Contacts of the strand formed by residues 197 - 205 (chain B) in PDB entry 1P13
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 TYR 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B TYR* 3.5 33.9 + + - -
187B VAL* 4.2 3.8 - - + -
188B ARG 3.2 16.6 - - - +
189B GLU* 3.7 23.5 + - + -
195B GLY* 3.4 29.4 - - - -
196B ALA* 1.3 71.7 - - - +
198B CYS* 1.3 59.3 + - - +
217B ILE* 2.8 48.8 + - + +
225B PHE* 4.7 11.9 - + - -
236B LEU* 3.7 34.8 - - + -
399B CAC 3.2 13.7 - - - +
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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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187B VAL* 3.4 6.6 - - - +
188B ARG* 2.9 48.3 + - + +
197B TYR* 1.3 72.2 - - - +
199B LEU* 1.3 63.3 + - - +
200B SER* 4.9 0.2 - - - +
215B TYR 3.1 11.7 - - - +
216B LYS* 3.9 4.5 - - - -
217B ILE* 3.8 5.4 - - - -
399B CAC 2.0 57.2 - - - +
3C PTR 3.7 22.4 - - + -
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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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185B PHE* 3.7 30.3 - - + -
186B LEU 3.7 7.2 - - - +
187B VAL* 4.1 9.6 - - + +
198B CYS* 1.3 73.7 - - - +
200B SER* 1.3 60.3 + - - +
201B VAL* 3.7 21.5 - - + -
213B LYS 3.6 1.7 - - - +
214B HIS* 3.5 2.1 - - - -
215B TYR* 2.8 45.8 + - + +
217B ILE* 3.9 16.7 - - + +
227B ILE* 3.9 28.7 - - + -
239B LEU* 4.7 8.1 - - + -
240B VAL* 5.2 3.1 - - + -
243B TYR* 5.3 0.4 - - + -
250B LEU* 4.9 4.3 - - + -
254B LEU* 4.2 19.7 - - + -
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Residues in contact with SER 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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171B SER* 4.4 1.8 - - - -
175B LEU* 3.4 21.9 - - - +
185B PHE* 3.2 5.4 - - - +
186B LEU* 2.9 43.3 + - - -
188B ARG* 3.0 21.0 + - - -
198B CYS* 4.0 0.8 - - - +
199B LEU* 1.3 71.3 - - - +
201B VAL* 1.3 61.8 + - - +
213B LYS 3.4 4.7 - - - -
214B HIS* 2.8 29.3 + - - -
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Residues in contact with VAL 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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175B LEU* 4.4 0.4 - - - -
183B GLY* 3.8 19.3 - - - +
184B THR 3.4 9.2 - - - +
185B PHE* 4.1 0.7 - - + -
199B LEU* 3.7 27.6 - - + -
200B SER* 1.3 80.1 - - - +
202B SER* 1.3 74.4 + - - +
203B ASP* 4.4 0.8 - - + +
212B VAL* 3.3 6.2 - - - +
213B LYS* 2.8 45.8 + - + +
215B TYR* 4.4 13.7 - - + -
250B LEU* 5.5 2.5 - - + -
252B HIS* 5.3 5.4 - - + +
254B LEU* 3.8 20.6 - - + -
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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
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175B LEU* 3.7 28.5 - - - +
176B LEU* 6.0 0.9 - - - -
180B ASN* 4.6 2.8 - - - +
181B PRO 3.0 25.1 + - - -
182B ARG* 3.9 3.0 - - - +
183B GLY* 3.0 22.3 + - - -
184B THR* 2.8 25.2 + - - -
201B VAL* 1.3 79.3 - - - +
203B ASP* 1.3 62.1 + - - +
210B LEU* 5.7 6.3 - - - -
211B ASN 3.7 6.7 - - - -
212B VAL* 4.5 4.0 - - - +
252B HIS* 5.8 0.5 - - - +
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Residues in contact with ASP 203 (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 ARG* 2.7 43.1 + - - +
201B VAL* 4.4 1.8 - - + +
202B SER* 1.3 75.7 - - - +
204B PHE* 1.3 76.5 + - - +
205B ASP* 3.7 2.6 - - - +
210B LEU* 3.6 12.2 - - - +
211B ASN* 2.8 35.3 + - - +
213B LYS* 2.3 51.0 + - + +
251B CYS* 3.5 9.6 - - - +
252B HIS* 4.8 2.1 - - - +
352B CAC 4.9 0.2 - - - +
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Residues in contact with PHE 204 (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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173A ARG* 3.6 53.2 - - + +
176A LEU* 3.7 24.9 - - + -
177A ASN 5.5 0.2 - - - -
182B ARG* 3.4 31.3 + - + +
203B ASP* 1.3 82.8 + - - +
205B ASP* 1.3 61.8 + - - +
206B ASN* 3.4 33.4 + - - +
209B GLY* 3.3 33.9 - - - -
210B LEU* 3.5 12.8 - - + -
211B ASN* 3.5 3.6 - - - +
352B CAC 5.4 0.9 - - - +
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Residues in contact with ASP 205 (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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203B ASP* 3.7 2.6 - - - +
204B PHE* 1.3 75.0 - - - +
206B ASN* 1.3 61.2 + - - +
207B ALA* 3.0 2.2 - - + +
208B LYS* 3.2 41.7 + - + +
209B GLY* 2.3 42.6 + - - -
211B ASN* 2.6 31.4 + - - +
213B LYS* 3.4 16.2 + - - -
352B CAC 5.0 10.7 - - - +
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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