Contacts of the strand formed by residues 34 - 40 (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 TYR 34 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33J TYR* 1.3 87.4 - - + +
35J TRP* 1.3 66.0 + - - +
36J ASN* 3.3 3.1 + - - +
51J TYR* 4.1 36.0 + + + -
52J ILE 4.3 0.2 - - - -
53J SER* 3.5 33.7 - - - -
54J ASN* 5.2 2.2 - - - -
98J ARG* 3.2 10.4 - - - +
99J SER* 2.9 48.5 + - - +
101J TYR* 4.1 19.1 - + + -
107J TYR* 3.5 39.2 + + - -
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Residues in contact with TRP 35 (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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2J VAL* 5.5 1.3 - - + -
4J LEU* 4.5 7.9 - - + -
24J VAL* 4.1 20.4 - - + -
27J TYR* 4.4 14.4 - + + -
28J SER 4.3 6.5 - - - -
29J ILE* 3.2 66.1 + - + -
33J TYR 3.7 22.7 + - - +
34J TYR* 1.3 76.0 - - - +
36J ASN* 1.3 61.3 + - - +
37J TRP* 5.2 0.2 - - - -
51J TYR* 3.1 5.1 - - - -
52J ILE* 3.0 47.9 + - + +
53J SER 4.2 3.4 - - - -
70J ILE* 5.1 1.0 - - - +
79J PHE* 3.5 35.8 - + + -
97J ALA 3.6 3.4 - - - -
98J ARG* 3.5 44.2 - - + -
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Residues in contact with ASN 36 (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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34J TYR* 3.3 14.3 + - - +
35J TRP* 1.3 75.3 - - - +
37J TRP* 1.3 63.6 + - - +
38J ILE* 4.9 1.1 - - + -
48J TRP* 3.3 15.1 + - + +
50J GLY 3.4 9.6 - - - +
51J TYR* 3.6 10.9 - - - +
79J PHE* 3.5 7.6 - - - -
96J CYS* 3.4 5.4 - - - -
97J ALA 2.8 32.6 + - - +
99J SER* 2.9 26.1 + - - +
109J MET* 4.3 13.9 - - - +
96K TRP* 3.2 30.9 - - - -
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Residues in contact with TRP 37 (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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6J GLU* 3.5 24.9 - - + -
20J LEU* 3.9 36.3 - - + -
21J THR 4.3 5.6 - - - -
22J CYS* 3.8 22.0 - - + -
35J TRP 5.2 0.2 - - - -
36J ASN* 1.3 76.4 - - - +
38J ILE* 1.3 66.8 + - - +
48J TRP* 4.2 1.0 - - - -
49J VAL* 3.0 39.0 + - + +
50J GLY 3.0 11.5 + - - +
70J ILE* 4.1 20.4 - - + -
79J PHE* 4.0 10.0 - + - -
80J PHE 2.8 29.2 + - - -
81J LEU* 3.4 31.2 - - + +
94J TYR* 4.5 2.2 - - + -
95J TYR 3.1 27.8 - - - -
96J CYS* 3.5 19.3 - - + -
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Residues in contact with ILE 38 (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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36J ASN* 4.9 0.7 - - + -
37J TRP* 1.3 82.2 - - - +
39J ARG* 1.3 57.0 + - - +
46J LEU* 3.6 29.2 - - + -
47J GLU 3.4 16.4 - - - +
48J TRP* 4.1 20.2 - - + -
49J VAL* 3.8 4.3 - - - -
94J TYR* 3.4 3.4 - - - +
95J TYR* 2.7 43.7 + - + +
97J ALA* 6.0 0.7 - - + +
109J MET* 4.3 16.6 - - - -
112J TRP* 3.3 36.6 - - + -
44K ILE* 4.2 3.1 - - + -
98K PHE* 4.0 15.0 - - + -
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Residues in contact with ARG 39 (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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38J ILE* 1.3 75.5 - - - +
40J LEU* 1.3 61.3 + - - +
41J PHE* 2.9 45.1 - - + -
45J LYS 3.8 0.9 - - - +
46J LEU* 3.4 9.1 - - - +
47J GLU* 2.7 70.0 + - - -
49J VAL* 4.0 10.0 - - - +
64J LEU* 4.0 15.4 - - - +
83J LEU* 3.7 12.7 - - - +
90J ASP* 2.9 30.5 + - - +
92J ALA* 3.9 5.4 - - + -
93J THR 3.6 4.5 - - - -
94J TYR* 3.6 44.5 + - + +
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Residues in contact with LEU 40 (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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39J ARG* 1.3 73.5 - - - +
41J PHE* 1.3 72.3 + - - +
42J PRO* 3.8 0.9 - - - +
44J ASN* 4.5 6.3 - - - +
45J LYS 4.1 6.3 - - - +
46J LEU* 3.5 29.2 - - + -
92J ALA* 3.5 6.3 - - - +
93J THR* 2.8 49.7 + - + +
95J TYR* 3.9 24.7 - - + +
38K GLN* 3.0 26.5 - - + +
87K PHE* 4.0 16.6 - - + -
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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