Contacts of the strand formed by residues 565 - 569 (chain A) in PDB entry 3I7K
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 SER 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A ILE 3.8 0.7 - - - +
559A GLY* 3.5 2.6 - - - -
560A LEU* 2.9 29.3 + - - +
563A ASP* 2.6 33.7 + - - -
564A ILE* 1.3 78.0 - - - +
566A ALA* 1.3 61.0 + - - +
567A ARG* 2.7 26.0 + - - -
579A LYS* 4.7 0.2 - - - -
580A GLU 3.2 16.2 - - - -
581A MET* 3.7 11.9 - - - -
582A LEU* 4.7 2.0 - - - -
588A PRO* 4.4 4.7 - - - +
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Residues in contact with ALA 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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558A ILE 3.1 4.5 - - - +
559A GLY* 5.0 0.7 - - - -
565A SER* 1.3 74.6 - - - +
567A ARG* 1.3 61.1 + - - +
568A ILE* 5.9 0.4 - - - -
578A HIS 4.2 0.2 - - - +
579A LYS* 3.3 1.2 - - - -
580A GLU* 2.7 43.9 + - + +
582A LEU* 4.9 7.2 - - + +
591A ILE* 3.6 26.7 - - + -
604A CYS* 4.5 15.0 - - + -
614A PHE* 6.3 3.6 - - + -
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Residues in contact with ARG 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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534A MET* 3.5 23.9 - - + +
535A GLU* 3.9 15.2 + - - +
556A CYS 3.5 3.3 - - - +
557A ALA* 3.6 3.1 - - - +
558A ILE* 2.8 59.7 + - + +
560A LEU* 3.5 19.1 - - + +
563A ASP* 2.6 29.9 + - - -
565A SER* 2.7 27.8 + - - -
566A ALA* 1.3 73.7 - - - +
568A ILE* 1.3 69.9 + - - +
569A LEU* 4.5 1.8 - - + -
576A LEU* 3.8 20.4 - - + +
578A HIS 3.3 12.6 - - - +
579A LYS* 3.2 43.3 - - + +
591A ILE* 5.1 1.0 - - - +
602A LEU* 5.0 0.7 - - - +
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Residues in contact with ILE 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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555A LEU* 3.8 30.5 - - + -
556A CYS 3.3 6.5 - - - +
567A ARG* 1.3 77.9 - - - +
569A LEU* 1.3 69.5 + - - +
576A LEU* 4.4 0.2 - - - +
577A LEU* 3.4 32.1 + - + +
578A HIS* 3.0 30.9 + - + +
593A MET* 5.2 0.4 - - + -
602A LEU* 3.7 23.3 - - + -
616A LEU* 3.6 38.1 - - + -
620A THR 4.4 6.5 - - - +
621A GLY* 4.7 3.6 - - - -
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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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516A LEU* 4.4 22.2 - - + -
532A THR* 6.5 0.2 - - + -
534A MET* 4.6 14.4 - - - -
541A LEU* 6.2 0.4 - - + -
555A LEU* 3.5 13.2 - - - +
556A CYS* 2.8 48.1 + - + +
558A ILE* 4.0 27.6 - - + -
567A ARG* 4.5 1.3 - - + -
568A ILE* 1.3 85.6 - - - +
570A LYS* 1.3 60.7 + - - +
571A LEU 4.0 0.2 - - - -
574A PHE* 3.6 28.7 - - + +
575A GLU 3.9 0.2 - - - -
576A LEU* 3.9 34.3 - - + -
577A LEU* 3.6 7.1 - - - +
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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