Contacts of the strand formed by residues 195 - 200 (chain A) in PDB entry 3SOQ
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 LYS 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A LEU* 3.6 2.9 - - - -
190A ASP* 2.8 35.0 + - + +
193A GLU* 3.8 22.0 - - + +
194A GLN* 1.3 80.0 - - - +
196A LEU* 1.3 60.8 + - - +
197A TYR* 4.1 19.7 - - + +
208A LYS* 4.2 25.1 - - + +
209A SER* 3.4 17.0 - - - +
210A ASN* 2.5 30.1 + - - +
211A LEU* 3.7 8.8 - - - +
215A ASN* 3.2 25.7 + - - +
217A GLN* 5.2 3.6 + - - -
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Residues in contact with LEU 196 (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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153A TYR* 4.2 15.7 - - + -
163A ILE* 4.1 7.2 - - + -
176A ILE* 3.7 29.4 - - + -
187A LEU* 3.5 37.0 - - + -
188A THR 3.6 12.6 - - - +
189A LEU* 3.7 20.9 - - + -
195A LYS* 1.3 74.7 - - - +
197A TYR* 1.3 63.4 + - - +
198A TRP* 4.1 12.9 - - + -
208A LYS* 3.1 5.9 - - - +
209A SER* 2.8 42.2 + - - +
210A ASN 4.3 3.6 - - - +
211A LEU* 3.9 9.8 - - + +
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Residues in contact with TYR 197 (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 LEU* 3.3 5.1 - - - +
188A THR* 2.8 40.9 + - + +
190A ASP* 4.0 13.8 + - + -
193A GLU* 6.0 0.5 - - - +
195A LYS* 4.1 16.6 - - + +
196A LEU* 1.3 79.5 - - - +
198A TRP* 1.3 64.8 + - - +
206A ILE* 4.4 1.6 - - + -
207A HIS 3.4 5.6 - - - +
208A LYS* 2.9 29.1 + - + -
219A VAL* 3.7 15.9 - - + -
230A LEU* 3.7 15.9 - - + +
232A LEU* 3.8 23.8 - - + -
237A LEU* 3.6 31.2 - - + -
252A LYS* 2.8 46.9 + - + +
253A TYR* 5.0 0.5 - - - -
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Residues in contact with TRP 198 (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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155A THR* 5.2 1.6 - - + -
163A ILE* 3.4 30.8 - - + +
177A ILE* 3.9 22.0 - - + -
180A GLU 5.3 0.4 + - - -
181A ILE* 4.9 7.5 - - - +
184A PRO* 4.6 9.9 - - + -
186A GLY 3.1 15.0 - - - +
187A LEU* 4.0 5.2 - - + -
196A LEU* 4.1 10.1 - - + -
197A TYR* 1.3 80.4 - - - +
199A ALA* 1.3 69.5 + - - +
200A ASP* 4.6 6.0 + - + +
205A PHE* 4.3 14.3 - + - -
206A ILE* 3.2 5.0 - - - +
207A HIS* 3.0 50.1 + - + -
208A LYS* 3.9 12.3 - - - -
209A SER* 3.5 22.2 - - - -
216A ARG* 3.5 49.7 - - + +
230A LEU* 3.8 5.8 - - - -
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Residues in contact with ALA 199 (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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183A TRP 3.6 0.2 - - - +
184A PRO* 3.5 3.6 - - - +
185A ASN* 2.9 26.0 + - - +
186A GLY* 3.0 20.0 + - - +
198A TRP* 1.3 76.1 - - - +
200A ASP* 1.3 61.2 + - - +
201A ALA 4.0 0.8 + - - -
205A PHE 3.4 4.7 - - - +
206A ILE* 3.7 20.4 - - + -
227A PRO* 3.9 24.9 - - + -
228A PHE 5.8 0.7 - - - -
229A ALA 5.9 0.2 - - - -
230A LEU* 4.6 8.1 - - + -
239A TRP* 5.7 1.6 - - + -
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Residues in contact with ASP 200 (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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180A GLU 4.5 0.5 - - - +
181A ILE* 3.5 16.5 - - - +
182A TYR 2.9 24.4 + - - -
183A TRP 3.0 25.4 + - - -
184A PRO* 3.7 2.9 - - + +
198A TRP* 4.3 3.9 + - + -
199A ALA* 1.3 73.5 - - - +
201A ALA* 1.3 56.9 + - - +
202A LYS 3.1 10.4 + - - -
203A LEU* 3.2 18.3 + - + +
204A ASN* 2.8 24.3 + - - -
205A PHE* 2.9 42.1 + - + +
227A PRO* 3.9 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