Contacts of the strand formed by residues 134 - 143 (chain A) in PDB entry 3O7O
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A THR 4.0 0.2 - - - +
119A TRP* 3.4 9.5 - - - +
120A LEU* 2.7 50.5 + - + +
133A ASP* 1.4 80.2 - - - +
135A GLU* 1.3 64.9 + - - +
136A ILE* 3.8 22.2 + - + -
179A TRP* 4.9 0.4 - - - -
180A ASP* 3.4 11.2 - - + +
182A LEU* 4.0 8.5 - - + -
210A LEU* 3.9 21.3 - - + -
216A VAL* 3.8 35.2 - - + -
219A PHE* 4.8 2.2 - - + -
222A LEU* 4.1 11.7 - - + -
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Residues in contact with GLU 135 (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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117A GLU* 2.6 34.1 - - - +
118A THR 3.5 4.3 - - - +
119A TRP* 3.4 29.2 - - + -
134A VAL* 1.3 71.5 - - - +
136A ILE* 1.3 57.7 + - - +
137A MET* 4.0 11.8 - - + +
177A TRP* 4.9 1.2 - - - -
179A TRP* 2.8 41.4 + - + -
180A ASP 2.7 9.5 + - - +
181A TYR* 3.5 23.2 - - - -
182A LEU* 2.7 36.5 + - - +
232A GLU* 5.3 1.6 - - - +
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Residues in contact with ILE 136 (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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117A GLU* 3.2 4.4 - - - -
118A THR* 3.0 41.1 + - + +
120A LEU* 3.7 33.9 - - + -
134A VAL* 3.8 15.3 - - + -
135A GLU* 1.3 76.2 - - - +
137A MET* 1.3 65.0 + - - +
138A VAL* 5.0 2.7 - - + -
182A LEU* 3.3 10.3 - - + +
184A PHE* 3.8 32.3 - - + -
202A PHE* 4.8 10.1 - - + +
203A LEU* 3.8 18.4 - - + -
206A ALA* 3.8 17.3 - - + -
219A PHE* 4.2 0.7 - - + -
227A TRP* 4.5 5.0 - - + -
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Residues in contact with MET 137 (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 TYR* 4.7 5.2 - - + +
115A ALA* 3.7 19.3 - - + -
116A MET 3.2 4.7 - - - -
117A GLU* 3.4 36.3 - - + +
135A GLU* 4.0 8.3 - - - +
136A ILE* 1.3 74.2 - - - +
138A VAL* 1.3 66.7 + - - +
139A TRP* 3.6 21.3 - - + +
181A TYR* 3.7 27.6 - - + -
182A LEU 2.8 16.2 + - - +
183A ALA* 3.7 2.9 - - + -
184A PHE* 2.9 28.8 + - - +
232A GLU* 3.5 35.4 - - + +
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Residues in contact with VAL 138 (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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115A ALA* 3.3 1.2 - - - -
116A MET* 2.7 42.8 + - + +
136A ILE* 5.0 2.2 - - + -
137A MET* 1.3 77.5 - - - +
139A TRP* 1.3 60.5 + - - +
140A PHE* 3.6 23.9 + - + -
170A TRP* 3.5 27.4 - - + -
184A PHE* 3.4 3.8 - - + -
197A PHE* 4.7 2.5 - - + -
202A PHE* 3.6 43.7 - - + -
227A TRP* 4.1 24.5 - - + -
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Residues in contact with TRP 139 (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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113A ASN* 3.2 39.0 - - + +
114A PHE 3.4 6.5 - - - +
115A ALA* 3.6 14.3 - - + +
137A MET* 3.6 30.6 - - + +
138A VAL* 1.3 72.8 - - - +
140A PHE* 1.3 62.7 + - - +
141A TYR 3.4 3.8 + - - +
142A PHE* 3.8 7.1 - - + -
145A LEU* 3.7 32.3 - - + -
146A THR 3.6 5.4 - - - -
147A PRO* 3.4 43.1 - - + -
170A TRP* 3.6 3.3 - - - -
181A TYR* 3.9 6.7 - - - -
183A ALA* 4.1 6.1 - - + +
184A PHE 2.8 18.3 + - - +
185A ARG* 3.7 26.8 - - + +
186A LEU* 3.1 26.7 + - - +
232A GLU* 3.8 7.0 - - - -
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Residues in contact with PHE 140 (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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102A PHE* 4.7 1.1 - - + -
114A PHE* 2.9 28.1 + + + -
116A MET* 3.8 20.0 - - + -
138A VAL* 3.6 26.5 - - + -
139A TRP* 1.3 73.3 - - - +
141A TYR* 1.4 58.7 + - - +
142A PHE* 5.9 0.4 - - - -
159A PHE* 3.8 15.5 - + - -
170A TRP* 3.6 20.2 - + - -
186A LEU* 3.8 20.1 - - + +
189A PRO* 3.4 7.1 - - - +
190A VAL* 2.9 34.3 + - + +
195A VAL* 3.7 30.1 - - + -
197A PHE* 3.6 43.3 - + + -
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Residues in contact with TYR 141 (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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104A ILE* 4.6 5.8 - - + -
106A HIS* 2.6 43.1 + + - -
112A LEU* 3.9 20.2 - - + -
113A ASN* 3.3 7.6 - - - +
114A PHE* 2.9 36.7 + - + +
139A TRP* 3.4 5.3 - - - +
140A PHE* 1.4 75.3 - - - +
142A PHE* 1.3 86.4 + - - +
143A ASN* 3.6 14.5 + - + +
189A PRO* 3.8 19.5 - - + -
190A VAL 3.3 14.8 - - - +
191A LYS* 3.4 46.5 + - + +
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Residues in contact with PHE 142 (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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112A LEU 3.3 9.9 - - - +
139A TRP* 3.8 20.2 - - + -
140A PHE 5.9 0.2 - - - -
141A TYR* 1.3 94.1 - - - +
143A ASN* 1.3 66.2 + - - +
144A ASN 4.9 1.8 - - - -
145A LEU 3.5 22.7 - - - +
185A ARG* 3.4 40.4 - - + -
186A LEU 3.7 16.6 - - - -
187A LYS* 4.7 4.7 - - - -
189A PRO* 3.7 34.0 - - + +
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Residues in contact with ASN 143 (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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106A HIS* 3.3 22.4 + - + +
108A PRO 3.1 23.0 + - - +
110A LEU 2.9 21.6 - - - +
111A PRO* 3.3 2.1 - - - +
112A LEU* 2.6 40.2 + - + +
141A TYR* 3.6 16.0 + - + +
142A PHE* 1.3 77.6 + - - +
144A ASN* 1.4 79.6 + - - +
145A LEU 3.0 2.8 + - - -
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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