Contacts of the strand formed by residues 195 - 203 (chain A) in PDB entry 1S3Y
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 PHE 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PRO 3.3 22.0 - - - -
27A TRP* 3.4 29.2 - + + -
28A LYS* 4.3 5.6 - - + -
29A LEU* 3.8 19.3 - - + -
146A ILE* 3.9 17.7 - - + -
148A LYS* 3.4 45.3 - - + -
150A ILE* 4.3 4.9 - - + -
190A ILE 3.2 3.5 - - - +
191A ASN* 3.0 9.2 + - - -
192A GLU 2.8 38.2 + - - +
193A ASP* 3.1 27.8 - - + -
194A GLY* 1.3 78.9 - - - +
196A ASP* 1.3 60.3 + - - +
197A TYR* 4.0 4.7 - - + -
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Residues in contact with ASP 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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146A ILE* 3.7 2.7 - - - +
147A TYR* 2.9 47.1 + - + +
148A LYS* 5.6 1.4 - - - +
189A LYS* 2.8 48.3 + - + +
190A ILE 3.9 1.8 - - - -
191A ASN* 2.7 30.3 - - - +
194A GLY 4.4 1.8 + - - +
195A PHE* 1.3 72.7 - - - +
197A TYR* 1.3 62.6 + - - +
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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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29A LEU* 3.5 32.8 - - + -
31A LYS* 3.1 17.8 - - - +
32A GLU* 3.7 8.0 + - + -
144A THR* 3.9 13.2 - - + -
145A ILE 3.0 18.6 - - - +
146A ILE* 4.1 7.9 - - + -
147A TYR* 4.4 2.5 - - - -
189A LYS* 3.1 6.5 - - - +
190A ILE* 2.8 64.7 + - + +
192A GLU* 2.7 29.9 + - + -
195A PHE* 4.0 6.5 - - + -
196A ASP* 1.3 75.5 - - - +
198A GLU* 1.3 62.6 + - - +
199A PHE* 3.6 37.6 - + - -
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Residues in contact with GLU 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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144A THR* 3.3 4.2 - - - -
145A ILE* 2.9 33.2 + - + +
147A TYR* 3.7 28.2 + - + +
171A LYS* 5.9 0.7 + - - -
186A PRO 6.0 0.4 - - - +
187A HIS* 5.0 4.7 - - - -
188A GLY* 3.4 38.0 + - - +
189A LYS* 4.4 4.4 + - + +
190A ILE* 4.7 1.6 - - - -
197A TYR* 1.3 79.6 - - - +
199A PHE* 1.3 80.2 + - - +
200A GLU* 4.0 12.8 + - + +
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Residues in contact with PHE 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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31A LYS* 5.2 3.4 - - + -
32A GLU* 4.3 6.5 - - + -
35A TYR* 3.9 49.1 - + + +
143A ALA 3.6 3.4 - - - +
144A THR* 3.5 21.1 - - - -
174A HIS* 4.9 9.2 + - + -
177A LEU* 3.9 11.7 - - + +
185A VAL* 3.7 28.7 - - + -
186A PRO* 4.0 21.9 + - + +
188A GLY 4.8 0.4 + - - -
190A ILE* 3.5 19.7 - - + -
197A TYR* 3.6 35.0 - + - -
198A GLU* 1.3 86.7 - - - +
200A GLU* 1.3 65.0 + - - +
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Residues in contact with GLU 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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35A TYR* 5.4 1.6 + - - -
142A MET* 3.8 2.9 - - - +
143A ALA* 2.8 36.1 + - + +
145A ILE* 3.3 21.3 - - + +
147A TYR* 4.2 7.4 + - - -
161A ARG* 3.0 35.6 + - - -
171A LYS* 3.8 30.6 + - + +
177A LEU* 3.7 7.1 - - - +
198A GLU* 4.7 14.3 - - - +
199A PHE* 1.3 80.3 - - - +
201A MET* 1.3 61.8 + - - +
202A TRP* 2.9 26.8 + - + +
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Residues in contact with MET 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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140A ARG* 3.3 34.5 - - + +
141A ILE 3.5 3.8 - - - +
142A MET* 3.4 40.2 - - + +
171A LYS* 3.5 6.2 - - - +
172A GLU* 2.9 44.9 + - + -
176A ASP* 4.7 2.5 - - - +
177A LEU* 3.2 51.0 - - + +
180A TRP* 3.3 22.7 - - + -
200A GLU* 1.3 75.3 - - - +
202A TRP* 1.3 64.9 + - - +
203A THR* 4.6 0.2 - - + -
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Residues in contact with TRP 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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140A ARG* 3.3 3.1 - - - +
141A ILE* 2.7 43.2 + - + +
143A ALA* 4.6 3.3 - - + +
160A PHE* 3.6 42.5 - + + -
161A ARG* 3.6 42.0 - - + -
166A SER* 6.3 0.7 - - - -
169A TRP* 3.7 25.7 - - + -
170A LYS 3.3 12.6 - - - -
171A LYS* 3.5 42.3 - - + +
200A GLU* 2.9 37.0 + - + +
201A MET* 1.3 79.5 - - - +
203A THR* 1.3 64.4 + - - +
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Residues in contact with THR 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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139A ASP* 3.1 16.4 - - - +
140A ARG* 3.4 34.5 - - + +
168A VAL 3.8 0.5 - - - +
169A TRP* 3.7 5.0 - - - -
170A LYS* 3.0 32.1 + - - +
172A GLU* 2.7 36.7 + - + -
201A MET* 4.6 1.3 - - + -
202A TRP* 1.3 80.5 - - - +
204A ARG* 1.3 65.2 + - - +
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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