Contacts of the strand formed by residues 153 - 159 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 4.0 9.6 - - + -
114B ALA* 3.7 17.9 - - + +
115B ILE* 3.6 45.8 - - + +
118B ARG* 2.7 35.9 + - + +
119B TRP* 3.8 18.3 - - + -
144B LEU* 4.1 11.7 - - + -
145B VAL 3.3 13.2 - - - +
146B THR* 4.1 2.5 - - - -
151B GLY 4.4 1.3 - - - +
152B LYS* 1.3 74.9 - - - +
154B ASP* 1.3 68.5 + - - +
170B VAL* 4.4 1.6 - - + -
208B TYR* 3.6 33.9 - - + -
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Residues in contact with ASP 154 (chain B).
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* 2.9 24.9 + - - +
119B TRP* 4.3 4.0 - - - -
144B LEU* 3.3 6.1 - - - +
145B VAL* 2.8 46.7 + - + +
147B ASP* 6.0 0.5 - - - +
152B LYS* 2.6 32.7 + - - +
153B LEU* 1.3 80.6 - - - +
155B ILE* 1.3 68.8 + - - +
156B THR* 4.0 5.8 - - + -
154X ASP* 4.4 4.0 - - - +
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B TRP* 3.5 31.0 - - + +
125B PHE* 3.8 21.8 - - + -
128B ALA* 3.7 28.5 - - + -
129B PHE* 3.8 20.6 - - + +
132B THR* 3.6 35.9 - - + +
143B TRP 3.3 9.2 - - - +
144B LEU* 4.6 0.9 - - + -
154B ASP* 1.3 75.5 + - - +
156B THR* 1.3 70.4 + - - +
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLY* 3.7 0.3 - - - -
143B TRP* 2.7 50.7 + - - +
145B VAL* 4.2 25.6 - - + +
154B ASP* 4.6 5.8 - - + -
155B ILE* 1.3 83.9 - - - +
157B THR* 1.3 70.4 + - - +
158B THR* 5.4 1.0 - - - +
164B VAL* 4.6 4.3 - - - +
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Residues in contact with THR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B THR* 3.2 34.5 - - + +
136B ILE* 4.0 22.7 - - + +
141B TRP 3.1 15.9 - - - +
142B GLY* 4.4 1.1 - - - -
143B TRP* 4.3 1.1 - - - -
156B THR* 1.3 78.5 - - - +
158B THR* 1.3 72.1 + - - +
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ILE* 5.3 0.9 - - - +
140B GLY* 3.2 3.3 - - - -
141B TRP* 2.8 35.5 + - - +
143B TRP* 2.9 29.0 + - + +
156B THR* 5.4 1.6 - - - +
157B THR* 1.3 83.5 - - - +
159B HIS* 1.3 59.9 + - - +
160B ASP 4.7 0.4 - - - +
162B ASP* 2.9 32.7 + - + +
163B PRO 3.8 17.3 - - - +
164B VAL* 4.3 7.0 - - + +
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Residues in contact with HIS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A HIS* 2.8 35.4 + + - -
160A ASP* 2.9 22.1 + - - -
136B ILE* 5.3 2.4 - - - +
137B GLN 3.0 28.3 + - - -
139B SER 3.0 19.0 + - - -
140B GLY* 4.2 1.0 - - - -
158B THR* 1.3 73.6 - - - +
160B ASP* 1.3 81.2 + - - +
161B GLN 3.1 0.2 + - - -
162B ASP* 2.9 34.2 + - - +
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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