Contacts of the strand formed by residues 209 - 219 (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 GLY 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B PHE* 3.3 23.1 - - - -
205B ASP 2.3 43.2 + - - -
206B ASN 4.2 2.9 + - - -
208B LYS* 1.3 70.9 - - - +
210B LEU* 1.3 67.7 + - - -
211B ASN* 3.3 4.2 + - - -
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Residues in contact with LEU 210 (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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170A GLU* 5.7 0.4 - - - +
173A ARG* 3.6 49.8 - - - +
175B LEU 6.0 0.4 - - - +
176B LEU* 4.0 39.5 - - + +
177B ASN 5.7 0.9 - - - +
178B PRO* 5.2 8.1 - - + -
180B ASN 5.7 0.4 - - - +
202B SER* 5.7 6.3 - - - -
203B ASP 3.6 15.9 - - - +
204B PHE* 3.5 8.7 - - + -
208B LYS 3.8 6.1 + - - +
209B GLY* 1.3 72.3 - - - -
211B ASN* 1.3 61.8 + - - +
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Residues in contact with ASN 211 (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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176B LEU* 4.0 6.8 - - - +
202B SER* 3.7 3.6 - - - -
203B ASP* 2.8 43.2 + - - +
204B PHE 3.4 0.4 - - - +
205B ASP* 2.6 38.4 + - - +
208B LYS* 5.1 7.0 - - + -
209B GLY 3.3 9.6 + - - +
210B LEU* 1.3 79.0 - - - +
212B VAL* 1.3 68.4 + - - +
213B LYS* 3.2 27.4 + - - +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 5.2 1.0 + - - -
172B GLU* 3.8 28.4 + - + +
175B LEU* 3.7 35.4 - - + -
176B LEU* 3.7 27.1 - - + +
201B VAL 3.3 11.4 - - - +
202B SER* 4.8 1.3 - - - -
211B ASN* 1.3 86.2 - - - +
213B LYS* 1.3 65.1 + - - +
214B HIS* 3.4 35.8 - - + +
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Residues in contact with LYS 213 (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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199B LEU 3.6 1.6 - - - +
200B SER* 3.4 3.5 - - - -
201B VAL* 2.8 38.5 + - + +
203B ASP* 2.3 41.1 + - + +
205B ASP* 3.4 16.7 + - - -
211B ASN* 3.2 18.4 + - - +
212B VAL* 1.3 73.6 - - - +
214B HIS* 1.3 60.9 + - - +
215B TYR* 3.5 35.0 - - + +
251B CYS* 3.8 20.8 - - + -
352B CAC 5.0 5.2 - - - -
4C ALA* 4.4 11.4 - - + -
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Residues in contact with HIS 214 (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 ARG* 3.5 46.4 - - + +
171B SER* 4.8 1.8 - - - -
172B GLU* 2.7 31.0 + - + -
188B ARG* 3.1 12.7 + - - +
198B CYS* 5.6 0.4 - - + -
199B LEU 3.5 3.8 - - - +
200B SER* 2.8 27.3 + - - -
212B VAL* 3.4 27.5 - - + +
213B LYS* 1.3 74.2 - - - +
215B TYR* 1.3 59.2 + - - +
2C ASP 4.1 3.3 + - - +
3C PTR 3.3 26.4 - - + -
4C ALA 2.7 34.1 + - - +
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Residues in contact with TYR 215 (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 CYS* 3.1 4.8 - - - -
199B LEU* 2.8 56.7 + - + +
201B VAL* 4.4 8.7 - - + -
213B LYS* 3.5 40.3 - - + +
214B HIS* 1.3 74.1 - - - +
216B LYS* 1.3 62.5 + - - +
217B ILE* 4.1 0.5 - - - +
227B ILE* 3.8 28.5 - - + +
250B LEU* 3.4 29.3 - - + +
251B CYS* 4.8 3.8 + - - -
3C PTR 4.3 1.8 - - - -
4C ALA* 3.4 36.5 - - + +
5C ASN* 4.1 2.6 + - - -
6C PHE* 3.7 32.9 - + - +
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Residues in contact with LYS 216 (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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197B TYR 3.9 5.2 - - - +
198B CYS* 3.9 6.7 - - - -
215B TYR* 1.3 73.8 - - - +
217B ILE* 1.3 61.7 + - - +
218B ARG* 3.6 49.6 + - - +
226B TYR 3.6 6.2 - - - +
227B ILE* 3.8 12.1 - - - +
399B CAC 4.9 11.0 - - + -
3C PTR 3.5 53.6 - - + +
4C ALA 5.0 1.8 + - - -
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Residues in contact with ILE 217 (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* 4.4 9.0 - - + -
195B GLY 5.7 0.2 - - - +
196B ALA* 5.1 2.8 - - - +
197B TYR* 2.8 37.4 + - + +
198B CYS 3.8 19.7 - - - +
199B LEU* 3.9 16.2 - - + +
216B LYS* 1.3 71.1 - - - +
218B ARG* 1.3 62.8 + - - +
219B LYS* 5.2 1.0 - - - +
225B PHE* 3.9 26.0 - - + -
226B TYR 3.4 4.3 - - - +
227B ILE* 3.7 17.7 - - + -
236B LEU* 3.9 32.8 - - + -
239B LEU* 4.0 18.8 - - + -
399B CAC 5.7 0.2 - - - +
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Residues in contact with ARG 218 (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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216B LYS* 3.8 46.8 + - - +
217B ILE* 1.3 77.1 - - - +
219B LYS* 1.3 62.2 + - - +
220B LEU* 5.5 2.9 - - + -
225B PHE* 3.2 5.2 - - - -
226B TYR* 2.8 75.1 + - + +
227B ILE* 5.8 0.7 - - - +
3C PTR 6.0 1.2 - - - +
5C ASN* 5.8 4.2 + - - +
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Residues in contact with LYS 219 (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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195B GLY 5.9 2.5 - - - +
217B ILE 4.2 1.1 + - - +
218B ARG* 1.3 77.8 - - - +
220B LEU* 1.3 71.8 + - - +
221B ASP* 4.3 3.0 + - - +
223B GLY 3.9 15.3 - - - -
224B GLY* 3.6 24.9 - - - -
225B PHE* 3.7 45.7 - - + +
226B TYR* 4.8 0.2 - - - -
234B SER 5.7 0.7 - - - -
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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