Contacts of the helix formed by residues 565 - 571 (chain A) in PDB entry 5HLB
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 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A TYR* 3.7 25.0 - - + -
520A ALA* 4.4 5.2 - - + -
521A LEU* 3.9 28.5 - - + -
527A TYR* 4.2 20.9 - - + -
528A ARG 3.3 24.9 - - - +
529A LEU* 3.5 14.5 + - + +
531A THR* 2.8 18.6 + - - +
533A ILE* 3.7 18.1 - - + +
564A MET* 1.4 70.9 - - - +
566A VAL* 1.3 60.8 + - - +
568A ALA* 3.5 2.8 + - - +
569A LEU* 3.4 20.3 + - + +
580A LEU* 4.2 19.5 - - + -
673A THR* 5.0 2.0 - - + +
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Residues in contact with VAL 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* 3.0 30.9 + - + +
564A MET* 3.9 20.0 - - + -
565A LEU* 1.3 78.3 - - - +
567A ASP* 1.3 55.1 + - - +
570A THR* 2.6 40.0 + - - +
672A TRP* 4.0 26.9 - - + -
673A THR* 3.5 19.6 - - + +
676A GLN* 4.9 4.0 - - + -
781A ARG* 3.5 26.2 - - - +
783A LEU* 4.0 12.8 - - + -
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Residues in contact with ASP 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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563A VAL* 5.2 4.9 - - + -
564A MET* 3.1 20.5 + - - +
566A VAL* 1.3 76.5 - - - +
568A ALA* 1.4 64.4 + - - +
570A THR* 4.0 9.9 + - - +
571A ARG* 3.0 44.2 + - - +
573A MET* 4.1 2.6 - - - +
680A ARG* 4.3 9.0 + - - -
781A ARG* 2.6 44.5 + - - -
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Residues in contact with ALA 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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517A TYR* 3.5 21.1 + - + +
533A ILE* 4.3 6.1 - - + -
563A VAL* 3.8 17.6 - - + +
564A MET 3.0 14.6 + - - +
565A LEU 3.5 6.7 + - - +
567A ASP* 1.4 75.7 - - - +
569A LEU* 1.4 57.0 + - - +
572A SER* 3.3 4.2 + - - -
573A MET* 2.9 42.3 + - - +
576A PRO* 3.9 11.9 - - + -
577A THR* 4.7 0.2 + - - -
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Residues in contact with LEU 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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513A LYS* 3.9 20.0 - - + -
514A PRO* 4.2 13.9 - - + -
517A TYR* 3.6 55.6 + - + -
521A LEU* 6.1 0.4 - - + -
565A LEU* 3.4 5.0 + - + +
567A ASP 3.3 0.4 - - - -
568A ALA* 1.4 73.1 - - - +
570A THR* 1.4 66.9 + - - +
571A ARG 3.2 1.8 - - - -
572A SER* 3.1 11.2 + - - +
670A THR* 4.7 13.9 - - + +
673A THR* 3.9 30.1 - - + -
674A MET* 5.1 3.6 - - + -
677A VAL* 4.1 10.4 - - + +
698A LYS* 4.0 17.7 - - + -
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Residues in contact with THR 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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566A VAL* 2.6 25.3 + - - +
567A ASP* 3.4 12.3 + - - +
569A LEU* 1.4 76.2 - - - +
571A ARG* 1.3 63.0 - - + +
572A SER 3.4 0.9 + - - -
673A THR* 3.9 4.8 - - - +
676A GLN* 3.4 44.3 - - + +
677A VAL* 3.4 24.0 - - - +
680A ARG* 4.2 12.3 - - + +
681A GLY* 3.8 12.6 - - - +
682A THR* 3.4 14.0 + - - -
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Residues in contact with ARG 571 (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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553A ASP* 5.5 5.2 - - - +
554A ASP* 5.0 9.3 + - - -
558A SER* 5.2 1.8 + - - -
563A VAL* 5.1 4.6 - - - +
567A ASP* 3.0 28.1 + - - +
570A THR* 1.3 84.7 - - + +
572A SER* 1.4 69.5 + - - +
573A MET* 3.2 43.6 + - + +
680A ARG 5.8 0.7 - - - +
681A GLY* 4.9 6.3 - - - -
682A THR* 3.7 14.4 - - - +
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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