Contacts of the strand formed by residues 182 - 190 (chain A) in PDB entry 3SDE
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LYS* 3.3 24.4 + - - +
173A GLU* 3.8 27.0 - - + +
176A PHE* 3.7 7.0 - - + -
177A SER* 3.7 27.6 - - - +
180A GLY 3.7 2.2 - - - +
181A PRO* 1.3 73.1 - - - +
183A GLU* 1.3 64.0 + - - +
184A LYS* 3.6 28.7 - - - +
185A ALA* 4.2 2.0 - - + +
201A VAL* 4.2 8.3 - - + -
202A GLU 3.7 5.4 - - - +
203A PHE* 3.6 26.5 - - + +
204A ALA* 5.6 0.4 - - - -
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Residues in contact with GLU 183 (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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76A LYS* 3.2 36.3 + - - +
79A THR* 3.5 25.6 + - + +
80A GLN* 2.7 40.6 + - - +
81A ARG* 4.1 2.8 + - - +
123A ARG* 4.6 2.1 + - - -
154A HIS* 2.9 23.0 + - - -
181A PRO 4.0 1.0 + - - -
182A VAL* 1.3 72.2 - - - +
184A LYS* 1.4 63.5 + - + +
202A GLU* 2.8 17.2 + - + +
203A PHE 3.7 10.3 - - - -
204A ALA* 3.6 28.1 - - + +
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Residues in contact with LYS 184 (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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81A ARG* 4.2 25.5 - - - +
173A GLU* 5.0 4.0 - - - -
182A VAL* 3.5 7.0 - - - +
183A GLU* 1.4 84.3 - - + +
185A ALA* 1.3 66.4 + - - +
186A VAL* 3.5 22.1 - - + +
200A PHE* 4.4 10.5 - - + -
201A VAL* 3.6 0.2 - - - -
202A GLU* 2.8 44.6 + - - +
232B ASP 4.5 0.2 + - - -
233B GLU* 3.2 42.2 + - - +
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Residues in contact with ALA 185 (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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169A ASN* 3.6 20.3 - - - +
172A LEU* 4.1 11.9 - - + -
173A GLU* 3.7 42.7 + - + +
182A VAL* 4.2 5.1 - - + +
184A LYS* 1.3 79.5 - - - +
186A VAL* 1.3 66.5 + - - +
200A PHE* 3.3 11.4 - - - +
201A VAL* 4.3 6.3 - - + -
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Residues in contact with VAL 186 (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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169A ASN* 3.5 8.3 - - - +
172A LEU* 3.7 3.8 - - - +
184A LYS* 3.5 32.8 - - + +
185A ALA* 1.3 80.3 - - - +
187A VAL* 1.3 74.9 + - - +
188A VAL* 4.3 1.5 - - + +
199A GLY* 3.0 6.6 - - - -
200A PHE* 3.0 53.6 + - + -
232B ASP* 3.5 27.8 - - - +
233B GLU 4.1 4.5 - - - +
235B GLY* 3.9 12.6 - - - +
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Residues in contact with VAL 187 (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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163A LEU* 4.2 11.2 - - + -
164A SER 5.8 0.7 - - - +
167A VAL* 3.5 30.7 - - + +
168A SER 3.4 31.4 - - - +
169A ASN* 2.8 12.8 + - - +
172A LEU* 4.1 10.3 - - + -
186A VAL* 1.3 72.8 - - - +
188A VAL* 1.3 66.7 + - - +
189A VAL* 4.1 0.2 - - - +
195A ALA* 4.5 10.1 - - + -
197A GLY 5.9 0.9 - - - +
198A LYS 4.0 7.9 - - - +
199A GLY* 4.3 0.7 - - - -
235B GLY* 2.9 25.5 - - - -
236B LEU* 3.1 22.3 + - + -
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Residues in contact with VAL 188 (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 VAL* 4.5 5.6 - - + +
187A VAL* 1.3 72.1 - - - +
189A VAL* 1.3 62.2 + - - +
195A ALA* 3.8 3.6 - - - -
196A THR* 2.9 41.0 + - + +
198A LYS* 2.9 27.5 + - + +
199A GLY* 4.0 14.8 - - - +
200A PHE* 4.6 5.2 - - + -
230B LEU* 3.7 35.0 - - + -
231B ASP 3.8 11.9 - - - +
232B ASP* 4.0 22.4 - - + -
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Residues in contact with VAL 189 (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 VAL 3.5 0.4 + - - -
188A VAL* 1.3 78.4 - - - +
190A ASP* 1.4 62.3 + - - +
193A GLY* 3.8 26.7 - - - +
194A ARG 3.3 14.6 - - - +
195A ALA* 4.1 3.8 - - - +
196A THR* 3.9 4.3 - - - -
230B LEU* 3.6 2.9 - - - -
231B ASP* 2.8 52.6 + - + +
235B GLY 3.5 20.4 - - - +
236B LEU* 3.7 32.3 - - + -
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Residues in contact with ASP 190 (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 VAL* 1.4 78.7 - - - +
191A ASP* 1.4 62.3 + - - +
192A ARG* 3.1 35.1 + - - +
193A GLY* 2.9 23.4 + - - -
194A ARG* 2.9 39.9 + - - +
195A ALA 5.3 1.2 - - - +
196A THR* 3.8 12.1 - - + +
228B ASP* 5.9 0.7 - - - +
229B GLN 4.0 3.1 - - - +
230B LEU* 4.1 16.4 - - + -
231B ASP* 5.0 3.5 + - - +
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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