Contacts of the strand formed by residues 202 - 215 (chain B) in PDB entry 4RE1
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 ARG 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A GLU* 5.8 0.2 - - - -
300A SER* 4.7 9.4 - - - +
331A ASN 4.9 4.0 + - - -
332A GLY 3.4 24.4 + - - -
333A ARG* 3.8 34.8 - - - +
194B ARG* 4.0 27.0 - - + +
196B ILE 3.8 4.9 - - - +
197B GLY* 4.1 8.1 - - - -
198B THR 3.1 30.9 + - - +
199B THR* 3.2 21.4 + - - +
201B LEU* 1.3 74.5 - - - +
203B LEU* 1.3 61.8 + - - +
204B VAL* 3.4 3.7 + - + +
297B TYR* 3.1 7.6 - - - +
298B GLU* 3.0 41.4 + - + +
299B SER* 3.7 26.6 - - - +
300B SER 3.9 4.9 - - - +
333B ARG* 6.0 0.8 - - - +
386B LEU* 4.2 3.1 - - - -
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ARG* 4.1 16.1 - - - +
195B SER 5.3 0.2 + - - -
196B ILE* 2.8 46.4 + - + +
202B ARG* 1.3 70.0 - - - +
204B VAL* 1.3 59.8 + - - +
205B GLU 3.3 28.3 - - - +
206B PHE* 4.1 21.1 - - + -
227B ILE* 4.2 15.3 - - + +
295B SER* 4.7 0.9 - - - -
296B GLN 3.6 7.4 - - - +
297B TYR* 3.6 36.1 - - + +
386B LEU* 3.8 3.6 - - + +
388B MET* 4.0 24.2 - - + -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ARG* 3.5 35.3 + - - +
202B ARG 4.0 7.9 - - - +
203B LEU* 1.3 77.1 - - - +
205B GLU* 1.3 66.3 + - + +
227B ILE* 6.0 0.7 - - - -
228B GLY* 3.6 20.3 - - - -
296B GLN* 2.8 24.8 + - + +
298B GLU* 3.4 46.0 - - + +
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Residues in contact with GLU 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 LEU* 3.3 10.9 - - - +
204B VAL* 1.3 85.6 - - + +
206B PHE* 1.3 65.6 + - - +
207B SER* 3.7 18.2 + - - -
226B HIS* 4.2 14.9 - - + +
227B ILE 3.4 10.5 - - - +
228B GLY* 5.5 1.3 - - - -
294B THR* 3.7 22.5 - - - +
295B SER* 3.1 4.1 - - - -
296B GLN* 2.9 35.3 + - + +
337B ARG* 3.5 21.9 + - - -
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Residues in contact with PHE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 4.1 21.8 - - + -
205B GLU* 1.3 76.7 - - - +
207B SER* 1.3 68.6 + - - +
208B ALA* 4.8 2.5 - - + -
225B VAL* 4.1 24.9 - - + -
226B HIS* 3.1 2.8 + - - -
227B ILE* 2.6 47.2 + - + +
275B PHE* 4.7 17.0 - + - -
293B VAL* 3.8 27.6 - - + -
294B THR 3.5 3.6 - - - -
295B SER* 3.8 18.6 - - - -
297B TYR* 5.0 0.7 - - - -
374B LEU* 4.0 28.7 - - + -
388B MET* 5.6 3.8 - - + -
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Residues in contact with SER 207 (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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205B GLU* 3.7 12.8 + - - -
206B PHE* 1.3 82.8 - - - +
208B ALA* 1.3 60.0 + - - +
209B PHE* 3.7 13.3 - - - -
221B LYS* 5.1 2.9 + - - -
223B LEU* 4.5 12.4 - - - +
225B VAL 3.3 9.6 - - - -
226B HIS* 3.4 23.3 - - - -
293B VAL* 3.4 6.1 - - - +
294B THR* 2.9 34.7 + - - -
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Residues in contact with ALA 208 (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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206B PHE* 5.0 3.6 - - + -
207B SER* 1.3 72.7 - - - +
209B PHE* 1.3 62.4 + - - +
223B LEU* 3.5 2.8 - - - +
224B PHE* 2.8 32.1 + - + -
225B VAL* 3.1 28.1 + - + +
