Contacts of the strand formed by residues 106 - 112 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100U GLU 3.5 6.4 - - - +
101U TYR* 3.6 20.1 - - - -
102U TYR* 2.7 28.5 + - - +
103U SER 4.4 0.2 + - - -
104U VAL 3.5 2.8 + - - -
105U THR* 1.3 82.3 + - - +
107U TYR* 1.3 61.5 + - - -
108U ALA* 4.8 2.4 - - - +
32V PHE* 3.8 17.4 - - - -
49V TYR* 5.7 0.7 - - - -
91V HIS* 4.0 2.7 - - - -
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Residues in contact with TYR 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U TYR* 3.2 36.8 + + - -
51U TYR* 4.7 2.3 + + - -
99U SER* 3.7 14.8 - - - +
100U GLU 2.8 7.0 - - - +
101U TYR* 4.0 30.6 - + + -
105U THR 4.3 1.0 - - - +
106U GLY* 1.3 75.3 - - - -
108U ALA* 1.3 64.5 + - - +
34V ASN* 3.2 2.7 + - - +
89V GLN* 5.2 2.5 - - - +
91V HIS* 2.8 56.9 + + + -
94V PHE* 3.9 26.1 - + - -
96V TRP* 3.6 32.1 - + + -
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Residues in contact with ALA 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U SER* 3.2 2.5 + - - -
100U GLU* 2.7 45.8 + - + +
106U GLY 4.8 1.6 - - - +
107U TYR* 1.3 79.9 - - - +
109U MET* 1.3 62.1 + - - +
110U ASP* 3.4 2.6 + - - +
34V ASN* 3.9 8.7 - - - +
36V TYR* 4.2 1.6 - - - -
46V LEU* 4.2 11.9 - - + -
49V TYR* 3.9 32.3 - - + -
89V GLN* 4.8 1.3 - - - +
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Residues in contact with MET 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U ASN* 4.1 20.9 - - - +
38U ILE* 4.3 12.3 - - + -
48U TRP* 5.6 0.7 - - + -
97U ALA* 4.1 8.5 - - + -
98U ARG 3.2 9.0 - - - +
99U SER* 3.7 17.7 - - - +
108U ALA* 1.3 70.1 - - - +
110U ASP* 1.3 58.9 + - - +
111U TYR 3.8 0.9 - - - -
112U TRP* 3.3 41.1 + - + +
36V TYR* 3.3 22.3 + - + +
46V LEU* 3.2 13.7 - - - +
89V GLN* 3.4 26.2 - - - +
96V TRP* 4.3 11.9 - - + -
98V PHE* 3.7 26.7 - - + -
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Residues in contact with ASP 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127P GLN* 4.9 2.3 + - - +
130P ASN* 4.1 2.8 - - - +
98U ARG* 2.7 49.3 + - - +
100U GLU* 2.9 23.2 - - - +
108U ALA 3.4 1.7 + - - +
109U MET* 1.3 74.8 - - - +
111U TYR* 1.3 81.0 + - - +
112U TRP* 4.1 6.2 + - - -
46V LEU* 3.8 13.1 + - + +
55V HIS* 3.3 36.1 + - + +
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Residues in contact with TYR 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127P GLN* 3.4 28.6 + - - +
131P SER* 2.9 27.4 + - - -
1U GLU* 4.7 5.0 - - + +
2U VAL* 3.4 52.0 + - + -
4U LEU* 3.4 22.6 - - + +
97U ALA* 3.0 4.7 - - - -
98U ARG* 3.0 52.7 + - + -
110U ASP* 1.3 108.4 + - - +
112U TRP* 1.3 60.7 + - - +
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Residues in contact with TRP 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U LEU* 4.4 9.0 + - - +
38U ILE* 3.3 37.2 - - + -
95U TYR* 3.8 22.0 - - + -
96U CYS 3.7 2.9 - - - -
97U ALA* 3.5 17.5 - - + -
109U MET* 3.3 44.2 + - + +
110U ASP 4.2 4.4 + - - -
111U TYR* 1.3 80.1 - - - +
113U GLY* 1.3 64.1 - - - +
36V TYR* 3.6 33.7 - + - -
44V ILE* 3.4 60.7 + - + +
45V LYS* 4.7 6.5 - - - -
98V PHE* 5.0 2.5 - + - -
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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