Contacts of the strand formed by residues 193 - 203 (chain B) in PDB entry 4K71
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 PHE 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PRO* 3.8 2.9 - - - +
189B SER* 2.9 32.6 + - - +
190B SER* 2.8 35.3 + - - +
191B PRO 3.6 8.3 - - - -
192B GLY* 1.3 86.6 - - - +
194B SER* 1.3 62.0 + - - +
241B THR* 3.8 19.5 - - + -
242B VAL* 3.4 18.8 - - - +
243B LYS* 4.5 14.8 - - + -
244B SER* 3.0 8.4 + - - +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ALA* 4.8 1.5 - - - +
187B ARG 3.2 16.9 + - - -
188B PRO* 4.3 5.4 - - - +
189B SER* 3.5 5.7 + - - -
193B PHE* 1.3 75.8 + - - +
195B VAL* 1.3 63.8 + - - +
241B THR* 3.4 4.5 - - - +
242B VAL* 2.9 37.3 + - - +
243B LYS 4.8 0.2 - - - -
244B SER* 4.1 5.3 + - - +
247B GLU* 2.5 41.7 + - - -
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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
----------------------------------------------------------
185B LYS 3.8 0.9 - - - +
186B ALA* 3.3 3.3 - - - -
187B ARG* 2.9 37.5 + - + +
188B PRO 4.7 1.8 - - - +
189B SER* 3.7 17.7 - - - -
194B SER* 1.3 73.0 - - - +
196B LEU* 1.3 63.1 + - - +
197B THR* 3.9 6.1 - - - +
239B SER* 3.7 28.0 - - - +
240B LEU 3.7 8.7 - - - +
241B THR* 4.6 4.0 - - - +
99C MET* 3.5 20.1 - - + +
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Residues in contact with LEU 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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184B LEU* 4.4 16.6 - - + -
185B LYS 3.4 3.1 - - - +
186B ALA* 3.3 30.1 - - + +
194B SER* 4.1 0.4 - - - -
195B VAL* 1.3 73.7 - - - +
197B THR* 1.3 60.3 + - - +
198B CYS 4.2 0.7 - - - -
212B PHE* 4.0 19.2 - - + -
238B SER 3.8 0.7 - - - +
239B SER* 3.1 6.4 - - - -
240B LEU* 2.8 34.1 + - + +
242B VAL* 4.0 16.8 - - + -
247B GLU* 3.9 21.1 - - + +
250B TYR* 3.5 40.6 - - + -
267B LEU* 4.8 2.7 - - + -
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Residues in contact with THR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ARG 3.6 1.7 - - - +
184B LEU* 3.5 5.5 - - - -
185B LYS* 2.9 29.6 + - - -
195B VAL* 3.9 3.1 - - - +
196B LEU* 1.3 73.3 - - - +
198B CYS* 1.3 61.1 + - - +
199B SER* 3.7 13.6 + - - +
237B SER* 3.9 10.5 - - - -
238B SER 3.4 5.4 - - - +
239B SER* 3.1 24.1 + - - +
98C ASP 3.8 12.8 - - - +
99C MET* 3.2 49.6 + - - +
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Residues in contact with CYS 198 (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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182B MET* 3.6 23.3 - - - -
183B ARG 3.5 7.0 - - - -
184B LEU* 3.9 7.0 - - + +
196B LEU 4.2 0.6 - - - -
197B THR* 1.3 70.6 - - - +
199B SER* 1.3 59.4 + - - +
210B LEU* 3.8 8.2 - - + +
212B PHE* 4.1 8.4 - - + -
237B SER* 3.1 4.7 - - - -
238B SER* 2.8 37.9 + - - +
252B CYS* 2.0 53.4 - - + -
265B VAL* 4.7 2.9 - - - -
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Residues in contact with SER 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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181B SER 3.7 0.9 - - - +
182B MET* 3.2 12.1 - - - +
183B ARG* 2.8 34.0 + - - -
197B THR* 3.7 8.5 + - - +
198B CYS* 1.3 75.3 - - - +
200B ALA* 1.3 59.5 + - - +
201B PHE* 3.6 27.0 - - - -
210B LEU* 5.4 0.2 - - - -
235B HIS* 4.7 4.4 + - - -
236B ALA 3.6 6.3 - - - -
237B SER* 3.8 5.0 - - - -
98C ASP* 3.4 26.4 + - - -
99C MET* 4.2 1.2 + - - -
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Residues in contact with ALA 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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180B PRO* 3.8 7.2 - - + -
181B SER 3.6 4.5 - - - -
182B MET* 3.7 20.2 - - + -
198B CYS 4.4 0.2 + - - -
199B SER* 1.3 73.1 - - - +
201B PHE* 1.3 60.7 + - - +
203B PHE* 3.6 19.2 - - + -
208B LEU* 3.9 19.5 - - + -
210B LEU* 4.7 1.3 - - + -
235B HIS* 3.4 9.0 - - - -
236B ALA 2.9 30.7 + - - +
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Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PRO* 3.4 2.1 - - - +
181B SER* 2.9 40.7 + - - +
183B ARG* 4.1 11.9 - - + -
199B SER* 3.6 28.7 - - - -
200B ALA* 1.3 75.7 - - - +
202B SER* 1.3 69.5 + - - +
203B PHE* 3.6 1.3 - - - -
234B PHE 4.3 0.2 - - - -
235B HIS* 3.6 17.5 - + - -
10C TYR* 5.5 0.4 - - + -
11C SER* 3.4 41.5 - - - -
12C ARG 3.6 7.6 - - - +
13C HIS* 3.6 11.0 - - - +
14C PRO* 3.6 29.8 - - + -
98C ASP* 3.4 28.7 - - - -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 3.1 30.4 - - - +
179B PRO 3.6 5.2 - - - +
181B SER* 5.8 0.9 - - - -
201B PHE* 1.3 76.0 - - - +
203B PHE* 1.3 56.4 + - - +
229B ASN* 3.7 11.3 + - - +
233B SER* 3.7 6.8 + - - -
234B PHE 2.9 15.3 + - - -
235B HIS* 4.8 0.2 - - - +
12C ARG* 2.7 39.8 + - - +
13C HIS* 3.5 21.6 - - - -
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 3.2 14.1 - - - +
180B PRO* 3.6 31.6 - - + -
200B ALA* 3.6 30.3 - - + -
202B SER* 1.3 76.1 - - - +
204B TYR* 1.3 62.7 - - - +
205B PRO 3.4 13.7 - - - -
206B PRO 3.5 22.7 - - - -
208B LEU* 4.0 13.9 - - + -
226B PHE* 3.8 13.7 - + - -
233B SER* 4.2 1.8 - - - -
234B PHE* 2.7 70.9 + - + +
236B ALA* 3.8 13.9 - - + -
256B HIS* 3.6 8.5 - + - +
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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