292B GLY 3.4 4.9 - - - -
293B VAL* 4.0 12.1 - - + -
343B MET* 3.9 20.9 - - + -
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Residues in contact with PHE 209 (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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207B SER* 3.7 17.3 - - - -
208B ALA* 1.3 75.5 - - - +
210B LEU* 1.3 61.7 - - - +
211B GLU* 3.8 34.3 - - + -
221B LYS* 4.0 18.6 - - + -
222B HIS 3.1 13.0 - - - +
223B LEU* 3.8 13.9 - - + -
224B PHE* 3.6 12.9 - - - -
290B PHE* 4.1 15.9 - + - -
291B TYR* 3.5 3.6 - - - -
292B GLY* 2.9 50.4 + - - +
293B VAL 4.3 0.4 - - - -
294B THR* 3.6 30.3 - - - -
340B ARG* 4.2 17.9 - - + -
343B MET* 4.3 0.5 - - - +
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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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209B PHE* 1.3 74.5 - - - +
211B GLU* 1.3 73.2 + - - +
212B GLN* 4.2 26.7 + - + +
220B ASN* 3.7 1.6 + - - +
221B LYS* 3.3 3.8 - - - -
222B HIS* 2.7 43.8 + - + +
224B PHE* 3.7 15.9 - - + -
281B CYS* 4.3 24.5 - - + -
282B ASN 5.5 4.0 - - - +
289B ALA* 4.3 6.7 - - + -
290B PHE 3.5 9.6 - - - +
291B TYR* 3.6 44.4 - - + +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 3.8 22.8 - - + -
210B LEU* 1.3 73.3 - - - +
212B GLN* 1.3 62.1 + - - +
219B TYR* 2.5 42.4 + - + +
220B ASN 3.3 3.6 - - - +
221B LYS* 4.2 6.6 - - + +
288B GLY 3.8 0.2 - - - +
289B ALA* 3.2 5.2 - - - -
290B PHE* 2.7 48.8 + - + +
340B ARG* 2.6 41.2 + - - -
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Residues in contact with GLN 212 (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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210B LEU* 4.2 28.5 + - + +
211B GLU* 1.3 79.7 - - - +
213B GLN* 1.3 60.9 + - - +
214B ARG* 3.9 3.1 + - + +
219B TYR* 3.6 5.7 - - - -
220B ASN* 2.8 61.3 + - + +
222B HIS* 5.9 1.6 - - - +
281B CYS* 5.6 2.0 - - - +
282B ASN 4.0 30.9 - - - +
288B GLY 3.3 8.1 - - - +
289B ALA* 4.4 7.2 - - + +
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Residues in contact with GLN 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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212B GLN* 1.3 72.3 - - - +
214B ARG* 1.3 65.7 + - - +
215B ASP* 3.0 24.9 + - - +
216B PRO* 3.7 16.9 + - + +
217B ASP 4.9 0.2 - - - -
218B SER 3.2 13.2 + - - -
219B TYR* 3.4 26.1 - - + +
288B GLY* 2.9 30.9 + - - +
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Residues in contact with ARG 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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212B GLN* 3.9 3.0 + - - +
213B GLN* 1.3 75.4 - - - +
215B ASP* 1.3 65.2 + - - +
218B SER* 3.5 18.7 + - - -
288B GLY 5.3 2.9 - - - +
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Residues in contact with ASP 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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213B GLN* 3.0 21.2 + - - -
214B ARG* 1.3 81.2 - - - +
216B PRO* 1.3 76.4 - - + +
217B ASP* 2.7 37.2 + - - +
218B SER* 2.7 30.2 + - - +
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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