Contacts of the strand formed by residues 198 - 208 (chain B) in PDB entry 4EOH
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 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B ASP* 5.5 1.4 - - - -
190B LEU 4.9 4.3 - - - +
192B SER* 3.7 24.4 - - - +
194B GLN* 3.6 58.8 + - + -
195B GLY 3.5 9.4 + - - +
196B SER* 3.1 1.5 - - - +
197B ASN* 1.3 89.9 - - + +
199B LEU* 1.3 60.9 + - - +
222B ASP 3.7 10.1 - - - -
223B ILE 3.2 7.9 - - - +
224B ARG* 3.2 55.7 + - + -
225B LYS* 3.4 15.2 + - - -
411B MPD 3.9 19.4 - - + +
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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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186B THR 4.0 7.9 - - - +
187B SER* 4.4 9.9 - - - -
188B SER* 3.3 11.0 - - - +
189B ASP* 4.9 2.7 - - - +
190B LEU 5.8 0.2 - - - -
198B TYR* 1.3 74.1 - - - +
200B ILE* 1.3 75.0 + - - +
201B VAL* 3.8 19.1 - - + -
222B ASP* 3.4 4.2 - - - -
223B ILE* 2.7 51.3 + - + +
224B ARG 5.1 0.4 - - - +
225B LYS* 3.9 30.5 - - + +
408B MPD 3.8 22.0 - - + +
410B MPD 6.2 0.2 - - - -
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Residues in contact with ILE 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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185B ILE 4.1 1.7 - - - +
187B SER 3.7 4.5 - - - -
188B SER* 2.2 60.9 + - - +
190B LEU* 3.8 26.0 - - + +
191B PRO 4.0 1.1 - - - +
192B SER* 3.8 8.1 - - - -
199B LEU* 1.3 74.0 - - - +
201B VAL* 1.3 68.4 + - - +
202B LEU* 3.9 27.2 + - + +
220B ARG* 3.0 35.2 - - - +
221B MET 3.4 4.5 - - - +
222B ASP* 2.8 37.9 - - - +
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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
----------------------------------------------------------
184B VAL* 4.2 18.4 - - + -
185B ILE 3.7 7.6 - - - +
186B THR* 3.1 23.6 - - - +
199B LEU* 3.8 6.7 - - + -
200B ILE* 1.3 74.7 - - - +
202B LEU* 1.3 68.0 + - - +
219B ILE* 4.9 4.3 - - + -
220B ARG* 3.2 5.5 - - - +
221B MET* 2.8 50.7 + - + +
223B ILE* 3.7 22.7 - - + -
237B PHE* 4.9 6.5 - - + -
256B CYS* 5.8 2.7 - - - -
260B VAL* 5.1 4.0 - - + -
408B MPD 4.0 11.9 - - + -
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Residues in contact with LEU 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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165B GLN* 4.4 13.0 - - + +
168B ALA* 3.5 20.0 - - + -
169B LEU* 4.8 2.2 - - + -
172B MET* 3.3 35.5 - - + +
183B VAL 4.1 0.3 - - - +
184B VAL* 3.3 4.3 - - - +
185B ILE* 2.9 39.5 + - + +
188B SER* 6.3 0.4 - - - -
190B LEU* 4.2 16.6 - - + -
200B ILE* 3.9 10.7 - - + +
201B VAL* 1.3 80.7 - - - +
203B GLY* 1.3 59.6 + - - +
219B ILE 3.5 4.9 - - - +
220B ARG* 3.7 34.5 - - + -
312B LEU* 3.9 12.8 - - + -
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Residues in contact with GLY 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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169B LEU* 5.6 1.0 - - - +
172B MET* 4.6 2.6 - - - +
183B VAL 3.4 7.4 - - - -
184B VAL* 4.2 9.0 - - - -
202B LEU* 1.3 75.1 - - - +
204B SER* 1.3 61.5 + - - -
218B ARG* 3.2 5.0 - - - +
219B ILE* 2.9 41.3 + - - +
252B LEU* 3.5 14.6 - - - -
256B CYS* 5.2 0.4 - - - -
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Residues in contact with SER 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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172B MET* 4.3 19.5 - - - +
173B ASP* 5.0 0.3 + - - -
176B HIS* 2.7 30.3 + - - -
182B THR* 3.4 1.7 - - - +
183B VAL 2.8 36.3 + - - +
203B GLY* 1.3 75.5 - - - -
205B GLN* 1.3 61.7 + - - +
216B MET* 3.4 22.0 - - - +
217B GLU 3.3 5.8 - - - -
218B ARG* 4.0 9.4 + - - +
252B LEU* 3.6 3.4 - - - +
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Residues in contact with GLN 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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181B ASP 3.2 3.1 - - - +
182B THR* 2.8 31.4 + - - +
204B SER* 1.3 75.8 + - - +
206B ARG* 1.3 71.1 + - - +
207B ARG* 2.8 35.5 + - + +
215B VAL 3.9 0.3 - - - +
216B MET* 3.2 2.8 - - - -
217B GLU* 2.8 38.5 + - - +
245B THR* 4.5 6.7 - - - +
248B HIS 5.7 0.6 + - - -
249B PRO 3.2 17.9 + - - +
252B LEU* 3.9 32.7 + - + +
409B MPD 3.7 21.0 - - - +
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Residues in contact with ARG 206 (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 HIS* 3.5 37.9 + - + +
181B ASP* 2.7 42.3 + - - +
205B GLN* 1.3 76.2 - - - +
207B ARG* 1.3 65.7 + - - +
214B VAL* 3.6 23.7 - - + +
215B VAL 3.3 7.4 - - - +
216B MET* 3.3 38.7 - - + +
404B MPD 3.8 30.3 + - - +
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Residues in contact with ARG 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 GLN* 2.8 35.4 + - + +
206B ARG* 1.3 75.2 - - - +
208B ARG* 1.3 65.0 + - - +
209B ASN* 5.0 2.5 - - + +
213B SER 3.5 0.7 - - - +
214B VAL* 4.3 3.1 - - - +
215B VAL* 2.8 52.0 + - + +
217B GLU* 2.7 43.2 + - - +
249B PRO 4.4 1.6 - - - -
250B ASN* 2.8 52.3 + - - +
252B LEU 4.0 0.2 - - - +
404B MPD 3.8 12.1 + - - +
409B MPD 6.3 3.6 - - + -
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 1.3 76.3 - - - +
209B ASN* 1.3 62.4 + - - +
212B GLY* 2.7 53.1 + - - +
213B SER 3.3 4.7 - - - +
214B VAL* 3.6 25.6 - - + +
250B ASN* 5.5 2.3 - - - +
404B MPD 3.5 37.9 + - + +
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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