Contacts of the helix formed by residues 536 - 545 (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 GLY 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A LEU 3.5 2.2 + - - -
532A LEU* 3.3 26.2 + - - +
533A GLN 4.8 0.2 - - - -
534A GLU 3.6 1.0 - - - -
535A SER* 1.3 73.7 - - - +
537A ASN* 1.3 58.3 + - - -
538A GLY 3.0 0.2 - - - -
539A PHE* 3.0 21.7 + - - +
540A VAL* 3.3 14.2 + - - +
616A ASN* 3.5 25.1 - - - -
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Residues in contact with ASN 537 (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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535A SER 3.0 4.2 + - - +
536A GLY* 1.3 68.7 - - - -
538A GLY* 1.3 62.7 + - - +
539A PHE 3.2 0.2 - - - -
540A VAL* 3.7 6.9 - - + +
541A ARG* 2.9 75.1 + - - +
613A THR* 3.5 4.3 + - + +
614A THR* 3.8 17.7 - - - +
615A PHE 2.8 31.0 + - - +
616A ASN* 4.1 8.6 + - + +
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Residues in contact with GLY 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A PHE* 4.2 14.4 - - - +
509A SER* 5.0 8.7 + - - -
535A SER* 2.9 17.4 + - - -
537A ASN* 1.3 83.9 - - - +
539A PHE* 1.3 57.4 + - - +
541A ARG* 3.5 7.3 + - - +
542A HIS* 3.0 27.4 + - - +
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Residues in contact with PHE 539 (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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507A PHE* 3.3 29.8 - + + -
523A PHE* 4.2 28.7 - + - -
528A ALA* 3.9 14.8 - - - -
531A LEU* 3.7 33.7 - - + +
532A LEU* 3.3 29.6 - - + -
535A SER* 4.1 4.2 + - - -
536A GLY 3.0 11.7 + - - +
538A GLY* 1.3 74.6 - - - +
540A VAL* 1.3 66.9 + - - +
542A HIS* 3.1 7.4 + - - +
543A ASN* 3.0 43.1 + - - -
548A SER* 4.1 7.0 - - - -
550A ILE* 4.9 1.1 - - + -
570A GLY 4.1 0.9 - - - -
572A CYS* 4.0 16.2 - - - -
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Residues in contact with VAL 540 (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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532A LEU* 5.5 0.4 - - + -
536A GLY 3.3 13.6 + - - +
537A ASN* 3.8 8.1 - - - +
538A GLY 3.4 0.2 - - - -
539A PHE* 1.3 75.4 - - - +
541A ARG* 1.3 62.5 + - - +
543A ASN* 3.2 13.2 + - - +
544A VAL* 3.5 11.3 + - - +
569A ASN 4.1 6.3 - - - +
570A GLY* 3.5 31.2 + - - +
571A GLY* 5.0 1.4 - - - +
608A LEU* 3.3 34.3 - - + +
613A THR* 4.0 20.6 - - + -
615A PHE* 4.0 20.2 - - + +
616A ASN* 5.2 1.8 - - - -
617A SER* 5.6 0.9 - - - +
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Residues in contact with ARG 541 (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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509A SER* 4.2 28.5 + - - +
510A PRO* 5.4 2.0 - - + -
537A ASN* 2.9 39.2 + - - +
538A GLY* 3.7 6.0 - - - +
540A VAL* 1.3 77.1 - - - +
542A HIS* 1.3 62.8 + - - +
544A VAL* 3.1 27.3 + - - +
545A SER* 4.0 4.9 + - - -
611A PRO* 3.1 22.0 + - - +
612A ASN* 2.8 32.8 + - - +
613A THR* 2.6 29.1 + - + +
614A THR* 3.2 18.8 - - - +
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Residues in contact with HIS 542 (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* 4.3 12.0 - + - -
506A GLY 5.2 1.3 - - - -
507A PHE* 3.6 35.1 - + + -
508A SER 5.7 0.7 - - - -
509A SER* 6.2 3.8 - - - +
515A GLN* 3.3 44.5 + - + +
523A PHE* 5.1 2.7 - + - -
538A GLY 3.0 15.3 + - - +
539A PHE* 3.2 10.7 - + - +
541A ARG* 1.3 76.0 - - - +
543A ASN* 1.3 67.9 + - - +
544A VAL 3.2 1.4 + - - -
545A SER* 3.4 7.5 + - - -
546A CYS* 3.1 38.1 + - + +
548A SER* 3.7 16.5 + - - -
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Residues in contact with ASN 543 (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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303A SER 2.9 22.2 - - - +
539A PHE* 3.0 28.3 + - - -
540A VAL 3.2 9.6 + - - +
542A HIS* 1.3 79.4 + - - +
544A VAL* 1.3 60.0 + - - +
545A SER 3.4 0.2 - - - -
546A CYS 3.3 7.8 - - - +
548A SER* 2.5 29.4 + - - -
570A GLY 2.8 22.6 + - - -
571A GLY* 3.4 17.9 - - - +
572A CYS* 3.2 15.2 - - - +
573A GLN* 3.1 12.2 + - - +
604A LYS* 3.0 5.4 + - - -
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Residues in contact with VAL 544 (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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303A SER* 2.7 21.5 + - - -
304A HIS* 2.9 38.9 + - + +
540A VAL 3.6 9.4 - - - +
541A ARG* 3.1 18.7 + - - +
543A ASN* 1.3 78.4 - - - +
545A SER* 1.3 57.0 + - - +
608A LEU 3.4 22.9 - - - +
609A ARG 3.7 16.6 - - - +
610A ASP 3.7 21.5 - - - +
611A PRO* 4.1 17.0 - - + -
613A THR* 5.1 0.4 - - + -
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Residues in contact with SER 545 (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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303A SER* 3.4 11.3 + - - -
304A HIS* 5.4 0.2 - - - -
424A SER* 5.9 3.4 - - - -
425A LEU* 4.1 5.2 + - - +
517A PHE* 3.7 25.6 - - - +
541A ARG 4.2 5.0 + - - -
542A HIS* 3.4 8.2 + - - -
544A VAL* 1.3 83.3 - - - +
546A CYS* 1.3 65.0 + - - +
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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