Contacts of the strand formed by residues 203 - 210 (chain B) in PDB entry 1MS4
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 VAL 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B TRP* 4.6 10.8 - - + -
121B THR* 5.0 10.1 - - + -
195B GLN* 4.4 7.0 - - + +
196B VAL 3.3 17.0 - - - +
197B THR* 4.9 4.9 - - + -
201B LYS 3.8 1.2 + - - +
202B GLN* 1.3 75.6 - - - +
204B PHE* 1.3 70.3 + - - +
226B PHE* 3.3 4.9 - - - -
227B GLY* 2.8 52.3 + - - +
228B CYS 4.0 11.4 - - - +
229B SER* 4.4 14.8 - - - +
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Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B MET* 4.2 9.4 - - - -
170B MET* 3.3 31.9 - - + -
172B THR* 5.6 2.0 - - + -
195B GLN* 3.6 1.3 - - - -
196B VAL* 2.8 69.4 + - + +
197B THR 4.7 1.6 - - - -
198B ASN* 4.1 20.0 - - + -
202B GLN 4.2 1.3 - - - -
203B VAL* 1.3 81.6 - - - +
205B SER* 1.3 57.1 + - - +
206B LYS* 4.0 16.6 - - + -
223B ARG* 4.0 26.5 - - + -
224B SER* 3.8 9.0 - - - +
225B ALA 4.1 7.4 - - - +
226B PHE* 3.8 20.9 - + + -
228B CYS 3.4 12.3 - - - -
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL 3.1 10.8 - - - -
195B GLN* 4.9 0.2 - - - -
204B PHE* 1.3 71.2 - - - +
206B LYS* 1.3 68.3 + - - +
223B ARG* 3.5 2.9 - - - +
224B SER* 2.9 35.8 + - - -
228B CYS* 2.9 24.4 + - - +
231B PRO* 3.5 29.4 - - - +
244B THR* 4.0 4.2 - - - +
263B TRP* 3.3 12.7 - - - -
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Residues in contact with LYS 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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167B MET* 3.4 27.8 - - - +
168B GLU* 3.2 27.1 + - - -
193B PRO* 3.3 6.4 - - - +
194B VAL* 2.7 35.9 + - + -
196B VAL* 3.9 17.9 - - + -
204B PHE* 4.0 7.1 - - + -
205B SER* 1.3 76.4 - - - +
207B ILE* 1.3 65.7 + - - +
219B PHE* 3.9 16.9 - - + +
220B GLY 3.1 23.7 + - - +
221B LYS 3.4 7.5 + - - -
222B GLY 3.1 18.1 + - - +
223B ARG* 3.7 13.1 - - + +
263B TRP* 3.3 16.3 - - - -
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Residues in contact with ILE 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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191B VAL* 3.9 25.1 - - + -
192B TYR 3.8 0.9 - - - -
193B PRO* 4.5 9.9 - - + -
206B LYS* 1.3 80.8 - - - +
208B PHE* 1.3 62.0 + - - +
209B TYR* 3.9 16.4 - - + -
218B LYS 3.8 0.2 - - - +
219B PHE* 3.3 8.7 - - - -
220B GLY* 3.0 26.9 + - - +
222B GLY 5.3 0.2 + - - -
233B ALA* 5.3 2.0 - - + -
240B LEU* 3.9 17.3 - - + -
242B ILE* 3.9 27.6 - - + -
259B MET* 3.7 23.6 - - - +
260B GLY* 3.7 22.9 - - - +
263B TRP* 3.7 9.2 - - + +
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Residues in contact with PHE 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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109B LEU* 4.5 7.4 - - + -
159B LEU* 3.7 25.8 - - + -
162B PHE* 4.5 7.6 - - + -
175B PHE* 3.7 29.6 - + - -
191B VAL 3.8 0.2 - - - -
192B TYR* 2.8 44.5 + + - +
194B VAL* 3.6 22.4 - - + -
207B ILE* 1.3 73.3 - - - +
209B TYR* 1.3 58.4 + - - +
217B TRP* 3.4 52.4 - + + -
218B LYS 3.4 9.0 - - - -
219B PHE* 3.5 33.2 - + + -
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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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189B ASN* 3.9 18.4 - - + -
190B LEU 3.1 13.9 - - - +
191B VAL* 4.3 2.9 - - + -
207B ILE* 3.9 22.9 - - + -
208B PHE* 1.3 73.9 - - - +
210B SER* 1.3 60.6 + - - +
211B GLU* 3.7 29.2 + - + -
217B TRP* 3.4 10.1 - - - -
218B LYS* 2.9 72.9 + - + +
219B PHE 4.2 2.3 + - - -
220B GLY* 4.1 11.4 - - - -
259B MET* 3.8 38.0 - - + +
261B ASN* 5.2 7.6 + - - -
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Residues in contact with SER 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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188B GLY 4.6 0.3 - - - +
189B ASN* 3.3 7.6 - - - -
190B LEU* 2.9 33.2 + - - +
209B TYR* 1.3 74.5 - - - +
211B GLU* 1.3 61.3 + - - +
212B ASP* 2.9 7.3 + - - -
213B GLU 4.8 0.7 + - - -
214B GLY* 2.8 31.9 + - - -
216B THR 2.7 25.6 + - - -
217B TRP* 3.6 20.6 - - - -
218B LYS* 6.2 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