Contacts of the strand formed by residues 106 - 112 (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 GLY 106 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100J GLU 3.5 0.9 - - - +
101J TYR* 3.1 23.9 - - - -
102J TYR* 2.9 33.4 + - - +
103J SER 4.4 0.2 + - - -
104J VAL 3.5 2.4 + - - -
105J THR* 1.3 79.7 + - - +
107J TYR* 1.3 60.7 + - - -
32K PHE* 3.8 21.7 - - - -
91K HIS* 3.9 0.7 - - - -
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Residues in contact with TYR 107 (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* 3.5 38.7 + + - -
51J TYR* 5.2 0.4 + + - -
99J SER* 4.4 1.8 - - - -
100J GLU 3.1 20.0 - - - +
101J TYR* 3.9 27.2 - + + -
105J THR 3.8 4.0 - - - +
106J GLY* 1.3 76.8 - - - -
108J ALA* 1.3 69.0 + - - +
34K ASN* 3.4 5.0 + - - +
49K TYR* 4.5 1.2 - - - +
89K GLN* 5.4 0.9 - - - +
91K HIS* 3.0 56.0 + + + -
94K PHE* 3.7 26.1 - + - -
96K TRP* 3.4 40.4 - + + -
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Residues in contact with ALA 108 (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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99J SER* 3.1 4.0 - - - -
100J GLU* 3.0 38.0 + - - +
107J TYR* 1.3 81.4 - - - +
109J MET* 1.3 61.0 + - - +
110J ASP 3.2 5.5 + - - -
34K ASN* 3.7 12.1 - - - +
36K TYR* 4.3 0.9 - - - -
46K LEU* 3.9 14.1 - - + -
49K TYR* 3.8 28.5 - - + -
89K GLN* 4.8 1.1 - - - +
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Residues in contact with MET 109 (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* 4.3 17.5 - - - +
38J ILE* 4.3 14.1 - - + -
48J TRP* 5.1 0.4 - - + -
97J ALA* 4.1 8.3 - - + -
98J ARG 3.2 9.6 - - - +
99J SER* 3.4 20.9 - - - +
108J ALA* 1.3 68.0 - - - +
110J ASP* 1.3 59.7 + - - +
111J TYR 3.8 0.4 - - - -
112J TRP* 3.0 47.9 + - + -
36K TYR* 3.2 37.2 + - + +
46K LEU* 3.6 7.5 - - - +
89K GLN* 3.5 10.8 - - - +
96K TRP* 4.3 12.6 - - + -
98K PHE* 3.5 31.4 - - + -
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Residues in contact with ASP 110 (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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127E GLN* 5.6 0.9 - - - +
130E ASN* 4.3 1.9 - - - +
98J ARG* 2.6 66.1 + - - +
100J GLU* 3.2 26.0 - - - +
108J ALA 3.2 1.8 + - - -
109J MET* 1.3 73.3 - - - +
111J TYR* 1.3 75.8 + - + -
112J TRP* 3.8 9.3 + - - -
45K LYS* 5.7 0.2 - - - -
46K LEU* 3.7 17.6 + - + +
55K HIS* 3.5 31.6 + - + +
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Residues in contact with TYR 111 (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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127E GLN* 2.5 35.8 + - + +
131E SER* 2.8 30.1 + - - -
1J GLU* 4.6 6.6 - - + +
2J VAL* 3.5 47.1 + - + +
4J LEU* 3.7 20.4 - - + +
97J ALA* 3.2 3.9 - - - -
98J ARG* 3.0 44.1 + - + -
110J ASP* 1.3 105.1 + - + +
112J TRP* 1.3 62.8 + - - +
55K HIS* 5.6 3.4 - + - -
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Residues in contact with TRP 112 (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* 4.0 14.9 + - - +
38J ILE* 3.3 42.6 - - + -
95J TYR* 3.9 13.5 - - + -
96J CYS 3.5 3.8 - - - -
97J ALA* 3.4 16.6 - - + -
109J MET* 3.0 53.7 + - + -
110J ASP 3.8 11.4 + - - -
111J TYR* 1.3 78.4 - - - +
113J GLY* 1.3 64.0 + - - +
36K TYR* 3.4 25.9 - + - -
43K THR* 6.4 0.2 - - + -
44K ILE* 3.0 58.4 + - + +
45K LYS* 4.4 6.4 - - - -
98K PHE* 4.8 1.1 - + - -
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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