Contacts of the strand formed by residues 78 - 83 (chain J) in PDB entry 1KYO
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 GLN 78 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J THR* 4.0 9.9 + - - +
22J CYS 3.0 20.4 - - - +
23J SER* 2.6 32.3 + - - -
24J VAL 4.5 0.7 - - - +
29J ILE* 4.2 6.5 - - - +
72J ARG* 3.5 2.9 - - - -
73J ASP* 3.0 29.0 + - + -
76J LYS* 3.5 44.5 + - + +
77J ASN* 1.3 73.6 - - - +
79J PHE* 1.3 61.4 + - - +
80J PHE* 3.8 24.7 - - + -
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Residues in contact with PHE 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 4.3 3.8 - - + -
22J CYS* 3.0 65.5 + - + +
24J VAL* 3.7 15.3 - - + -
29J ILE* 4.0 17.0 - - + -
35J TRP* 3.5 46.0 - + + -
36J ASN 3.5 21.3 - - - -
37J TRP* 4.0 15.4 - + - -
52J ILE* 4.1 16.4 - - + -
70J ILE* 4.7 0.2 - - + -
71J THR 3.4 11.9 - - - +
72J ARG* 4.1 7.0 - - + -
78J GLN* 1.3 73.7 - - - +
80J PHE* 1.3 63.1 + - - +
96J CYS* 3.7 11.2 - - + -
97J ALA 4.4 1.6 - - - -
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Residues in contact with PHE 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU 3.5 5.8 - - - +
21J THR* 3.3 33.4 - - - -
37J TRP* 2.8 23.8 + - - -
69J SER 4.7 0.7 - - - +
70J ILE* 3.1 19.3 - - - +
71J THR* 2.8 40.9 + - - +
72J ARG 4.4 1.8 - - - -
73J ASP* 4.2 20.9 - - + -
76J LYS* 5.9 0.2 - - + -
78J GLN* 3.8 38.1 - - + -
79J PHE* 1.3 77.5 - - - +
81J LEU* 1.3 58.4 + - - +
82J LYS* 6.1 0.9 - - + -
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Residues in contact with LEU 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J LEU* 3.9 6.5 - - + +
19J SER* 3.3 6.6 - - - -
20J LEU* 3.0 43.6 + - + +
37J TRP* 3.4 38.1 - - + +
49J VAL* 4.2 21.8 - - + -
68J LEU* 4.6 14.4 - - + -
69J SER 4.0 3.8 - - - -
70J ILE* 4.8 5.4 - - + +
80J PHE* 1.3 77.8 - - - +
82J LYS* 1.3 68.7 + - - +
83J LEU* 4.6 10.3 - - + +
94J TYR* 3.6 34.3 - - + -
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Residues in contact with LYS 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J SER* 4.0 25.6 - - - -
18J LEU 3.1 4.5 - - - +
19J SER* 3.6 20.9 + - - +
67J ARG 3.5 2.4 - - - +
68J LEU* 3.3 4.6 - - - -
69J SER* 3.2 40.5 + - - +
80J PHE* 6.1 1.1 - - + -
81J LEU* 1.3 78.1 - - - +
83J LEU* 1.3 58.5 + - - +
84J ASN* 3.5 17.4 + - - +
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Residues in contact with LEU 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J SER* 4.5 0.2 - - - -
18J LEU* 2.9 45.9 + - + -
39J ARG* 3.7 22.2 - - - +
49J VAL* 5.9 1.1 - - + -
64J LEU* 4.4 11.4 - - + -
67J ARG* 3.7 40.4 - - + +
68J LEU* 3.6 35.9 - - + +
81J LEU* 4.1 9.5 - - + +
82J LYS* 1.3 70.6 - - - +
84J ASN* 1.3 65.1 + - - +
86J VAL* 3.5 9.4 - - + +
90J ASP* 3.9 7.9 - - + +
94J TYR* 4.2 13.5 - - + +
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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