Contacts of the helix formed by residues 187 - 196 (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 ASP 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B TYR* 2.9 26.4 + - + +
185B LEU 3.2 0.4 - - - -
186B ASN* 1.3 80.4 - - - +
188B LYS* 1.3 60.3 + - - +
189B ALA* 3.4 11.4 + - - +
190B SER* 2.4 41.4 + - - -
191B TYR 3.4 6.4 + - - -
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Residues in contact with LYS 188 (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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133B LEU 5.3 1.1 + - - +
134B LEU* 3.2 45.3 + - + +
136B ILE 4.2 10.7 + - - -
175B MET* 4.2 15.5 - - + +
180B TYR* 3.8 32.9 - - + +
186B ASN 2.9 16.1 + - - +
187B ASP* 1.3 68.4 - - - +
189B ALA* 1.3 62.8 + - + +
191B TYR* 3.2 10.5 + - - +
192B ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 189 (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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134B LEU* 3.9 27.6 - - + -
187B ASP* 3.1 9.5 - - - +
188B LYS* 1.3 82.6 - - + +
190B SER* 1.3 57.8 + - - +
192B ALA* 3.4 2.5 + - - +
193B LYS* 3.0 28.6 + - - +
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Residues in contact with SER 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B TYR* 3.6 27.2 - - - -
187B ASP* 2.4 35.9 + - - -
189B ALA* 1.3 74.5 - - - +
191B TYR* 1.3 60.6 + - - +
193B LYS* 3.6 12.0 - - - +
194B GLY* 2.9 23.4 + - - -
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Residues in contact with TYR 191 (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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31B TYR 5.0 1.8 - - - -
32B ILE* 4.7 12.4 - - + +
91B PHE* 3.9 9.7 - - - -
173B VAL* 4.1 4.8 - - + +
174B ASP 3.0 28.6 + - - -
175B MET* 3.5 24.0 - - + -
179B ALA* 3.7 25.7 + - + +
180B TYR* 3.5 32.3 - + + -
184B TYR* 3.7 31.9 + + + -
187B ASP 3.4 2.8 + - - -
188B LYS* 3.2 13.1 + - - +
190B SER* 1.3 76.7 - - - +
192B ALA* 1.3 65.8 + - - +
194B GLY* 3.2 1.4 + - - -
195B ILE* 3.0 52.8 + - + +
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Residues in contact with ALA 192 (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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130B ASN* 3.7 19.9 - - + +
133B LEU* 4.0 18.2 - - + -
134B LEU* 4.0 15.9 - - + -
175B MET* 4.5 2.2 - - + -
188B LYS 2.9 15.8 + - - +
189B ALA* 3.8 4.3 - - - +
191B TYR* 1.3 79.0 - - - +
193B LYS* 1.3 62.8 - - - +
195B ILE* 3.3 18.4 - - - +
196B TRP* 3.1 21.0 + - - -
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Residues in contact with LYS 193 (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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130B ASN* 4.7 6.7 + - - +
189B ALA 3.0 18.6 + - - +
190B SER* 3.6 11.4 - - - +
192B ALA* 1.3 77.4 - - - +
194B GLY* 1.3 62.2 + - - +
196B TRP* 3.4 21.9 + - - +
197B ASN* 3.9 6.9 + - - -
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Residues in contact with GLY 194 (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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31B TYR* 3.4 25.5 - - - +
184B TYR* 4.5 7.0 - - - -
190B SER 2.9 16.2 + - - -
191B TYR 3.2 2.4 + - - -
193B LYS* 1.3 75.9 - - - +
195B ILE* 1.3 61.8 + - - +
196B TRP 3.1 2.5 - - - -
197B ASN* 2.9 28.6 + - - +
198B VAL 4.3 0.2 + - - -
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Residues in contact with ILE 195 (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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31B TYR* 5.1 2.0 + - - -
32B ILE* 4.3 7.6 - - + -
91B PHE* 3.9 22.0 - - + -
95B LEU* 4.0 20.0 - - + -
133B LEU* 5.3 2.0 - - + -
173B VAL* 3.9 29.8 - - + -
191B TYR* 3.0 44.5 + - + +
192B ALA* 3.3 21.3 - - - +
194B GLY* 1.3 76.5 - - - +
196B TRP* 1.3 68.0 + - + +
197B ASN 3.0 0.2 - - - -
198B VAL* 3.0 21.8 + - + +
199B ILE* 3.2 15.3 + - + +
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Residues in contact with TRP 196 (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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103B GLY* 3.2 21.3 - - - +
122B PHE* 4.6 4.0 - + + -
125B PHE* 3.7 29.6 - + - -
126B LYS* 3.8 44.7 - - + +
129B PHE* 3.7 37.0 - + + -
130B ASN* 2.8 33.9 + - - +
133B LEU* 5.4 0.7 - - + -
171B PHE* 4.0 10.3 - + - -
173B VAL* 6.3 0.4 - - + -
192B ALA 3.1 22.1 + - - -
193B LYS* 3.4 16.8 - - + +
194B GLY 3.1 1.0 - - - -
195B ILE* 1.3 81.4 - - + +
197B ASN* 1.3 58.6 + - - +
198B VAL 3.2 0.7 + - - -
199B ILE* 3.6 15.1 + - + +
201B TRP* 4.0 27.2 + + - -
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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