Contacts of the strand formed by residues 200 - 207 (chain A) in PDB entry 1O0W
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 ILE 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A THR* 2.9 7.3 - - - -
193A GLU* 2.5 59.9 + - + +
195A ASN* 3.6 39.3 - - + +
196A ASP* 4.4 5.6 - - - +
198A ASP* 3.7 12.1 - - + +
199A ARG* 1.3 80.5 - - - +
201A PHE* 1.3 73.8 + - - +
202A VAL* 4.7 1.1 - - + -
216A LYS* 4.0 20.0 - - + -
217A GLY* 3.4 13.5 - - - +
218A ARG* 5.3 3.4 - - + -
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Residues in contact with PHE 201 (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 LEU* 3.7 25.6 - - + -
191A ARG 3.9 3.4 - - - -
192A THR* 3.6 19.5 - - + -
199A ARG* 4.0 39.9 - - + -
200A ILE* 1.3 76.5 - - - +
202A VAL* 1.3 60.9 + - - +
216A LYS* 3.3 4.2 - - - -
217A GLY 2.9 29.2 + - - -
218A ARG 3.5 17.0 - - - -
219A THR* 3.5 35.2 - - - +
220A LYS* 3.7 18.4 - - + -
223A ALA* 3.2 10.0 - - + +
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Residues in contact with VAL 202 (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 LEU* 3.6 3.1 - - - +
190A VAL* 2.8 37.7 + - + +
191A ARG* 2.9 58.5 + - + +
193A GLU* 3.8 20.0 - - + -
200A ILE* 4.5 1.1 - - + +
201A PHE* 1.3 76.7 - - - +
203A VAL* 1.3 60.2 + - - +
214A THR* 3.4 29.6 - - + -
215A GLY 3.5 4.0 - - - +
216A LYS* 4.2 15.3 - - + -
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Residues in contact with VAL 203 (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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187A TYR* 4.1 10.8 - - + -
188A ILE 3.2 17.9 - - - +
189A LEU* 4.0 23.6 - - + +
202A VAL* 1.3 78.1 - - - +
204A GLU* 1.3 73.5 + - - +
214A THR* 3.3 2.8 - - - +
215A GLY 2.7 41.6 + - - +
220A LYS* 4.3 5.8 - - + +
223A ALA* 3.6 28.0 - - + -
224A GLU* 4.0 28.9 - - + -
227A ALA* 3.6 4.6 - - + +
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Residues in contact with GLU 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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186A GLU 3.6 1.2 - - - +
187A TYR* 3.6 1.9 - - - -
188A ILE* 3.0 32.4 + - - +
190A VAL* 3.4 31.6 - - + +
191A ARG* 5.8 1.0 + - - -
203A VAL* 1.3 76.9 - - - +
205A VAL* 1.3 61.5 + - - +
206A ARG* 2.8 36.7 + - - +
211A THR* 3.1 23.4 + - + +
213A ALA 3.2 9.2 - - - +
214A THR* 3.7 17.1 + - + +
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Residues in contact with VAL 205 (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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173A LEU* 3.6 24.2 - - + -
185A PRO* 3.8 11.2 - - + -
186A GLU 3.3 7.9 - - - +
187A TYR* 3.6 27.8 - - + +
203A VAL 4.2 0.6 + - - -
204A GLU* 1.3 75.0 - - - +
206A ARG* 1.3 64.0 + - - +
207A VAL* 5.9 0.4 - - + -
211A THR* 3.7 0.7 - - - -
212A ILE* 2.8 27.9 + - + -
213A ALA 2.8 19.1 + - - +
227A ALA* 3.8 11.9 - - + +
231A ALA* 3.4 30.5 - - + -
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Residues in contact with ARG 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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185A PRO* 3.5 6.4 - - - +
186A GLU* 2.8 57.5 + - + +
188A ILE* 3.6 31.9 - - + +
190A VAL* 3.9 13.1 - - - +
204A GLU* 2.8 33.2 + - + +
205A VAL* 1.3 80.6 - - - +
207A VAL* 1.3 64.4 + - - +
209A GLY* 3.9 16.6 + - - -
210A LYS 3.1 11.7 - - - +
211A THR* 3.4 17.5 + - - +
212A ILE 4.2 0.7 - - - +
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Residues in contact with VAL 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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173A LEU* 6.5 0.2 - - + -
177A VAL* 3.6 42.6 - - + -
181A HIS* 3.6 29.8 - - + +
183A VAL* 4.1 9.6 - - + -
184A PRO 5.0 3.6 - - - +
185A PRO* 4.8 3.8 - - + -
186A GLU* 4.2 0.4 - - - -
205A VAL* 5.9 0.9 - - + -
206A ARG* 1.3 79.0 - - - +
208A ASN* 1.3 78.5 - - - +
209A GLY 3.2 0.2 - - - -
210A LYS* 2.9 22.7 + - - +
212A ILE* 3.5 26.2 - - + -
235A LEU* 5.4 2.7 - - + -
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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