Contacts of the helix formed by residues 395 - 408 (chain A) in PDB entry 1QAS
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 LEU 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A SER* 1.3 73.9 - - - +
396A GLU* 1.3 57.5 + - - +
398A GLN* 3.6 16.2 + - - +
399A ARG* 3.0 47.6 + - - +
487A LYS* 3.6 33.2 - - - +
488A LEU 3.7 2.5 - - - +
489A VAL* 3.3 29.4 - - + +
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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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350A GLN* 2.9 32.6 + - - +
394A SER* 3.1 7.8 + - - +
395A LEU* 1.3 78.5 - - - +
397A GLN* 1.3 62.9 + - - +
399A ARG* 3.0 44.3 + - - +
400A VAL* 3.3 15.5 + - - +
403A ARG* 5.8 0.9 + - - -
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Residues in contact with GLN 397 (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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346A ASP* 3.1 33.6 + - - +
347A GLY 2.8 45.4 + - - +
350A GLN* 3.3 45.2 + - - +
352A PRO* 3.2 17.1 - - + +
393A CYS* 3.9 10.8 - - + -
394A SER* 3.2 7.5 + - - +
396A GLU* 1.3 76.2 - - - +
398A GLN* 1.3 59.3 + - - +
400A VAL* 3.1 7.9 + - - +
401A MET* 2.9 30.5 + - - +
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Residues in contact with GLN 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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391A ASN* 3.0 27.9 + - - +
393A CYS* 2.9 25.7 + - + +
394A SER 2.9 23.8 + - - +
395A LEU* 3.6 12.7 - - - +
397A GLN* 1.3 73.4 - - - +
399A ARG* 1.3 61.6 + - - +
401A MET* 3.2 11.5 - - - +
402A ALA* 2.9 29.1 + - - +
487A LYS* 3.0 24.6 + - - +
488A LEU* 3.4 8.7 - - - +
489A VAL* 3.1 36.8 + - + +
492A LEU* 3.7 9.3 - - + +
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Residues in contact with ARG 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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395A LEU* 3.0 44.5 + - - +
396A GLU* 3.0 37.7 + - - +
398A GLN* 1.3 79.5 - - - +
400A VAL* 1.3 50.9 + - - +
402A ALA* 3.4 7.4 + - - +
403A ARG* 2.7 63.2 + - - +
489A VAL* 3.4 13.1 - - + +
491A GLU* 3.0 27.2 + - - +
327B GLU* 3.0 30.2 + - - -
331B ARG* 3.9 19.2 - - - +
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Residues in contact with VAL 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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350A GLN* 3.3 25.4 - - + +
351A GLU* 3.7 5.6 - - - +
352A PRO* 3.4 24.0 - - + -
396A GLU* 3.4 23.3 - - - +
397A GLN* 3.1 12.3 + - + +
399A ARG* 1.3 77.8 - - - +
401A MET* 1.3 61.1 + - - +
403A ARG* 3.2 9.2 + - + +
404A HIS* 3.0 42.4 + - + +
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Residues in contact with MET 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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344A CYS* 3.3 29.6 - - + -
352A PRO* 3.9 17.3 - - + -
366A PHE* 3.5 29.2 - - + -
389A LEU* 4.5 15.7 - - + -
391A ASN* 3.2 30.5 - - + +
393A CYS* 3.8 14.4 - - - -
397A GLN 2.9 14.8 + - - +
398A GLN* 3.2 12.8 - - - +
400A VAL* 1.3 75.5 - - - +
402A ALA* 1.3 57.1 + - - +
404A HIS* 3.2 4.4 + - - +
405A LEU* 2.9 34.9 + - - +
492A LEU* 4.3 15.7 - - + -
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Residues in contact with ALA 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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398A GLN 2.9 16.7 + - - +
399A ARG 3.6 4.7 - - - +
401A MET* 1.3 75.3 - - - +
403A ARG* 1.3 65.1 + - + +
405A LEU* 3.3 3.3 + - - +
406A ARG* 3.1 31.5 + - - +
491A GLU* 3.8 26.2 - - + +
492A LEU* 4.0 4.7 - - + +
495A MET* 3.7 28.2 - - + +
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Residues in contact with ARG 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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396A GLU* 5.8 1.0 + - - -
399A ARG* 2.7 53.4 + - - +
400A VAL* 3.2 7.8 + - - +
402A ALA* 1.3 76.9 - - - +
404A HIS* 1.3 61.7 + - + +
406A ARG* 3.9 6.3 - - - +
407A ALA* 2.9 32.1 + - - +
491A GLU* 4.5 7.7 - - - +
316B LEU* 3.8 28.5 - - - +
317B GLU* 2.7 31.9 + - - +
323B PRO* 3.3 31.0 - - - +
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Residues in contact with HIS 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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351A GLU* 2.9 34.7 + - - -
352A PRO* 4.5 1.6 - - + -
366A PHE* 4.0 21.8 - + + -
367A CYS* 3.7 28.2 - - + +
370A LEU* 3.8 5.8 - - + -
371A ARG* 5.1 5.1 + - - -
400A VAL* 3.0 35.2 + - + +
401A MET 3.5 6.1 - - - +
403A ARG* 1.3 75.0 - - + +
405A LEU* 1.3 60.0 + - - +
407A ALA* 4.4 4.8 - - - +
408A ILE* 2.7 48.0 + - + +
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Residues in contact with LEU 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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366A PHE* 3.9 13.7 - - + -
370A LEU* 3.6 27.8 - - + -
387A LEU* 4.7 1.6 - - + -
389A LEU* 4.4 7.9 - - + -
401A MET 2.9 17.9 + - - +
402A ALA* 3.5 7.0 - - - +
404A HIS* 1.3 74.7 - - - +
406A ARG* 1.3 57.8 + - - +
409A LEU* 2.9 56.0 + - + +
413A LEU* 4.4 5.5 - - + +
437A LEU* 3.7 37.2 - - + -
492A LEU* 4.0 11.7 - - + -
495A MET* 3.8 21.5 - - + -
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Residues in contact with ARG 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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402A ALA* 3.1 16.4 + - - +
403A ARG* 4.1 6.1 - - - +
405A LEU* 1.3 78.8 - - - +
407A ALA* 1.3 55.2 + - - +
410A GLY* 3.1 26.2 + - - +
413A LEU* 4.3 9.7 - - + +
415A ASP* 4.4 24.2 + - - +
495A MET* 4.1 21.5 - - + -
321B THR 3.9 10.6 + - - +
323B PRO* 5.0 9.4 - - - +
360B PHE* 2.4 33.9 + - - +
361B THR 3.6 0.4 + - - -
362B SER* 3.1 38.9 - - - +
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Residues in contact with ALA 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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403A ARG 2.9 20.7 + - - +
404A HIS* 4.1 4.7 - - - +
406A ARG* 1.3 77.4 - - - +
408A ILE* 1.3 67.4 + - + +
410A GLY* 4.4 2.8 + - - -
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Residues in contact with ILE 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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367A CYS* 3.2 44.2 - - + +
370A LEU* 3.7 35.0 - - + +
371A ARG* 3.8 29.8 - - + +
374A ARG* 3.2 30.3 + - - +
404A HIS* 2.7 33.9 + - + +
407A ALA* 1.3 78.2 - - + +
409A LEU* 1.3 61.5 + - + +
410A GLY* 4.7 0.3 - - - -
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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