Contacts of the strand formed by residues 592 - 598 (chain B) in PDB entry 3K5N
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 592 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B LEU* 4.2 20.9 - - + +
419B ASP 3.4 10.1 - - - +
420B TYR* 2.9 35.4 - - + +
530B THR* 4.1 17.3 - - + -
549B THR* 6.3 1.1 - - + -
570B VAL* 3.3 30.0 - - + +
573B VAL* 3.9 27.6 - - + -
574B ASN* 3.3 26.4 + - - +
590B LEU 4.1 0.2 - - - -
591B GLU* 1.3 80.2 - - - +
593B GLU* 1.3 94.5 + - - +
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Residues in contact with GLU 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 2.8 5.7 - - - +
419B ASP* 2.4 60.9 + - - +
420B TYR 4.2 0.5 - - - -
421B LYS* 2.2 46.7 + - + +
570B VAL* 4.7 2.2 - - - -
591B GLU* 3.4 12.3 - - + +
592B LEU* 1.3 87.5 - - - +
594B TYR* 1.3 65.5 + - - +
595B GLU* 5.2 10.6 - - - +
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Residues in contact with TYR 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU* 3.9 25.6 - - + -
417B VAL 4.5 3.6 - - - -
418B LEU* 3.9 9.9 - - + -
559B GLU* 5.2 4.7 + - - -
562B ALA 4.3 2.0 - - - -
563B ALA* 4.0 24.8 + - + +
566B GLY* 3.9 22.7 - - - +
567B ARG* 4.3 17.0 - - + -
570B VAL* 3.7 22.9 - - + +
593B GLU* 1.3 74.7 - - - +
595B GLU* 1.3 71.9 + - - +
596B THR* 4.0 17.3 - - - -
597B HIS* 3.6 20.1 + - - +
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Residues in contact with GLU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B VAL* 2.7 27.3 + - + +
419B ASP* 3.5 47.6 - - + +
593B GLU* 4.1 11.8 - - - +
594B TYR* 1.3 88.9 - - - +
596B THR* 1.3 72.1 + - + +
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Residues in contact with THR 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B LEU* 3.5 4.0 - - - +
417B VAL* 2.7 45.9 + - + +
594B TYR* 4.0 9.8 - - - -
595B GLU* 1.3 93.3 - - + +
597B HIS* 1.3 61.1 + - - +
598B PHE* 4.1 22.8 - - + -
621B ILE* 5.8 8.1 - - + -
628B ARG* 6.2 2.5 - - - +
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Residues in contact with HIS 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B SER* 2.9 34.0 + - - -
415B VAL 3.4 3.6 - - - -
416B LEU* 3.0 32.8 - - + -
557B HIS* 4.8 7.6 - - - +
558B SER* 4.8 11.7 + - - -
559B GLU* 4.9 12.2 + - - +
562B ALA* 3.4 24.3 - - + +
594B TYR* 3.6 17.5 + - - +
596B THR* 1.3 76.8 - - - +
598B PHE* 1.3 72.3 + - - +
599B CYS* 4.0 19.4 + - + -
621B ILE* 4.1 14.1 - - - +
622B GLN 4.9 1.4 + - - -
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Residues in contact with PHE 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B SER* 2.7 7.5 - - - -
415B VAL* 2.6 44.6 + - - +
417B VAL* 5.0 8.3 - - + -
596B THR* 4.1 22.0 - - + -
597B HIS* 1.3 75.9 - - - +
599B CYS* 1.3 59.9 + - - +
600B ARG 3.9 0.9 - - - +
601B PHE* 3.0 50.0 - + + -
617B TYR* 4.5 12.3 - + - -
619B GLY* 4.3 3.1 - - - -
620B LEU 2.6 27.8 - - - +
621B ILE* 3.4 30.1 - - + -
630B VAL* 3.9 28.5 - - + -
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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