Contacts of the strand formed by residues 153 - 159 (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 LEU 153 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B LYS* 4.0 1.4 - - - -
111X LEU* 3.9 11.0 - - + -
114X ALA* 3.6 17.7 - - + +
115X ILE* 3.5 47.6 - - + +
118X ARG* 3.3 24.9 + - + +
119X TRP* 4.0 17.0 - - + -
144X LEU* 4.0 13.0 - - + -
145X VAL 3.3 12.6 - - - +
146X THR* 4.2 1.8 - - - -
151X GLY 3.7 0.4 + - - +
152X LYS* 1.3 71.9 - - - +
154X ASP* 1.3 74.3 + - - +
170X VAL* 4.4 1.3 - - + -
208X TYR* 3.5 33.7 - - + -
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Residues in contact with ASP 154 (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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118B ARG* 5.4 0.9 + - - -
152B LYS* 2.8 31.2 + - - -
154B ASP* 4.4 4.7 - - - +
118X ARG* 3.1 16.9 + - - +
119X TRP* 4.3 4.7 - - - -
144X LEU* 3.5 4.4 - - - +
145X VAL* 2.8 51.9 + - + +
147X ASP* 6.2 0.3 - - - +
152X LYS* 4.3 6.1 - - - +
153X LEU* 1.3 80.1 - - - +
155X ILE* 1.3 65.1 + - - +
156X THR* 4.6 8.1 - - + -
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Residues in contact with ILE 155 (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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119X TRP* 3.7 35.4 - - + +
125X PHE* 3.8 19.7 - - + -
128X ALA* 4.2 7.2 - - + +
129X PHE* 3.9 40.4 - - + +
132X THR* 3.5 35.7 - - + +
143X TRP 3.3 8.5 - - - +
144X LEU* 4.6 1.1 - - + -
154X ASP* 1.3 76.5 + - - +
156X THR* 1.3 68.8 + - - +
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Residues in contact with THR 156 (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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132X THR* 5.2 0.4 - - - -
142X GLY* 3.8 0.5 - - - -
143X TRP* 2.8 47.1 + - - +
145X VAL* 3.9 27.1 - - + +
154X ASP* 4.6 6.3 - - + -
155X ILE* 1.3 83.7 - - - +
157X THR* 1.3 75.3 + - - +
158X THR* 5.4 0.9 - - - +
164X VAL* 4.7 3.1 - - - +
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Residues in contact with THR 157 (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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132X THR* 3.2 36.3 - - + +
136X ILE* 3.8 23.0 - - + +
141X TRP 3.1 16.8 - - - +
142X GLY* 4.5 1.3 - - - -
143X TRP* 4.3 1.6 - - - -
156X THR* 1.3 78.6 - - - +
158X THR* 1.3 71.5 + - - +
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Residues in contact with THR 158 (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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136X ILE* 5.2 1.0 - - - +
140X GLY* 3.2 3.3 - - - -
141X TRP* 2.9 35.5 + - - +
143X TRP* 2.8 32.7 + - + +
156X THR* 5.4 1.6 - - - +
157X THR* 1.3 81.4 - - - +
159X HIS* 1.3 59.4 + - - +
160X ASP 4.7 0.2 - - - +
162X ASP* 3.1 31.1 + - + +
163X PRO 3.9 17.0 - - - +
164X VAL* 4.1 7.2 - - + -
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Residues in contact with HIS 159 (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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136X ILE* 5.5 1.8 - - - +
137X GLN 3.2 24.2 + - - -
139X SER 3.2 13.5 + - - -
140X GLY* 4.3 1.0 - - - -
158X THR* 1.3 72.5 - - - +
160X ASP* 1.3 91.5 + - - +
161X GLN 3.0 0.2 + - - -
162X ASP* 2.9 33.7 + - - +
159Y HIS* 3.0 18.4 + + - -
160Y ASP* 2.9 34.1 + - - -
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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