Contacts of the strand formed by residues 594 - 602 (chain A) in PDB entry 3KRL
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 GLY 594 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A ALA* 3.9 0.7 - - - +
591A GLY 3.2 24.8 + - - +
592A ALA 3.6 0.8 - - - -
593A PHE* 1.3 79.9 - - - +
595A LYS* 1.3 64.5 + - - +
617A MET 3.3 9.6 - - - -
618A LEU 4.0 0.2 - - - -
619A LYS* 3.7 17.7 - - - +
799A LEU* 3.2 20.4 + - - +
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Residues in contact with LYS 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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584A PHE* 5.8 2.4 - - - -
587A THR* 4.1 16.6 - - + -
589A GLY 3.5 12.8 - - - +
590A ALA* 4.0 12.3 - - + -
594A GLY* 1.3 76.3 - - - +
596A VAL* 1.3 62.1 + - - +
597A VAL* 3.5 28.0 - - + -
616A LYS* 3.7 1.4 - - - -
617A MET* 2.9 52.7 + - + +
619A LYS* 3.8 34.3 - - + +
799A LEU* 3.8 11.7 + - - +
800A ALA* 5.0 0.2 - - - -
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Residues in contact with VAL 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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1A KRL 3.9 35.0 - - + +
587A THR* 3.8 2.3 - - - +
588A LEU* 2.9 27.8 + - + +
589A GLY* 3.0 15.2 + - - +
595A LYS* 1.3 75.5 - - - +
597A VAL* 1.3 65.7 + - - +
614A ALA* 4.0 24.2 - - + -
615A VAL 3.3 14.8 - - - +
616A LYS* 4.3 6.1 - - + +
799A LEU* 5.9 0.9 - - + -
800A ALA* 3.2 28.0 - - + -
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Residues in contact with VAL 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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584A PHE* 4.1 31.4 - - + -
585A GLY 4.2 5.4 - - - +
586A LYS 3.5 13.5 - - - +
587A THR* 4.1 9.0 - - - +
588A LEU* 3.9 5.2 - - - +
595A LYS* 3.5 32.3 - - + -
596A VAL* 1.3 78.3 - - - +
598A GLU* 1.3 74.7 + - - +
599A ALA* 4.7 0.4 - - + -
614A ALA* 3.3 4.0 - - - +
615A VAL* 2.9 33.5 + - + -
617A MET* 3.6 17.9 - - + -
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Residues in contact with GLU 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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585A GLY* 2.7 39.4 + - - -
586A LYS* 2.9 44.1 + - + +
588A LEU* 3.8 17.0 - - + +
597A VAL* 1.3 72.6 - - - +
599A ALA* 1.3 59.5 + - - +
612A LYS* 2.9 34.7 + - + -
613A VAL 3.4 7.9 - - - +
665A TYR* 2.9 30.8 + - + -
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Residues in contact with ALA 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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582A LEU* 4.8 2.7 - - + -
583A GLN 3.2 24.0 - - - +
584A PHE* 3.9 9.4 - - + -
585A GLY* 4.2 1.1 - - - +
597A VAL* 4.7 0.2 - - + -
598A GLU* 1.3 79.1 - - - +
600A THR* 1.3 66.2 + - - +
612A LYS* 3.3 12.2 - - - +
613A VAL* 2.9 33.9 + - + +
615A VAL* 4.1 23.1 - - + -
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Residues in contact with THR 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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581A ASN 3.5 4.5 - - - +
582A LEU* 3.8 1.5 - - - -
583A GLN* 3.1 38.0 + - - +
599A ALA* 1.3 81.5 + - - +
601A ALA* 1.3 60.0 + - - +
602A PHE* 3.8 19.4 + - + -
610A VAL* 3.1 35.9 - - + -
611A LEU 3.8 7.0 - - - +
612A LYS* 4.7 6.8 - - + +
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Residues in contact with ALA 601 (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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577A PHE* 4.0 8.1 - - + -
581A ASN 3.5 5.6 - - - -
582A LEU* 4.3 10.8 - - + -
599A ALA 4.3 0.2 - - - -
600A THR* 1.3 71.7 - - - +
602A PHE* 1.3 64.3 + - - +
603A GLY 3.4 3.3 + - - -
604A LEU* 3.6 24.3 + - + -
609A ALA 3.5 10.7 - - - +
610A VAL* 3.8 1.2 - - - -
611A LEU* 3.0 43.0 + - + +
613A VAL* 4.4 6.0 - - + +
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Residues in contact with PHE 602 (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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577A PHE* 3.8 0.9 - - - -
581A ASN* 3.1 49.0 + - + +
583A GLN* 4.0 26.5 - - + -
600A THR* 4.0 19.3 - - + -
601A ALA* 1.3 69.2 - - - +
603A GLY* 1.3 60.7 + - - +
609A ALA 4.2 2.5 - - - -
610A VAL* 3.4 35.2 - - + -
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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