Contacts of the strand formed by residues 593 - 600 (chain A) in PDB entry 3VI4
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 ARG 593 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A GLN* 3.5 20.2 + - - +
509A TRP* 4.1 15.6 - - - +
566A ALA* 3.5 22.3 - - - +
567A LEU 3.4 8.5 - - - +
568A ASN* 4.1 16.8 - - + +
591A LYS* 4.0 20.5 - - - +
592A SER* 1.3 80.2 + - - +
594A ILE* 1.3 67.0 + - - +
595A GLU* 3.1 33.4 + - + +
2016A NAG 4.1 25.1 + - - -
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Residues in contact with ILE 594 (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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456A ALA* 3.5 28.5 - - + +
457A SER* 4.6 1.3 - - - -
458A LEU* 4.1 28.5 - - + +
565A ILE 4.1 0.2 - - - +
566A ALA* 3.5 2.6 - - - -
567A LEU* 2.7 69.7 + - + +
569A PHE* 6.1 0.7 - - + -
591A LYS* 5.5 5.8 - - + +
593A ARG* 1.3 76.1 - - - +
595A GLU* 1.3 70.1 + - - +
596A ASP* 6.3 0.4 - - + -
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Residues in contact with GLU 595 (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 TRP* 3.2 42.6 - - + -
565A ILE 3.4 3.4 - - - +
566A ALA* 4.1 11.7 - - + -
593A ARG* 3.1 35.8 + - + +
594A ILE* 1.3 85.5 - - - +
596A ASP* 1.3 62.2 + - - +
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Residues in contact with ASP 596 (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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458A LEU* 3.6 33.5 - - + +
459A THR* 4.5 1.2 - - - +
460A ILE* 3.5 29.9 + - + +
509A TRP* 5.4 0.2 - - - -
564A HIS* 3.6 3.1 + - - +
565A ILE* 2.7 41.1 + - + +
594A ILE* 6.3 0.4 - - + -
595A GLU* 1.3 75.4 - - - +
597A LYS* 1.3 80.2 + - - +
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Residues in contact with LYS 597 (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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460A ILE* 3.2 22.3 - - - +
463A ALA* 5.2 4.2 - - - +
562A PRO* 4.3 22.1 - - + +
563A ILE 3.3 8.5 - - - +
564A HIS* 3.6 34.6 + - + +
565A ILE* 4.5 0.2 - - - -
596A ASP* 1.3 87.7 + - - +
598A ALA* 1.3 61.9 + - - +
599A GLN* 4.4 15.7 - - - +
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Residues in contact with ALA 598 (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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460A ILE* 4.5 11.9 - - + -
463A ALA* 3.8 13.0 - - - +
465A PHE* 4.3 21.5 - - + -
482A ILE* 4.5 7.2 - - + -
548A ILE* 5.8 2.0 - - + -
563A ILE* 2.7 52.4 + - + +
565A ILE* 4.7 6.3 - - + -
597A LYS* 1.3 76.1 - - - +
599A GLN* 1.3 60.6 + - - +
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Residues in contact with GLN 599 (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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463A ALA 3.4 7.8 + - - +
464A MET* 3.5 7.4 - - - +
465A PHE* 2.6 32.3 + - - -
560A LEU 5.6 2.9 - - - +
562A PRO* 3.6 27.1 - - + +
597A LYS* 4.4 21.2 - - - +
598A ALA* 1.3 72.4 - - - +
600A ILE* 1.3 63.9 + - - +
601A LEU 3.9 0.2 + - - -
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Residues in contact with ILE 600 (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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465A PHE* 3.5 15.0 - - + +
467A PRO* 4.0 23.3 - - + -
518A ARG* 4.3 14.1 - - - +
550A LEU* 4.0 19.5 - - + -
556A PHE* 4.6 9.6 - - + -
558A ASP 4.5 2.0 - - - +
559A LYS* 3.8 44.3 - - + +
560A LEU 5.2 5.6 + - - +
561A SER 4.8 2.7 - - - +
562A PRO* 5.7 0.8 - - - +
563A ILE* 3.7 27.3 - - + +
599A GLN* 1.3 76.1 - - - +
601A LEU* 1.3 71.0 + - - +
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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