Contacts of the strand formed by residues 140 - 146 (chain Y) in PDB entry 1KKC
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 140 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136Y ILE* 4.1 15.7 - - - +
138Y GLY 3.9 2.2 + - - -
139Y SER* 1.3 77.6 - - - +
141Y TRP* 1.3 67.0 + - - -
158Y THR 3.2 13.2 - - - -
160Y ASP 3.8 8.7 - - - -
175Y MET* 2.9 28.3 + - - +
176Y TRP* 3.5 8.2 + - - +
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Residues in contact with TRP 141 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y ASN* 3.4 47.1 - - + +
88Y HIS* 3.6 19.5 - + - -
91Y PHE* 3.7 22.7 - + + -
136Y ILE* 3.6 5.5 - - - +
140Y GLY* 1.3 76.8 - - - -
142Y GLY* 1.3 60.7 + - - +
143Y TRP* 3.2 40.6 - + + +
157Y THR* 3.0 10.2 - - - -
158Y THR* 2.9 32.5 + - - +
160Y ASP 3.3 18.6 + - - -
161Y GLN* 2.9 19.2 + - - -
172Y GLY 4.7 0.9 - - - -
173Y VAL 3.5 11.2 - - - -
174Y ASP* 3.5 54.6 + - + -
176Y TRP* 3.8 1.0 - - - +
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Residues in contact with GLY 142 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Y PHE* 3.7 8.5 - - - -
132Y THR* 5.2 2.7 - - - -
133Y LEU* 3.6 22.7 - - - +
136Y ILE* 4.3 4.3 - - - -
141Y TRP* 1.3 73.9 - - - +
143Y TRP* 1.3 62.1 + - - -
156Y THR 3.6 5.4 - - - -
157Y THR* 4.3 3.1 - - - -
172Y GLY* 3.3 3.8 - - - -
173Y VAL 2.9 33.9 + - - -
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Residues in contact with TRP 143 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y ASN* 3.3 45.5 - - - -
90Y LEU* 4.1 25.6 - - + -
91Y PHE* 5.8 0.4 - - - -
94Y ASN* 5.1 0.9 - - - -
129Y PHE* 3.5 11.0 - - - -
141Y TRP* 3.2 37.3 - + + +
142Y GLY* 1.3 76.2 - - - -
144Y LEU* 1.3 59.2 + - - +
145Y VAL* 3.9 6.3 - - + -
155Y ILE* 3.2 4.9 - - - -
156Y THR* 2.7 51.0 + - - +
157Y THR* 4.2 0.9 - - - -
158Y THR* 2.8 34.8 + - + +
162Y ASP 4.9 0.9 - - - -
164Y VAL* 3.4 30.1 - - + -
169Y PRO* 4.4 9.4 - - + -
171Y PHE* 3.6 9.9 - - - +
172Y GLY* 3.4 25.1 - - - -
207Y ARG* 5.9 0.2 - - - -
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Residues in contact with LEU 144 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111Y LEU* 4.4 6.3 - - + -
115Y ILE* 4.0 20.0 - - + -
119Y TRP* 3.5 29.8 - - + -
125Y PHE* 3.6 15.5 - - + -
129Y PHE* 3.7 5.4 - - + -
143Y TRP* 1.3 72.6 - - - +
145Y VAL* 1.3 60.0 + - - +
153Y LEU* 4.1 5.8 - - + -
154Y ASP 3.3 19.1 - - - +
155Y ILE* 4.3 0.9 - - + -
169Y PRO* 4.2 0.2 - - - +
170Y VAL* 2.8 43.7 + - + +
171Y PHE* 3.1 46.1 + - + +
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Residues in contact with VAL 145 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y TRP* 4.1 9.4 - - + -
144Y LEU* 1.3 78.1 - - - +
146Y THR* 1.3 63.1 + - - +
153Y LEU* 3.3 8.7 - - - +
154Y ASP* 2.7 52.2 + - + +
156Y THR* 4.1 16.8 - - + +
164Y VAL* 3.6 37.7 - - + -
167Y ALA* 3.9 18.2 - - + -
168Y ALA 3.2 12.6 - - - +
169Y PRO* 4.2 2.7 - - + -
170Y VAL* 4.0 3.1 - - - -
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Residues in contact with THR 146 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145Y VAL* 1.3 77.2 - - - +
147Y ASP* 1.3 61.3 + - - +
148Y GLY 3.0 27.1 + - - +
151Y GLY 3.3 12.6 - - - -
152Y LYS 3.1 13.7 + - - -
153Y LEU* 4.2 0.9 - - - -
167Y ALA* 3.9 3.4 - - - -
168Y ALA* 2.9 50.8 + - + +
170Y VAL* 4.4 5.2 - - + -
207Y ARG 4.7 0.4 - - - +
208Y TYR* 3.3 27.8 - - + +
211Y GLY* 4.0 7.6 - - - -
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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