Contacts of the helix formed by residues 565 - 570 (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 VAL 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A SER* 3.4 13.1 - - - +
564A PRO* 1.3 75.6 - - + +
566A GLU* 1.3 59.8 + - - +
568A TRP* 2.9 19.5 + - + +
569A ASN* 2.8 42.7 + - - +
588A VAL* 3.7 29.4 - - + -
661A HIS* 4.2 16.2 - - + +
662A GLY* 3.5 35.4 - - - +
697A LEU 4.3 5.2 - - - +
699A LEU* 4.5 3.1 - - + -
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Residues in contact with GLU 566 (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* 4.0 14.4 - - + -
532A LEU* 3.4 20.8 - - + +
563A SER* 4.4 9.5 + - - +
564A PRO 3.5 0.4 - - - -
565A VAL* 1.3 77.9 - - - +
567A MET* 1.3 61.3 + - + +
569A ASN* 3.8 8.6 + - - +
570A GLY 3.7 6.9 + - - -
617A SER* 3.5 26.9 + - - -
618A ARG* 3.3 47.1 + - - +
664A GLY* 5.0 6.2 + - - -
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Residues in contact with MET 567 (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* 3.5 38.1 - - + +
528A ALA* 3.7 18.4 - - + -
529A LEU* 3.9 18.8 - - + -
532A LEU* 4.3 10.5 - - - -
550A ILE* 3.9 12.1 - - + -
562A TYR* 3.9 28.7 - - + -
563A SER 4.1 6.5 - - - +
564A PRO 3.1 11.0 - - - +
565A VAL 3.0 0.6 - - - -
566A GLU* 1.3 78.3 - - + +
568A TRP* 1.3 60.2 + - - +
570A GLY* 2.9 18.0 + - - -
572A CYS* 3.2 28.6 + - + +
575A VAL* 3.6 19.5 - - + -
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Residues in contact with TRP 568 (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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306A LEU* 3.5 44.5 - - + +
564A PRO* 3.0 30.7 + - + -
565A VAL* 2.9 24.7 + - + +
567A MET* 1.3 78.1 - - - +
569A ASN* 1.3 59.8 + - - +
570A GLY 2.9 0.2 - - - -
571A GLY* 2.9 20.1 + - - -
572A CYS 3.6 11.0 - - - -
573A GLN 5.0 2.6 + - - -
575A VAL* 3.9 18.1 - - + +
588A VAL* 3.7 22.9 - - + -
589A TYR* 3.8 18.2 + + - -
592A CYS* 3.3 32.8 - - + -
593A PHE* 3.7 25.5 - + - -
608A LEU* 3.8 10.9 - - - +
697A LEU* 5.0 3.7 - - + +
699A LEU* 4.5 8.5 - - + -
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Residues in contact with ASN 569 (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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540A VAL* 4.1 1.4 - - - +
565A VAL* 2.8 28.3 + - - +
566A GLU* 3.8 15.2 + - - +
567A MET 3.2 0.2 - - - -
568A TRP* 1.3 77.5 - - - +
570A GLY* 1.3 55.9 + - - +
571A GLY 3.3 1.1 + - - -
608A LEU* 3.8 4.6 - - - +
615A PHE* 3.3 25.6 - - - -
617A SER* 3.3 32.0 + - - +
662A GLY 3.5 23.4 + - - -
663A VAL* 3.5 9.3 - - - +
697A LEU* 3.6 36.6 - - + +
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Residues in contact with GLY 570 (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* 3.8 24.5 - - - +
539A PHE 4.1 0.7 - - - -
540A VAL* 3.5 25.5 + - - -
543A ASN* 2.8 19.9 + - - -
566A GLU* 3.7 2.2 + - - -
567A MET 2.9 9.8 + - - -
569A ASN* 1.3 78.2 - - - +
571A GLY* 1.3 57.0 + - - +
572A CYS* 3.1 6.9 - - - -
617A SER* 5.7 1.1 - - - -
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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