Contacts of the strand formed by residues 208 - 218 (chain B) in PDB entry 4JF7
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 PRO 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B TYR* 3.5 27.1 - - + +
146B LEU* 5.3 2.9 - - + -
148B MET* 3.7 14.5 - - - +
200B ILE* 3.5 22.0 - - + -
201B GLU 3.5 1.1 - - - +
203B THR* 4.5 0.6 - - - +
206B GLY 4.7 0.2 - - - +
207B PHE* 1.4 108.6 - - + +
209B PHE* 1.3 58.5 + - - +
210B PHE* 4.1 13.2 - - + -
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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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194A PHE* 4.5 13.9 - + - -
215A THR* 4.2 9.0 - - - -
216A LEU 4.4 0.9 - - - -
217A TYR* 3.3 36.1 - + + -
148B MET* 4.4 3.1 - - + -
149B PRO* 3.8 44.2 - - + -
200B ILE* 3.3 4.0 - - - -
201B GLU* 2.6 56.4 + - + +
203B THR* 3.9 16.8 - - + -
208B PRO* 1.3 74.8 - - - +
210B PHE* 1.3 74.0 + - - +
211B ARG* 3.3 42.1 + - + -
212B THR 5.0 0.2 - - - -
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Residues in contact with PHE 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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148B MET* 3.9 27.2 - - + -
149B PRO 4.8 1.1 - - - +
151B PHE* 3.5 44.6 - + + +
167B PHE* 3.6 27.6 - + - -
169B LEU* 5.1 4.9 - - + -
174B TRP* 3.2 35.9 - + - +
199B ILE 3.5 2.0 - - - -
200B ILE* 3.8 30.5 - - + -
208B PRO* 4.5 9.2 - - + -
209B PHE* 1.3 87.1 - - - +
211B ARG* 1.3 62.6 + - - +
212B THR 3.6 2.1 + - - -
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Residues in contact with ARG 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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214A LYS* 4.0 16.4 - - - +
215A THR* 2.8 30.6 + - - +
216A LEU* 4.0 19.4 - - - +
268A ASP* 4.4 7.9 + - - -
270A ILE* 5.7 2.8 - - - +
174B TRP* 3.8 1.6 - - - -
198B GLY* 3.1 4.3 - - - -
199B ILE* 2.6 59.5 + - + +
201B GLU* 3.4 34.5 + - + -
209B PHE* 3.3 28.9 + - + +
210B PHE* 1.3 70.4 - - - +
212B THR* 1.3 61.4 + - - +
213B LEU* 3.7 19.3 - - + +
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 4.6 10.1 - - + -
214A LYS 3.9 0.2 - - - -
215A THR* 2.8 53.9 + - + -
151B PHE* 3.5 29.5 + - - +
174B TRP* 3.7 7.0 - - - -
194B PHE* 6.0 0.2 - - + -
196B SER* 4.4 6.9 + - - -
197B MET 3.8 5.6 - - - +
209B PHE* 5.0 0.2 - - - -
210B PHE 3.6 2.2 + - - -
211B ARG* 1.3 70.0 - - - +
213B LEU* 1.3 64.5 + - - +
214B LYS* 3.7 24.5 - - - +
215B THR* 4.2 10.8 - - - +
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Residues in contact with LEU 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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213A LEU 2.8 24.4 - - - +
214A LYS* 4.4 12.3 - - + +
266A TYR* 5.1 0.5 + - - -
268A ASP* 5.5 1.8 - - - +
116B ALA* 3.6 34.8 - - + +
117B LEU* 3.8 19.1 - - + -
197B MET 2.8 10.5 + - - +
198B GLY* 4.2 2.2 - - - -
199B ILE* 4.1 15.0 - - + +
211B ARG* 3.5 42.6 + - - +
212B THR* 1.3 81.8 - - - +
214B LYS* 1.3 64.9 + - - +
266B TYR* 3.6 26.6 + - + +
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Residues in contact with LYS 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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112A SER* 3.6 9.5 + - - -
211A ARG* 4.0 10.5 - - - +
212A THR 4.0 6.3 - - - -
213A LEU* 4.5 9.5 - - + +
266A TYR* 4.2 6.3 + - - -
196B SER* 3.3 6.3 - - - -
197B MET* 3.0 46.1 + - + +
212B THR* 3.7 4.2 - - - +
213B LEU* 1.3 79.7 + - - +
215B THR* 1.3 70.5 + - - +
216B LEU* 4.0 19.5 - - + -
264B MET* 6.4 0.2 - - + -
265B TYR 3.6 8.3 - - - +
266B TYR* 2.9 48.9 + - + +
268B ASP* 2.7 28.4 + - - +
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Residues in contact with THR 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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209A PHE* 3.9 17.0 - - + -
211A ARG* 2.8 58.7 + - + -
212A THR* 3.1 32.0 + - - +
194B PHE* 3.1 28.7 - - + -
195B VAL 3.4 4.0 - - - -
196B SER* 3.7 4.5 - - - -
212B THR* 4.2 6.5 - - - +
214B LYS* 1.3 75.0 + - - +
216B LEU* 1.3 59.9 + - - +
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Residues in contact with LEU 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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209A PHE* 4.5 3.6 - - - -
211A ARG* 4.0 17.5 - - - +
193B GLN 4.6 0.2 - - - -
194B PHE* 3.6 7.6 - - - -
195B VAL* 2.7 56.8 + - + +
197B MET* 4.4 13.0 - - + -
214B LYS* 4.0 20.4 - - + -
215B THR* 1.3 82.6 - - - +
217B TYR* 1.3 62.2 + - - +
218B LEU* 4.1 10.5 - - + -
264B MET* 4.1 24.9 - - + -
270B ILE* 3.6 31.4 - - + -
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Residues in contact with TYR 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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147A ASN 4.8 1.6 + - - -
148A MET* 5.8 0.2 - - - -
149A PRO* 3.6 34.4 - - + +
201A GLU* 4.3 11.6 + - - +
203A THR* 3.7 25.4 - - + -
207A PHE* 6.4 0.7 - + - -
209A PHE* 3.4 40.4 - + + -
180B VAL* 3.5 29.2 - - + +
182B LEU* 4.3 4.5 - - - +
192B ASN* 2.9 44.5 + - + +
193B GLN 3.6 2.7 - - - -
194B PHE* 4.0 17.0 - + + -
216B LEU* 1.3 75.5 - - - +
218B LEU* 1.3 63.4 + - - +
219B SER* 3.2 15.3 + - - -
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Residues in contact with LEU 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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191B SER 4.6 0.7 - - - +
192B ASN* 3.3 6.8 - - - +
193B GLN* 2.9 37.7 + - + +
195B VAL* 4.4 9.6 - - + -
216B LEU* 4.8 18.4 - - + -
217B TYR* 1.3 70.7 - - - +
219B SER* 1.3 59.4 + - - +
220B ASP 4.0 1.3 - - - -
222B VAL 5.6 0.7 - - - +
224B ARG* 3.9 34.7 + - - +
238B MET* 3.7 30.1 - - + -
262B ILE* 4.7 13.0 - - + -
264B MET* 4.6 8.7 - - - -
270B ILE* 5.5 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