Contacts of the helix formed by residues 188 - 197 (chain B) in PDB entry 1KNY
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 SER 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LYS* 4.1 17.6 - - - -
161A PHE* 3.9 22.4 - - - -
168A GLN* 6.1 1.1 - - - -
98B LEU* 4.1 17.3 - - - +
171B MET* 5.6 2.4 - - - +
187B THR* 1.3 81.5 + - - +
189B ALA* 1.3 58.6 + - - -
191B VAL* 3.3 18.4 + - - +
192B LEU 5.0 0.2 + - - -
557B APC 3.1 31.1 + - - -
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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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149A LYS* 6.1 0.4 - - + -
153A ILE* 5.4 0.4 - - + -
158A PRO* 4.2 25.2 - - + +
160A THR* 4.7 1.2 + - - -
161A PHE* 3.0 52.6 - - + +
187B THR* 3.4 8.5 + - + +
188B SER* 1.3 77.8 - - - +
190B SER* 1.3 58.5 + - - +
191B VAL 3.4 0.4 + - - -
192B LEU* 4.8 3.9 + - - +
193B THR* 4.5 9.5 - - - +
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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
----------------------------------------------------------
185B TYR* 4.5 0.2 - - - -
186B THR* 2.7 28.1 + - - -
187B THR* 2.6 30.2 + - - +
189B ALA* 1.3 78.5 - - - +
191B VAL* 1.4 65.5 + - - +
192B LEU 3.4 1.3 - - - -
193B THR* 2.8 25.2 + - - -
194B GLU* 3.0 22.0 + - - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.8 26.5 - - + -
171B MET* 3.7 24.0 - - + -
174B ALA* 3.5 27.6 - - + -
175B MET* 4.3 4.7 - - + -
185B TYR* 3.0 43.8 - - + -
187B THR 3.3 4.8 + - - +
188B SER 3.3 17.1 + - - +
189B ALA 3.4 0.2 - - - -
190B SER* 1.4 75.6 - - - +
192B LEU* 1.3 60.6 + - + +
195B ALA* 2.8 25.8 + - - +
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Residues in contact with LEU 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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160A THR* 5.0 3.1 - - - +
161A PHE* 6.5 1.3 - - + -
164A SER* 4.7 5.2 - - - +
170B ALA* 4.0 5.8 - - + +
171B MET* 3.7 29.4 - - + -
188B SER 5.0 0.4 + - - -
189B ALA 4.8 3.9 + - - +
190B SER 3.4 0.4 - - - -
191B VAL* 1.3 81.1 - - + +
193B THR* 1.3 68.4 + - + +
195B ALA* 2.9 14.0 + - - +
196B VAL* 3.0 19.1 + - - +
205B TYR* 3.6 23.2 + - - +
209B CYS* 4.3 12.5 - - - -
212B VAL* 3.6 29.2 - - + -
213B MET* 3.6 32.5 - - + -
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Residues in contact with THR 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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158A PRO* 5.4 4.0 - - + -
160A THR* 3.5 25.8 - - + +
189B ALA 4.5 9.2 - - - +
190B SER* 2.8 19.6 + - - -
192B LEU* 1.3 78.3 - - + +
194B GLU* 1.3 70.3 + - - +
196B VAL* 2.7 25.4 - - - +
197B LYS* 3.4 20.1 + - - +
213B MET* 3.8 14.4 - - - -
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Residues in contact with GLU 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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183B ILE* 5.2 3.3 - - - +
184B CYS 4.1 4.7 - - - +
185B TYR* 3.2 30.9 - - + -
186B THR* 2.8 32.1 + - - +
190B SER* 3.0 21.0 + - - +
191B VAL 3.5 3.1 - - - +
193B THR* 1.3 85.2 + - - +
195B ALA* 1.3 64.6 + - - +
197B LYS* 3.1 35.1 + - - +
198B GLN* 3.1 19.2 + - - +
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Residues in contact with ALA 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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174B ALA* 3.9 19.1 - - + -
177B ILE* 3.7 12.2 - - + +
185B TYR* 3.2 23.1 - - + +
191B VAL 2.8 19.1 + - - +
192B LEU 2.9 4.9 + - - +
194B GLU* 1.3 72.6 - - - +
196B VAL* 1.3 57.8 + - - +
197B LYS 2.9 10.5 + - - -
198B GLN* 2.9 27.5 + - - +
201B LEU* 3.7 0.7 - - - +
205B TYR* 4.1 11.7 - - + +
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Residues in contact with VAL 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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192B LEU 3.0 13.7 + - - +
193B THR* 2.7 34.3 - - - +
195B ALA* 1.3 75.5 - - - +
197B LYS* 1.3 56.8 + - + +
198B GLN 3.3 3.7 - - - +
201B LEU* 4.1 18.5 - - + +
205B TYR* 4.6 8.9 - - + -
206B ASP* 4.2 32.8 - - + +
209B CYS* 4.8 3.4 - - + -
213B MET* 4.2 18.4 - - + -
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Residues in contact with LYS 197 (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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193B THR* 3.4 25.3 + - - +
194B GLU* 3.1 36.2 + - - +
195B ALA 2.9 1.2 - - - -
196B VAL* 1.3 78.5 - - + +
198B GLN* 1.3 73.2 + - - +
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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