Contacts of the strand formed by residues 208 - 216 (chain B) in PDB entry 1EQR
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 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TYR* 4.2 9.0 + - - -
41A ARG* 3.1 11.0 + - - +
155B HIS* 2.7 40.8 + - - +
156B GLY* 3.5 11.1 - - - +
157B PHE* 3.8 27.2 - - + -
158B LEU* 2.9 30.0 + - - +
202B MET* 4.4 1.6 - - - -
206B PHE* 5.2 1.4 - - - +
207B ASP* 1.3 99.2 + - - +
209B TYR* 1.3 60.8 + - - +
235B GLU 3.5 5.6 - - - -
236B THR* 4.5 7.4 - - + -
237B SER 5.0 0.2 - - - +
239B MET* 3.1 43.0 - - - +
247B VAL* 5.6 3.0 - - - +
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Residues in contact with TYR 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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157B PHE* 3.5 8.3 - - - -
158B LEU 3.3 8.3 - - - +
160B ILE* 3.3 32.1 - - + -
162B THR* 4.3 2.0 - - + -
194B PRO* 3.4 8.9 - - + +
198B LYS* 3.4 31.4 - - + -
201B LEU* 3.7 27.1 - - + -
202B MET* 3.9 18.1 - - + +
206B PHE* 5.7 0.7 - - + -
208B ARG* 1.3 75.4 - - - +
210B TYR* 1.3 76.3 + - - +
211B GLN* 2.9 28.1 + - + +
233B ASP* 2.7 36.9 + - - -
234B VAL* 3.5 0.5 - - - -
235B GLU* 2.9 37.4 + - + +
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Residues in contact with TYR 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 VAL* 4.8 3.8 - - + -
149B ARG* 3.5 28.3 + - + +
152B MET* 3.6 41.7 - - + -
153B ASP* 2.4 35.1 + - - -
157B PHE* 3.3 28.5 - - + -
158B LEU 2.9 20.5 + - - +
159B ASP* 3.3 38.0 + - + +
160B ILE 3.7 0.2 + - - -
209B TYR* 1.3 84.9 - - - +
211B GLN* 1.3 83.2 + - - +
212B ILE* 4.8 9.9 - - + -
232B ILE* 5.1 2.2 - - + -
233B ASP 2.8 15.3 - - - +
234B VAL* 4.6 2.2 - - + -
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Residues in contact with GLN 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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159B ASP* 4.4 12.3 - - - +
160B ILE 3.6 9.6 - - - +
161B GLU* 2.8 37.4 - - - +
162B THR* 3.1 23.2 + - - +
164B MET* 6.1 0.2 - - - +
194B PRO* 3.7 4.7 - - - +
209B TYR* 2.9 32.2 + - + +
210B TYR* 1.3 84.9 - - - +
212B ILE* 1.3 69.1 + - - +
213B VAL* 3.4 24.6 + - + +
232B ILE* 3.8 1.4 - - - -
233B ASP* 2.9 29.6 + - - +
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Residues in contact with ILE 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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161A GLU* 4.6 4.7 - - - +
145B THR* 4.6 6.5 - - + -
148B VAL* 3.8 22.7 - - + -
149B ARG* 3.1 53.1 + - + +
159B ASP* 5.1 2.2 + - - -
210B TYR* 4.7 5.9 - - + -
211B GLN* 1.3 74.6 - - - +
213B VAL* 1.3 58.3 + - - +
230B THR* 3.6 24.2 - - + +
231B GLN 3.6 2.7 - - - +
232B ILE* 3.8 31.0 - - + -
535B LEU* 4.1 13.9 - - + -
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Residues in contact with VAL 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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162B THR* 5.0 0.9 - - - +
164B MET* 3.4 25.4 - - + -
194B PRO* 3.8 31.9 - - + -
211B GLN* 3.7 27.4 - - + +
212B ILE* 1.3 75.4 - - - +
214B LYS* 1.3 70.0 + - - +
215B CYS* 3.8 4.3 + - - -
230B THR* 4.0 5.2 - - - -
231B GLN* 2.9 36.8 + - + +
233B ASP* 3.9 22.7 - - + -
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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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161A GLU* 3.5 25.6 + - - +
162A THR 3.2 28.0 + - - -
163A PRO* 4.9 0.8 - - - +
164A MET* 4.0 28.0 - - + +
211A GLN* 5.3 2.7 - - - +
164B MET* 3.5 21.1 - - + +
191B PRO* 4.6 3.8 - - - +
193B SER* 5.1 0.7 - - - -
194B PRO* 5.1 0.3 - - - +
213B VAL* 1.3 87.8 - - - +
215B CYS* 1.3 67.5 + - - +
216B PHE* 4.4 10.5 - - + -
228B GLU* 3.2 34.0 + - + +
229B PHE* 3.8 5.7 - - - +
230B THR* 3.8 14.5 + - - +
552B ILE* 6.3 0.6 - - - +
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Residues in contact with CYS 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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191B PRO 3.6 4.5 - - - -
192B GLN 2.6 25.8 - - - +
193B SER* 3.5 21.1 - - - -
194B PRO* 4.3 4.7 - - - -
213B VAL* 4.0 4.7 - - - -
214B LYS* 1.3 82.0 - - - +
216B PHE* 1.3 64.3 + - - +
228B GLU* 3.1 6.8 - - - +
229B PHE* 2.9 51.5 + - + +
231B GLN* 3.6 22.9 - - - -
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Residues in contact with PHE 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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164A MET* 4.0 23.8 - - + -
165A LEU* 4.0 15.3 - - + -
164B MET* 3.9 24.7 - - - -
176B TYR* 3.6 22.4 - + + -
190B LEU* 3.7 44.0 - - + +
191B PRO 2.9 24.0 + - - +
192B GLN* 2.6 36.2 - - - +
214B LYS* 4.4 7.6 - - + -
215B CYS* 1.3 81.0 - - - +
217B ARG* 1.3 56.5 + - - +
227B PRO 3.5 6.7 - - - -
228B GLU* 3.7 29.2 - - + -
229B PHE* 4.3 3.9 - - - -
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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