Contacts of the strand formed by residues 113 - 120 (chain A) in PDB entry 2KTY
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LEU* 4.4 5.0 - - + +
87A TYR* 3.0 33.4 - + + +
88A GLN* 3.3 34.8 - - + +
91A ALA* 3.4 28.7 - - + +
92A LYS 5.7 0.2 - - - +
111A PRO 3.9 1.4 + - - -
112A LYS* 1.3 84.6 + - - +
114A TRP* 1.3 75.1 + - - +
115A GLY* 2.9 40.1 - - - -
116A SER* 2.6 28.2 + - - -
129A MET* 4.8 1.1 - - + -
130A ILE 3.6 5.4 - - - -
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Residues in contact with TRP 114 (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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31A ASP* 5.4 0.7 - - - +
33A ALA* 6.1 1.2 - - - +
37A TRP* 6.2 4.2 - - + -
67A PRO 5.0 1.1 - - - -
68A CYS* 4.2 24.0 - - - -
112A LYS* 3.2 56.5 + - + +
113A TYR* 1.3 87.3 - - - +
115A GLY* 1.3 60.8 + - - +
130A ILE* 3.3 32.1 + - + -
131A MET* 3.6 14.4 + - - -
132A ASP* 3.8 13.3 - - - +
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Residues in contact with GLY 115 (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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31A ASP* 4.7 13.2 - - - -
33A ALA* 6.3 0.9 - - - -
37A TRP* 5.5 3.1 - - - -
113A TYR* 2.9 24.8 - - - -
114A TRP* 1.3 82.5 - - - +
116A SER* 1.3 57.3 + - - -
130A ILE* 3.0 30.2 + - - +
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Residues in contact with SER 116 (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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31A ASP* 3.1 9.5 - - - +
32A MET* 2.7 42.5 + - - +
84A LEU* 3.6 12.3 - - - +
113A TYR* 2.6 30.2 + - - -
115A GLY* 1.3 69.8 - - - -
117A GLY* 1.3 53.9 + - - +
127A ARG* 6.2 1.6 - - - -
128A PHE* 3.5 8.1 - - - -
129A MET* 2.9 32.9 - - - +
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Residues in contact with GLY 117 (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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30A THR 3.8 7.4 - - - -
31A ASP* 4.1 1.6 - - - -
32A MET* 4.2 12.3 - - - +
116A SER* 1.3 78.5 - - - +
118A LEU* 1.3 57.2 + - - +
127A ARG* 3.7 4.0 - - - +
128A PHE* 2.8 57.3 + - - +
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Residues in contact with LEU 118 (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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30A THR 4.3 4.4 + - - +
32A MET* 4.4 12.8 - - + +
77A ASN* 4.9 7.0 - - - +
117A GLY* 1.3 75.1 - - - +
119A HIS* 1.3 61.2 + - - +
120A ASP* 3.9 14.4 + - + +
125A SER* 3.2 44.6 - - - +
126A TYR 3.1 9.4 - - - +
127A ARG* 3.5 27.8 - - + +
128A PHE* 3.4 5.7 - - - -
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Residues in contact with HIS 119 (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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29A ILE* 5.9 2.9 - - + -
30A THR* 5.6 3.4 + - - -
118A LEU* 1.3 74.1 + - - +
120A ASP* 1.3 76.3 + - - +
121A LYS* 3.2 10.8 + - + -
126A TYR* 2.7 43.3 + + + +
128A PHE* 3.7 12.2 - - + -
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Residues in contact with ASP 120 (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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118A LEU* 3.9 11.5 + - + +
119A HIS* 1.3 83.9 + - - +
121A LYS* 1.3 58.3 + - - +
122A ASN* 3.2 29.0 + - - +
123A GLY* 3.7 10.6 + - - -
124A LYS 4.0 5.8 + - - -
125A SER* 4.1 14.2 + - - +
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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