Contacts of the strand formed by residues 689 - 696 (chain A) in PDB entry 1K2N
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 689 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585A ASP* 3.0 31.0 - - - +
586A SER* 3.1 0.9 - - - -
587A ILE* 3.1 26.5 + - + +
679A LYS* 5.7 5.6 - - + -
681A ILE 3.4 2.0 - - - +
682A TRP* 4.2 23.3 - - + -
687A LYS 3.1 11.6 + - - +
688A PHE* 1.3 74.4 - - - +
690A ILE* 1.3 69.4 + - - +
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Residues in contact with ILE 690 (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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586A SER* 3.2 11.0 - - - +
587A ILE* 3.3 32.3 - - + -
588A ILE* 3.7 14.1 - - + -
613A ILE* 5.2 0.2 - - + -
615A ASP* 4.0 12.3 - - + -
618A LEU* 5.0 0.7 - - + -
679A LYS* 3.5 12.5 - - - +
680A ILE* 3.3 30.7 + - + -
681A ILE* 2.7 37.3 + - + +
688A PHE* 3.5 14.6 - - + -
689A VAL* 1.3 84.2 - - - +
691A GLY* 1.3 62.9 + - - +
692A PHE* 3.7 22.0 - - + -
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Residues in contact with GLY 691 (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 PRO* 3.5 0.5 - - - +
583A LEU* 3.2 30.4 + - - +
586A SER* 3.2 8.4 - - - -
678A ILE 2.9 15.9 - - - -
679A LYS* 4.1 4.7 - - - -
680A ILE* 4.2 2.0 - - - -
690A ILE* 1.3 82.8 - - - +
692A PHE* 1.3 70.0 + - - -
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Residues in contact with PHE 692 (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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580A LEU* 3.5 27.6 - - + -
581A LYS 3.8 4.7 - - - +
582A PRO* 3.2 33.4 - - + -
583A LEU* 3.5 4.7 - - - -
588A ILE* 4.1 4.0 - - + -
592A LEU* 3.1 27.1 - - + -
603A ILE* 4.0 4.9 - - + -
613A ILE* 3.3 41.7 - - + -
676A ASP 3.6 1.2 - - - +
677A GLU* 3.5 1.2 - - - -
678A ILE* 2.9 38.4 + - + +
680A ILE* 3.6 25.1 - - + +
690A ILE* 3.7 20.2 - - + -
691A GLY* 1.3 79.7 - - - -
693A LYS* 1.3 59.9 + - - +
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Residues in contact with LYS 693 (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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579A THR 2.6 21.1 - - - +
580A LEU* 3.7 2.2 - - - -
581A LYS* 2.8 46.0 + - + +
583A LEU* 3.4 16.1 - - + +
675A GLY* 4.2 21.5 + - - -
676A ASP 3.6 3.1 - - - +
677A GLU* 3.5 31.9 - - + +
692A PHE* 1.3 72.4 - - - +
694A VAL* 1.3 61.9 + - - +
695A GLU* 3.5 7.7 + - + +
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Residues in contact with VAL 694 (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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578A LEU* 3.2 40.2 - - + -
579A THR 3.0 2.0 - - - -
580A LEU* 3.0 31.8 - - + +
647A ILE* 4.6 0.2 - - + -
672A LEU* 3.4 20.2 - - + -
673A GLN 3.3 24.0 - - - +
675A GLY* 2.5 40.8 + - - +
676A ASP* 2.5 25.4 + - + +
678A ILE* 5.1 0.4 - - + -
693A LYS* 1.3 71.3 - - - +
695A GLU* 1.3 52.8 + - - +
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Residues in contact with GLU 695 (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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578A LEU* 3.6 0.9 - - - +
579A THR* 2.5 57.0 + - - +
581A LYS* 4.1 25.1 + - - -
674A ASP* 3.8 16.3 - - - +
675A GLY* 4.6 5.4 - - - +
693A LYS* 4.6 8.5 + - + +
694A VAL* 1.3 75.8 - - - +
696A ILE* 1.3 59.9 + - - +
697A ASN* 3.0 27.8 + - - -
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Residues in contact with ILE 696 (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* 3.1 23.6 - - + +
578A LEU* 3.2 20.4 - - + -
647A ILE* 3.9 9.0 - - + -
672A LEU 4.1 0.2 - - - +
673A GLN 3.9 3.1 - - - -
674A ASP* 2.8 52.2 + - + +
695A GLU* 1.3 68.4 - - - +
697A ASN* 1.3 62.9 + - - +
698A ASP 3.2 26.0 - - - +
699A THR* 4.2 12.6 - - + +
705A GLU* 3.0 44.1 - - + +
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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