Contacts of the strand formed by residues 613 - 621 (chain A) in PDB entry 5NK4
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 VAL 613 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A ILE* 3.8 25.6 - - + -
609A HIS 4.0 1.6 - - - +
610A PRO 3.0 15.5 + - - +
611A SER 3.3 2.4 - - - +
612A CYS* 1.3 81.4 - - - +
614A THR* 1.3 66.8 + - - +
615A ARG* 4.2 3.8 + - + +
631A MET 3.6 3.8 - - - +
632A LEU* 4.0 6.7 - - + -
643A VAL* 5.5 1.1 - - + -
645A ILE* 3.7 32.3 - - + -
682A ILE* 4.0 12.3 - - + -
689A MET* 4.3 17.3 - - + -
691A ILE* 3.9 17.0 - - + -
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Residues in contact with THR 614 (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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611A SER 5.5 1.4 + - - -
612A CYS 4.1 1.8 + - - -
613A VAL* 1.3 74.7 + - - +
615A ARG* 1.3 70.4 + - - +
616A GLN* 3.7 14.2 + - + +
630A GLY* 3.1 6.2 - - - -
631A MET* 3.0 41.2 + - - +
645A ILE* 4.0 2.5 - - - +
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Residues in contact with ARG 615 (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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613A VAL* 4.1 5.3 + - + +
614A THR* 1.3 79.7 - - - +
616A GLN* 1.3 60.3 + - - +
626A GLU* 5.1 0.4 + - - -
628A TYR* 3.5 57.6 + - + -
629A LYS 4.2 3.1 - - - -
645A ILE* 3.9 19.7 - - + -
647A THR* 4.0 12.9 - - - +
687A PRO* 4.5 15.4 - - - +
689A MET* 3.3 30.1 - - - +
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Residues in contact with GLN 616 (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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614A THR* 3.8 19.0 - - + +
615A ARG* 1.3 77.9 - - - +
617A LYS* 1.3 65.4 + - + +
618A VAL* 5.8 0.2 - - - +
628A TYR* 5.3 1.8 - - - -
629A LYS* 2.8 45.9 + - + +
630A GLY* 3.7 2.0 - - - -
631A MET* 3.2 25.1 - - - +
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Residues in contact with LYS 617 (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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616A GLN* 1.3 82.9 - - + +
618A VAL* 1.3 76.6 + - - +
619A ILE* 3.9 11.8 - - + +
628A TYR* 3.1 7.6 - - - -
629A LYS* 2.8 41.7 + - + -
1001A 90E 5.3 14.3 - - - -
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Residues in contact with VAL 618 (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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616A GLN 5.8 0.2 - - - +
617A LYS* 1.3 84.8 - - - +
619A ILE* 1.3 62.6 + - - +
620A GLY 3.9 18.4 - - - +
621A ALA* 4.9 5.4 - - + -
626A GLU* 4.7 11.2 - - + -
627A VAL 3.7 5.4 - - - +
628A TYR* 3.5 25.6 - - + +
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Residues in contact with ILE 619 (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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617A LYS* 3.9 20.0 - - + +
618A VAL* 1.3 79.9 - - - +
620A GLY* 1.3 58.8 + - - +
627A VAL* 2.8 39.1 + - + +
628A TYR 4.0 2.7 - - - +
629A LYS* 4.0 21.3 - - + +
644A ALA* 4.9 0.4 - - + -
694A TYR* 4.1 9.9 - - + +
1001A 90E 3.6 73.7 - - + +
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Residues in contact with GLY 620 (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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618A VAL* 3.7 5.3 - - - +
619A ILE* 1.3 78.4 - - - +
621A ALA* 1.3 64.6 + - - +
626A GLU* 3.5 4.2 - - - +
627A VAL* 2.8 42.3 + - - +
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Residues in contact with ALA 621 (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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618A VAL* 4.9 6.5 - - + -
620A GLY* 1.3 77.1 - - - +
622A GLY* 1.3 60.1 - - - +
625A GLY 3.9 5.2 - - - -
626A GLU* 4.2 14.1 - - + +
627A VAL* 5.1 0.6 - - - +
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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