Contacts of the strand formed by residues 184 - 193 (chain A) in PDB entry 3WOO
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 THR 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ASP* 4.3 6.7 - - - +
134A THR* 3.4 15.6 - - - +
178A SER* 3.7 2.8 + - - -
179A PHE* 2.8 42.7 + - + +
180A SER* 5.3 2.6 + - - -
182A GLY 3.3 0.8 - - - -
183A ASN* 1.3 87.3 + - - +
185A TYR* 1.3 69.0 + - - +
186A ARG* 3.8 36.0 + - - +
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Residues in contact with TYR 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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132A ASP* 3.3 2.4 - - - +
133A VAL* 2.9 39.2 + - + -
134A THR* 2.8 25.5 + - + -
137A ALA* 3.6 25.6 - - + -
138A LYS* 4.7 6.7 - - + -
141A ILE* 3.5 27.7 - - + +
155A LEU* 4.1 17.9 - - + +
176A LEU* 4.1 15.9 - - + -
177A TYR 3.3 13.0 - - - +
178A SER* 3.8 20.1 + - - -
182A GLY* 3.5 35.6 + - - -
184A THR* 1.3 75.7 - - - +
186A ARG* 1.3 66.7 + - - +
550A LEU* 4.0 13.9 - - - +
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Residues in contact with ARG 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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30A VAL* 4.2 10.9 - - - +
32A GLN* 3.5 54.9 + - - +
130A ILE* 3.9 16.2 - - + -
131A THR 3.2 11.2 - - - +
132A ASP* 4.3 15.5 + - - +
133A VAL 4.4 0.2 - - - +
175A ARG 3.8 0.5 - - - +
176A LEU* 3.7 5.1 - - - -
177A TYR* 2.8 43.3 + - - +
179A PHE* 3.5 50.4 - - + +
184A THR* 3.8 19.9 + - + +
185A TYR* 1.3 80.4 - - - +
187A LEU* 1.3 59.0 + - - +
188A PHE* 4.5 4.9 - - + -
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Residues in contact with LEU 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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129A GLU 3.7 0.5 - - - +
130A ILE* 3.3 5.2 - - - -
131A THR* 2.8 51.0 + - + +
133A VAL* 4.3 6.8 - - + +
162A LEU* 3.9 46.2 - - + -
163A ILE* 4.5 7.6 - - + -
166A CYS* 4.0 22.7 - - + -
174A CYS* 4.1 10.3 - - + -
175A ARG 3.5 28.0 - - - +
176A LEU* 4.2 3.6 - - - +
186A ARG* 1.3 72.1 - - - +
188A PHE* 1.3 66.9 + - - +
189A LYS* 5.8 0.4 - - + -
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Residues in contact with PHE 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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31A PRO* 5.7 2.9 - - + -
32A GLN* 6.0 0.2 - - - -
127A LEU* 3.8 20.2 - - + -
129A GLU 3.5 2.9 - - - +
130A ILE* 3.6 39.9 - - + -
173A ARG 4.2 0.3 - - - +
174A CYS* 3.1 7.1 - - - +
175A ARG* 2.8 39.7 + - + +
177A TYR* 3.5 39.0 - + + -
179A PHE* 4.6 6.3 - + - -
186A ARG* 4.5 10.5 - - + -
187A LEU* 1.3 82.4 - - - +
189A LYS* 1.3 58.8 + - - +
190A ASN* 4.2 13.6 - - - +
272A TYR* 4.5 8.3 - + - -
578A SER* 3.9 16.8 - - - -
579A LEU* 4.0 27.8 - - + -
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Residues in contact with LYS 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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127A LEU* 3.9 0.9 - - - +
128A ASP* 2.8 46.2 + - - +
129A GLU* 2.8 38.4 + - + +
166A CYS* 3.7 32.2 + - - +
169A GLU* 2.7 31.0 + - - +
172A PHE* 3.5 35.6 - - + -
174A CYS* 3.9 11.0 - - - -
187A LEU* 4.1 0.6 + - + +
188A PHE* 1.3 73.9 - - - +
190A ASN* 1.3 59.2 + - - +
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Residues in contact with ASN 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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66A ALA* 6.0 1.0 - - - +
125A PHE* 3.9 31.9 + - + +
126A VAL 3.2 5.8 - - - +
127A LEU* 3.4 36.1 - - - +
128A ASP 4.3 0.2 - - - +
172A PHE* 3.2 9.8 - - - -
173A ARG 2.8 42.7 + - - +
175A ARG* 5.4 1.2 - - - +
177A TYR* 5.5 1.0 + - - -
188A PHE* 4.3 16.2 - - - +
189A LYS* 1.3 77.1 + - - +
191A LEU* 1.3 60.8 + - - +
192A GLU 3.4 0.2 + - - -
272A TYR* 5.0 5.5 + - - -
803A GOL 3.7 19.8 + - - -
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Residues in contact with LEU 191 (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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124A VAL 3.5 2.4 - - - +
125A PHE* 3.4 5.7 - - - -
126A VAL* 2.8 42.7 + - + +
128A ASP* 4.6 1.3 - - + +
170A ALA 5.5 0.2 - - - +
171A GLY 3.5 16.8 - - - +
172A PHE* 3.7 33.2 - - + -
190A ASN* 1.3 72.5 - - - +
192A GLU* 1.3 58.1 + - - +
193A ILE* 3.6 14.5 + - + -
232A VAL* 5.5 1.1 - - + -
238A PRO* 3.6 22.9 - - + -
248A TYR* 3.7 38.6 - - + +
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Residues in contact with GLU 192 (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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123A ARG* 2.9 41.7 + - - +
124A VAL 3.9 2.0 - - - -
125A PHE* 3.8 13.3 - - + -
171A GLY 2.8 17.6 + - - +
172A PHE 4.7 3.1 - - - +
173A ARG* 3.8 47.2 + - + +
190A ASN 3.4 0.4 + - - -
191A LEU* 1.3 70.6 - - - +
193A ILE* 1.3 62.0 + - - +
194A LYS* 3.5 18.8 + - + +
238A PRO* 3.2 22.0 - - - +
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Residues in contact with ILE 193 (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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123A ARG* 3.3 13.9 - - - -
124A VAL* 2.8 39.0 + - + +
126A VAL* 4.0 22.0 - - + -
191A LEU* 4.2 11.2 - - + -
192A GLU* 1.3 73.8 - - - +
194A LYS* 1.3 60.3 + - - +
195A ASP 4.0 9.6 - - - +
196A VAL* 4.1 7.5 - - + +
230A ALA* 3.9 22.9 - - + -
231A TYR 3.6 19.1 - - - +
232A VAL* 4.1 16.2 - - + -
238A PRO* 4.6 3.1 - - + -
248A TYR* 3.8 34.8 - - + -
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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