Contacts of the strand formed by residues 140 - 146 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136X ILE* 4.0 15.8 - - - +
138X GLY 3.7 3.4 + - - -
139X SER* 1.3 77.9 - - - +
141X TRP* 1.3 66.3 + - - -
158X THR 3.2 13.0 - - - -
159X HIS* 4.3 0.2 - - - -
160X ASP 3.9 7.6 - - - -
175X MET* 2.9 26.3 + - - -
176X TRP* 3.5 12.3 - - - +
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Residues in contact with TRP 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X ASN* 3.6 41.6 - - + +
88X HIS* 3.8 17.5 - + - -
91X PHE* 3.6 28.0 - + + -
136X ILE* 3.3 6.6 - - - +
140X GLY* 1.3 76.3 - - - -
142X GLY* 1.3 59.5 + - - +
143X TRP* 3.3 38.6 - + - +
157X THR* 3.1 29.6 - - - -
158X THR* 2.9 14.1 + - - +
160X ASP 3.4 19.6 + - - -
161X GLN* 3.0 19.8 + - - -
172X GLY 4.5 1.3 - - - -
173X VAL 3.6 11.7 - - - -
174X ASP* 3.5 55.8 + - + -
175X MET 4.3 0.2 - - - +
176X TRP* 4.0 1.2 - - - +
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Residues in contact with GLY 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X PHE* 3.7 8.7 - - - -
132X THR* 5.5 1.6 - - - -
133X LEU* 3.5 23.1 - - - +
136X ILE* 3.9 5.8 - - - +
141X TRP* 1.3 75.2 - - - +
143X TRP* 1.3 60.5 + - - -
156X THR 3.8 4.7 - - - -
157X THR* 4.5 2.5 - - - -
172X GLY* 3.1 5.0 - - - -
173X VAL 2.8 33.7 + - - -
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Residues in contact with TRP 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X ASN* 3.3 45.3 - - - -
90X LEU* 4.2 24.7 - - + -
91X PHE* 5.8 0.4 - - - -
94X ASN* 5.1 0.4 - - - -
129X PHE* 3.6 10.5 - - - -
141X TRP* 3.3 34.5 - + + +
142X GLY* 1.3 76.0 - - - -
144X LEU* 1.3 60.2 + - - +
145X VAL* 3.9 10.8 - - + -
155X ILE* 3.3 4.9 - - - -
156X THR* 2.8 50.4 + - - +
157X THR* 4.3 0.4 - - - -
158X THR* 2.8 33.7 + - + -
164X VAL* 3.3 24.0 - - + +
169X PRO* 4.1 15.5 - - + -
171X PHE* 3.5 11.0 - - - -
172X GLY* 3.3 27.1 - - - -
207X ARG* 5.7 0.2 - - - -
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Residues in contact with LEU 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X LEU* 4.3 7.6 - - + -
115X ILE* 4.1 18.2 - - + -
119X TRP* 4.1 13.5 - - + -
125X PHE* 3.9 24.9 - - + -
129X PHE* 3.9 5.8 - - + -
143X TRP* 1.3 72.8 - - - +
145X VAL* 1.3 55.6 + - - +
153X LEU* 4.0 18.2 - - + -
154X ASP 3.5 14.1 - - - +
155X ILE* 4.6 0.7 - - + +
169X PRO* 4.0 0.3 - - - +
170X VAL* 2.8 49.3 + - + +
171X PHE* 3.1 47.4 + - + +
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Residues in contact with VAL 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143X TRP* 3.9 9.6 - - + -
144X LEU* 1.3 78.8 - - - +
146X THR* 1.3 64.6 + - - +
152X LYS 3.7 0.2 - - - +
153X LEU* 3.3 6.6 - - - +
154X ASP* 2.8 53.0 + - + +
156X THR* 3.9 25.6 - - + +
164X VAL* 3.8 27.1 - - + -
167X ALA* 3.7 19.5 - - + -
168X ALA 3.3 11.9 - - - +
169X PRO* 4.2 2.5 - - + -
170X VAL* 4.1 3.8 - - - -
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Residues in contact with THR 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X VAL* 1.3 79.4 - - - +
147X ASP* 1.3 60.6 + - - +
148X GLY 2.9 27.0 + - - +
151X GLY 3.2 21.8 + - - -
152X LYS 3.1 6.5 - - - -
153X LEU* 4.2 0.7 - - - -
167X ALA* 3.9 4.0 - - - -
168X ALA* 2.9 45.1 + - + +
170X VAL* 4.1 5.8 - - + -
207X ARG 4.8 0.2 - - - +
208X TYR* 3.4 27.5 - - + +
211X GLY* 4.1 7.4 - - - -
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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