Contacts of the strand formed by residues 203 - 210 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TRP* 4.4 19.1 - - + -
121A THR* 4.6 12.3 - - + -
195A GLN* 4.5 8.1 - - + -
196A VAL 3.3 15.7 - - - +
197A THR* 4.4 5.2 - - + -
201A LYS 3.8 1.2 + - - +
202A GLN* 1.3 74.5 - - - +
204A PHE* 1.3 69.2 + - - +
226A PHE* 3.3 4.7 - - - -
227A GLY* 2.7 54.2 + - - +
228A CYS 4.1 7.6 - - - +
229A SER* 4.4 11.7 - - - -
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET* 4.3 9.0 - - - -
170A MET* 3.4 30.5 - - + -
172A THR* 5.1 1.3 - - + -
195A GLN* 3.5 2.6 - - - +
196A VAL* 2.8 72.5 + - + +
197A THR 4.5 2.0 - - - -
198A ASN* 4.0 19.5 - - + -
202A GLN 4.3 1.1 - - - -
203A VAL* 1.3 81.0 - - - +
205A SER* 1.3 56.5 + - - +
206A LYS* 3.9 20.9 - - + -
223A ARG* 4.1 15.5 - - + -
224A SER* 3.8 16.6 - - - +
225A ALA 4.1 5.8 - - - +
226A PHE* 3.8 20.9 - + + -
228A CYS 3.5 11.4 - - - -
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL 3.1 10.5 - - - -
204A PHE* 1.3 71.0 - - - +
206A LYS* 1.3 63.9 + - - +
223A ARG* 3.4 7.8 - - - +
224A SER* 3.0 39.1 + - - -
228A CYS* 2.7 31.7 + - - +
231A PRO* 3.7 27.7 - - - +
244A THR* 4.0 3.2 - - - +
263A TRP* 3.5 11.9 - - - -
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET* 3.5 25.4 - - - +
168A GLU* 3.5 16.0 + - - -
193A PRO* 3.3 4.7 - - - +
194A VAL* 2.6 48.8 + - + +
196A VAL* 3.7 18.8 - - + -
204A PHE* 3.9 8.2 - - + -
205A SER* 1.3 74.3 - - - +
207A ILE* 1.3 60.8 + - - +
219A PHE* 3.7 16.3 - - + +
220A GLY 3.0 26.2 + - - +
221A LYS* 3.3 18.4 + - - +
222A GLY 3.1 17.0 + - - +
223A ARG* 3.8 12.8 - - + +
263A TRP* 3.5 12.6 - - - -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 3.8 24.7 - - + -
192A TYR 3.8 0.7 - - - -
193A PRO* 4.4 9.4 - - + -
206A LYS* 1.3 80.0 - - - +
208A PHE* 1.3 61.2 + - - +
209A TYR* 4.0 12.2 - - + -
218A LYS 3.8 0.3 - - - +
219A PHE* 3.4 7.3 - - - -
220A GLY* 3.0 28.1 + - - +
222A GLY 5.5 0.2 + - - -
233A ALA* 5.3 1.6 - - + -
240A LEU* 3.8 18.6 - - + -
242A ILE* 4.1 24.7 - - + -
259A MET* 3.3 29.6 - - + +
260A GLY* 3.6 21.7 + - - +
263A TRP* 3.8 10.5 - - + +
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Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.3 10.3 - - + -
159A LEU* 3.6 35.9 - - + -
162A PHE* 4.6 7.6 - - + -
175A PHE* 3.7 23.8 - + - -
192A TYR* 2.7 51.3 + + + +
194A VAL* 3.6 27.6 - - + -
207A ILE* 1.3 73.9 - - - +
209A TYR* 1.3 59.2 + - - +
217A TRP* 3.5 40.3 - + + -
218A LYS 3.3 10.1 - - - -
219A PHE* 3.6 32.8 - + + +
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Residues in contact with TYR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ASN* 3.8 20.2 - - + -
190A LEU 3.1 14.4 - - - +
191A VAL* 4.3 2.0 - - - -
207A ILE* 4.0 11.9 - - + -
208A PHE* 1.3 75.8 - - - +
210A SER* 1.3 60.3 + - - +
211A GLU* 3.8 28.0 + - + -
217A TRP* 3.2 9.9 - - - -
218A LYS* 2.8 70.9 + - + +
219A PHE 4.1 3.0 + - - -
220A GLY* 4.1 10.9 - - - -
259A MET* 3.8 50.3 - - + +
261A ASN* 5.4 6.8 + - - -
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLY 4.8 0.2 - - - +
189A ASN* 3.3 6.6 - - - -
190A LEU* 2.9 34.0 + - - +
209A TYR* 1.3 75.2 - - - +
211A GLU* 1.3 60.6 + - - +
212A ASP* 3.0 7.3 + - - -
213A GLU 4.8 0.7 + - - -
214A GLY* 2.8 31.9 + - - -
216A THR 2.9 24.2 + - - -
217A TRP* 3.5 20.8 - - - +
218A LYS* 6.1 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