Contacts of the helix formed by residues 187 - 202 (chain B) in PDB entry 5KAL
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 THR 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B ASN* 4.2 2.5 - - - -
179B ALA* 3.8 23.8 - - + +
186B ILE* 1.3 78.8 - - - +
188B SER* 1.3 64.9 + - - +
189B TYR* 3.6 12.7 + - - +
190B GLY* 3.1 22.5 + - - -
191B PHE* 3.2 14.0 + - - -
305B VAL* 4.6 10.4 + - + +
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Residues in contact with SER 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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169B LYS* 3.9 30.6 - - - +
173B LYS* 4.2 6.9 + - - -
178B ASN* 3.0 26.0 + - - +
187B THR* 1.3 74.2 - - - +
189B TYR* 1.3 63.5 + - - +
191B PHE* 3.1 8.7 + - - +
192B ASN* 2.9 28.3 + - - +
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Residues in contact with TYR 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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147B ASN* 3.4 42.0 + - + +
151B LEU* 4.2 21.3 - - + -
187B THR* 3.1 9.8 + - - +
188B SER* 1.3 78.3 - - - +
190B GLY* 1.3 63.2 + - - +
192B ASN* 3.2 10.2 + - - +
193B LEU* 3.0 48.7 + - + +
297B ASP* 3.6 17.9 + - - -
298B PRO* 3.4 27.9 - - - +
305B VAL* 4.3 13.9 - - + -
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Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 4.1 12.1 - - - -
187B THR* 3.1 12.3 + - - -
189B TYR* 1.3 80.4 - - - +
191B PHE* 1.3 56.9 + - - +
193B LEU* 3.2 10.4 + - - +
194B MET* 2.9 31.9 + - - +
295B ILE* 4.3 5.3 - - - +
305B VAL* 4.0 21.5 - - - -
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Residues in contact with PHE 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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168B ILE* 4.0 23.1 - - + -
169B LYS* 5.6 5.8 - - + -
171B TRP* 4.6 14.6 - + - -
172B SER* 3.6 33.9 - - - +
177B LEU* 4.2 18.2 - - + -
178B ASN* 4.6 3.4 - - - -
186B ILE* 3.5 37.9 - - + -
187B THR 3.2 22.6 + - - -
188B SER* 3.1 10.6 + - - +
190B GLY* 1.3 72.5 - - - +
192B ASN* 1.3 67.2 + - - +
194B MET* 3.2 27.7 + - + +
195B VAL* 2.9 28.4 + - - +
244B PHE* 5.9 1.6 - + - -
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Residues in contact with ASN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B SER* 6.0 3.2 - - - +
57B VAL* 4.2 20.8 - - - +
58B TYR* 3.6 9.2 + - - -
151B LEU* 4.3 20.3 - - + +
155B PHE* 4.3 12.0 - - + -
165B SER* 2.6 28.9 + - - -
169B LYS* 5.6 5.4 - - - +
188B SER* 2.9 17.4 + - - +
189B TYR* 3.4 11.6 - - - +
191B PHE* 1.3 76.4 - - - +
193B LEU* 1.3 63.4 + - - +
195B VAL* 3.1 5.9 + - - +
196B VAL* 2.9 29.4 + - - +
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Residues in contact with LEU 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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147B ASN* 6.3 0.2 - - + -
150B LEU* 6.5 0.2 - - + -
151B LEU* 4.3 10.3 - - + -
189B TYR* 3.0 58.9 + - + +
190B GLY* 3.2 9.4 + - - +
192B ASN* 1.3 75.7 - - - +
194B MET* 1.3 63.0 + - - +
196B VAL* 3.3 4.7 + - - +
197B TYR* 2.9 24.5 + - - +
259B ILE* 4.3 3.9 - - + +
261B LEU* 3.7 31.6 - - + +
295B ILE* 3.9 27.4 - - + -
296B GLU 4.6 7.6 - - - +
298B PRO* 4.8 9.6 - - + -
305B VAL* 4.2 9.2 - - + -
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Residues in contact with MET 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 4.7 6.3 - - - -
190B GLY 2.9 16.9 + - - +
191B PHE* 3.2 34.3 + - + +
193B LEU* 1.3 76.1 - - - +
195B VAL* 1.3 63.7 + - - +
197B TYR* 3.2 3.3 + - - +
198B TYR* 3.0 19.9 + - - +
244B PHE* 4.6 10.8 - - + -
248B PHE* 3.6 37.5 - - + -
259B ILE* 4.1 16.8 - - + -
293B TRP* 3.7 38.4 - - + -
295B ILE* 4.0 17.3 - - + -
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Residues in contact with VAL 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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155B PHE* 4.8 7.2 - - + -
161B CYS 5.6 0.2 - - - +
164B LEU* 4.3 17.0 - - + -
