* 2.7 38.5 + - - -
287A GLU* 4.3 1.7 - - - +
288A TYR* 2.6 24.2 + - - +
402A ARG 2.9 19.6 + - - +
403A LEU* 3.3 6.5 - - + +
404A VAL 3.0 0.2 - - - -
405A TYR* 1.3 77.0 - - - +
407A MET* 1.3 61.2 + - - +
409A SER* 2.7 24.7 + - - -
410A THR* 3.8 6.1 + - - -
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Residues in contact with MET 407 (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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280A PHE* 3.6 33.4 - - + -
281A VAL* 4.7 15.3 - - + -
284A LYS* 3.9 22.9 - - + -
285A LEU* 6.2 2.2 - - + -
382A ASP* 5.4 1.3 - - - +
403A LEU* 3.0 48.5 + - + +
404A VAL 3.7 2.0 - - - +
406A ASP* 1.3 75.6 - - - +
408A TYR* 1.3 68.0 + - + +
410A THR* 2.9 15.6 + - - -
411A PHE* 3.2 15.5 - - - -
512A ARG* 5.9 1.3 - - - +
514A ILE* 3.2 41.3 - - + -
515A LEU* 4.3 9.2 - - + -
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Residues in contact with TYR 408 (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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404A VAL* 2.9 38.9 + - + +
405A TYR* 4.4 3.4 - - - +
407A MET* 1.3 76.0 - - + +
409A SER* 1.3 62.5 + - - +
411A PHE* 3.1 15.6 + - - +
412A GLY 3.3 7.1 + - - -
413A PHE* 3.5 20.4 + + + -
416A ILE* 3.6 44.6 - - + -
468A PHE* 4.2 6.1 - - + +
470A LEU* 4.0 24.5 - - + -
480A CYS* 3.5 5.2 - - + +
481A GLY* 2.9 21.3 + - - -
514A ILE* 2.6 38.6 + - + -
515A LEU* 4.6 0.2 - - + -
521A PHE* 4.0 25.8 - + - -
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Residues in contact with SER 409 (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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405A TYR 3.1 18.2 + - - -
406A ASP* 2.7 16.6 + - - -
407A MET 3.1 0.6 - - - -
408A TYR* 1.3 79.9 - - - +
410A THR* 1.3 60.9 + - - +
411A PHE 3.1 0.2 - - - -
412A GLY* 3.3 13.6 + - - +
413A PHE 5.1 1.8 - - - +
637A LEU* 5.2 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