Contacts of the helix formed by residues 525 - 534 (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 GLU 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524A SER* 1.3 72.4 - - - +
526A SER* 1.3 67.6 + - - +
529A LEU* 3.1 37.5 + - + +
550A ILE* 4.1 2.9 - - - -
551A TYR 3.0 15.5 + - - +
552A PRO* 3.6 3.8 - - - +
553A ALA* 2.8 32.9 + - + +
555A TRP* 4.8 2.6 - - - -
556A ARG* 2.7 46.1 + - - -
562A TYR* 3.3 21.2 - - + +
567A MET* 3.5 21.7 - - + +
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Residues in contact with SER 526 (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 SER* 2.8 24.6 + - - -
525A GLU* 1.3 84.0 - - - +
527A ARG* 1.3 62.9 + - - +
529A LEU* 3.4 11.2 + - - +
530A ARG* 3.1 21.5 + - - +
553A ALA* 5.3 6.0 - - - +
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Residues in contact with ARG 527 (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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504A PHE* 3.2 53.3 + - - +
522A SER 3.3 22.6 + - - -
523A PHE* 3.7 20.3 - - + +
524A SER* 3.2 19.3 + - - +
526A SER* 1.3 78.1 + - - +
528A ALA* 1.3 56.3 + - - +
530A ARG* 2.9 36.5 + - - +
531A LEU* 2.8 40.6 + - + +
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Residues in contact with ALA 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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523A PHE* 4.0 8.0 - - + +
524A SER 3.0 16.9 + - - +
525A GLU 3.6 4.3 - - - +
527A ARG* 1.3 76.2 - - - +
529A LEU* 1.3 62.7 + - - +
531A LEU* 3.4 2.8 + - - +
532A LEU* 3.0 31.4 + - + +
539A PHE* 3.9 11.7 - - + -
550A ILE* 3.9 22.2 - - + -
567A MET* 3.7 22.9 - - + -
572A CYS* 5.4 0.2 - - - -
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Residues in contact with LEU 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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525A GLU* 3.1 29.5 + - + +
526A SER* 3.6 9.4 - - - +
528A ALA* 1.3 76.4 - - - +
530A ARG* 1.3 62.7 + - - +
532A LEU* 3.2 5.4 + - + +
533A GLN* 3.0 23.6 + - - +
566A GLU* 4.0 15.9 - - + -
567A MET* 3.9 19.3 - - + -
618A ARG* 3.3 28.5 + - - +
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Residues in contact with ARG 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 SER 3.1 12.2 + - - +
527A ARG* 2.9 41.2 + - - +
529A LEU* 1.3 77.4 - - - +
531A LEU* 1.3 68.7 + - - +
533A GLN* 3.1 7.1 + - - +
534A GLU* 2.8 66.2 + - + +
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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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504A PHE* 3.9 13.7 - - + -
507A PHE* 3.8 26.5 - - + -
523A PHE* 3.1 42.4 - - + -
527A ARG* 2.8 25.4 + - + +
530A ARG* 1.3 92.1 - - - +
532A LEU* 1.3 58.0 + - - +
534A GLU* 4.4 11.0 - - - +
535A SER* 2.8 35.9 + - - +
536A GLY 3.5 0.9 + - - -
539A PHE* 3.7 19.9 - - + -
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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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528A ALA* 3.0 30.2 + - + +
529A LEU* 3.5 7.9 - - - +
530A ARG 3.2 0.2 - - - -
531A LEU* 1.3 76.1 - - - +
533A GLN* 1.3 61.7 + - - +
536A GLY* 3.3 26.0 + - - +
539A PHE* 3.3 28.9 - - + -
540A VAL* 5.5 0.4 - - + -
566A GLU* 3.4 46.2 - - + +
567A MET* 4.3 13.7 - - - +
570A GLY* 3.8 24.7 - - - +
572A CYS* 5.0 2.5 - - - -
616A ASN* 4.4 2.1 + - - +
618A ARG* 4.1 17.0 - - + +
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Residues in contact with GLN 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 LEU 3.0 12.8 + - - +
530A ARG* 3.7 7.2 - - - +
532A LEU* 1.3 77.2 - - - +
534A GLU* 1.3 63.4 + - + +
536A GLY 4.8 0.2 - - - -
618A ARG* 3.1 47.0 + - - +
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Residues in contact with GLU 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 ARG* 2.8 54.4 + - + +
531A LEU* 4.2 9.0 - - - +
533A GLN* 1.3 85.1 - - + +
535A SER* 1.3 65.8 + - - +
536A GLY 3.6 0.7 - - - -
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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