165B SER* 4.4 32.3 - - - +
168B ILE* 4.5 14.4 - - + -
191B PHE 2.9 20.6 + - - +
192B ASN* 3.6 8.5 - - - +
194B MET* 1.3 74.1 - - - +
196B VAL* 1.3 64.1 + - - +
198B TYR* 3.2 3.1 + - - +
199B LEU* 2.9 41.8 + - + +
244B PHE* 4.1 24.9 - - + -
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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
----------------------------------------------------------
151B LEU* 3.9 20.2 - - + -
154B TYR* 3.9 34.8 - - + -
155B PHE* 4.5 20.6 - - + -
192B ASN 2.9 20.1 + - - +
193B LEU 3.8 3.6 - - - +
195B VAL* 1.3 76.7 - - + +
197B TYR* 1.3 62.8 + - - +
199B LEU* 3.5 7.1 + - + +
200B LEU* 2.9 24.6 + - + +
205B LEU* 4.5 8.2 - - + +
261B LEU* 3.8 28.7 - - + -
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Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU 2.9 17.6 + - - +
194B MET 3.2 3.6 + - - +
196B VAL* 1.3 77.2 - - - +
198B TYR* 1.3 65.2 + - - +
200B LEU* 2.9 16.9 + - + +
201B GLN* 3.0 51.6 + - + +
247B PHE* 4.0 15.9 - + - -
248B PHE* 4.3 11.9 - + - -
252B PHE* 4.6 18.4 - + - -
257B GLN* 4.9 5.9 + - - +
258B VAL 4.2 12.6 + - - -
259B ILE* 3.7 20.0 - - + -
260B SER 3.6 34.1 - - - -
261B LEU* 4.2 10.9 - - + +
265B GLY 4.5 10.1 + - - -
266B ILE* 4.8 12.1 - - - +
267B THR 6.1 0.4 - - - -
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Residues in contact with TYR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.4 8.5 - - + -
194B MET 3.0 13.3 + - - +
195B VAL 3.7 5.6 - - - +
197B TYR* 1.3 81.1 - - - +
199B LEU* 1.3 99.2 + - + +
201B GLN* 3.1 14.2 + - - +
202B ARG* 3.2 28.8 + - + +
204B HIS* 5.3 4.3 + + - -
240B GLN* 3.7 11.7 + - + +
243B ASP* 2.5 42.0 + - - +
244B PHE* 3.7 37.7 - + + -
247B PHE* 3.8 31.2 - + + -
248B PHE* 3.8 15.7 - - + -
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Residues in contact with LEU 199 (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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155B PHE* 5.0 6.7 - - + -
161B CYS* 4.1 32.1 - - + -
164B LEU* 4.2 11.2 - - + -
195B VAL* 2.9 37.3 + - + +
196B VAL* 3.9 1.3 - - + +
198B TYR* 1.3 99.5 - - + +
200B LEU* 1.3 58.8 + - - +
202B ARG* 3.5 2.8 + - - -
203B ASN 3.4 2.8 + - - -
204B HIS* 3.1 48.0 + - + +
205B LEU* 3.7 32.9 + - + -
240B GLN* 5.2 5.8 - - + +
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Residues in contact with LEU 200 (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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103A ARG* 4.1 10.5 + - - -
154B TYR* 4.0 30.3 - - + +
196B VAL* 2.9 14.9 + - + +
197B TYR* 2.9 9.1 + - + +
199B LEU* 1.3 76.1 - - - +
201B GLN* 1.3 68.2 + - + +
203B ASN* 3.2 13.7 + - - +
205B LEU* 3.5 40.7 - - + +
206B GLN 4.1 6.5 - - - +
207B PHE* 4.4 17.5 - - + +
260B SER 5.5 2.2 - - - +
261B LEU* 4.1 23.1 - - + -
263B ARG 5.9 1.3 - - - +
264B PRO* 6.4 0.4 - - + -
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Residues in contact with GLN 201 (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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103A ARG* 3.3 48.9 + - - +
197B TYR* 3.0 52.6 + - + +
198B TYR 3.1 6.5 + - - +
200B LEU* 1.3 79.8 - - - +
202B ARG* 1.3 63.4 + - + +
203B ASN* 3.3 0.4 + - - -
247B PHE* 4.1 23.7 - - + -
265B GLY* 3.4 22.4 + - - +
266B ILE* 4.5 16.6 - - - +
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Residues in contact with ARG 202 (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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198B TYR* 3.2 30.7 + - + +
199B LEU* 3.5 1.3 + - - +
200B LEU 3.2 0.8 - - - -
201B GLN* 1.3 77.8 + - - +
203B ASN* 1.3 70.1 + - - +
204B HIS* 3.2 33.6 + - + +
243B ASP* 2.9 37.5 + - - +
246B HIS* 5.1 1.0 - - - -
247B PHE* 3.7 22.8 - - - +
251B GLU* 2.6 42.2 + - - -
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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
------------------------------------------------------------
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