Contacts of the helix formed by residues 526 - 535 (chain A) in PDB entry 1QIH
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 526 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A VAL* 2.9 41.1 + - + +
524A TRP 3.7 0.2 - - - -
525A ASN* 1.3 86.3 - - + +
527A PHE* 1.3 64.9 + - - +
528A LEU 3.8 0.4 - - - -
529A PRO* 3.9 2.6 - - - +
530A LYS* 3.4 21.5 + - - +
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Residues in contact with PHE 527 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A ALA* 4.4 10.5 - - + -
522A VAL* 3.2 10.0 + - + +
523A PHE* 3.8 30.3 - + - +
526A GLN* 1.3 76.9 - - - +
528A LEU* 1.3 64.6 + - - +
530A LYS* 3.1 15.9 + - + +
531A LEU* 2.9 56.6 + - + +
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Residues in contact with LEU 528 (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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360A VAL* 4.5 10.5 - - + -
362A HIS* 5.8 1.3 - - - +
363A ALA* 5.7 0.4 - - + -
367A GLY* 4.2 25.1 - - - +
370A ALA* 4.6 1.1 - - + -
371A VAL* 4.1 11.4 - - + -
398A HIS* 6.0 0.2 - - + -
523A PHE* 2.9 32.6 + - + +
524A TRP* 3.3 38.4 - - + +
527A PHE* 1.3 71.2 - - - +
529A PRO* 1.3 74.6 - - + +
531A LEU* 3.0 15.3 + - + +
532A LEU* 2.9 44.8 + - + +
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Residues in contact with PRO 529 (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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524A TRP 3.4 23.8 - - - +
525A ASN* 3.8 13.9 - - - +
526A GLN 3.9 10.1 - - - +
527A PHE 3.6 2.9 - - - -
528A LEU* 1.3 93.9 - - + +
530A LYS* 1.3 56.1 + - - +
532A LEU* 3.4 10.0 + - + +
533A ASN* 3.0 29.9 + - - +
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Residues in contact with LYS 530 (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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526A GLN 3.4 13.4 + - - +
527A PHE* 3.1 16.7 + - + +
529A PRO* 1.3 77.0 - - - +
531A LEU* 1.3 65.5 + - - +
533A ASN* 3.3 6.0 + - - +
534A ALA* 3.0 26.0 + - + +
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Residues in contact with LEU 531 (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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364A ASN* 4.1 2.2 - - - +
366A LEU* 4.1 23.8 - - + +
367A GLY* 4.0 22.7 - - - +
370A ALA* 3.9 20.6 - - + -
527A PHE* 2.9 46.5 + - + +
528A LEU* 3.0 11.9 + - + +
530A LYS* 1.3 78.1 - - - +
532A LEU* 1.3 68.3 + - + +
534A ALA* 3.2 4.3 + - - -
535A THR* 2.9 43.8 + - + +
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Residues in contact with LEU 532 (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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362A HIS* 3.9 34.1 - - + +
363A ALA* 3.8 32.1 - - + -
364A ASN* 3.9 21.6 + - - +
367A GLY* 4.5 3.1 - - - -
528A LEU* 2.9 37.9 + - + +
529A PRO* 3.8 7.4 - - + +
531A LEU* 1.3 82.5 - - + +
533A ASN* 1.3 58.2 + - - +
535A THR* 3.0 23.0 - - - +
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Residues in contact with ASN 533 (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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529A PRO 3.0 18.1 + - - +
530A LYS* 3.8 6.5 - - - +
531A LEU 3.1 0.2 - - - -
532A LEU* 1.3 77.0 - - - +
534A ALA* 1.3 62.5 + - - +
535A THR 4.0 3.0 - - - +
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Residues in contact with ALA 534 (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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530A LYS* 3.0 20.1 + - + +
531A LEU* 3.9 4.0 - - - +
533A ASN* 1.3 80.2 - - - +
535A THR* 1.3 66.4 + - + +
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Residues in contact with THR 535 (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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364A ASN* 2.7 35.3 + - - -
366A LEU* 3.5 26.8 - - + +
531A LEU* 2.9 26.1 + - + +
532A LEU* 3.0 17.1 - - - +
533A ASN 4.0 2.9 - - - +
534A ALA* 1.3 87.4 - - + +
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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