Contacts of the strand formed by residues 115 - 122 (chain A) in PDB entry 1R7U
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASN 3.8 4.0 + - - -
114A THR* 1.3 72.7 - - - +
116A ILE* 1.3 65.7 + - - +
146A ARG* 3.3 41.3 + - + +
147A VAL 4.9 0.7 - - - +
148A HIS* 4.7 7.6 - - + -
203A GLU 3.4 25.6 + - - +
204A VAL* 3.7 13.2 - - + -
205A ASP* 2.9 39.2 + - - +
206A TYR 3.3 6.4 + - - -
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Residues in contact with ILE 116 (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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114A THR* 3.9 14.1 - - + +
115A THR* 1.3 78.1 - - - +
117A GLY* 1.3 65.8 + - - +
141A PHE* 3.9 15.7 - - + -
142A MET* 4.0 23.3 - - + -
145A HIS* 3.8 24.9 - - + -
146A ARG 2.8 20.8 + - - +
147A VAL* 3.3 8.6 - - + +
148A HIS 2.9 24.7 + - - +
204A VAL* 4.2 2.2 - - - -
206A TYR* 3.7 6.7 - - + +
208A VAL* 3.7 29.6 - - + -
225A LEU* 3.8 25.8 - - + -
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Residues in contact with GLY 117 (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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116A ILE* 1.3 75.6 - - - +
118A LEU* 1.3 55.2 + - - -
119A THR 4.0 0.7 - - - -
148A HIS 3.2 9.9 - - - -
150A TYR* 4.1 5.8 - - - -
204A VAL* 3.8 16.7 - - - +
206A TYR 2.8 14.6 + - - +
207A LEU* 3.5 9.2 - - - -
208A VAL* 2.8 34.1 + - - +
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Residues in contact with LEU 118 (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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116A ILE 3.9 0.6 + - - -
117A GLY* 1.3 72.5 - - - -
119A THR* 1.3 60.8 + - - +
120A VAL* 4.7 3.0 - - + +
133A PHE* 3.9 25.1 - - + -
137A ALA* 4.6 0.9 - - + -
141A PHE* 3.8 35.4 - - + -
147A VAL* 4.9 1.1 - - + -
148A HIS 3.0 7.6 + - - +
149A TYR* 3.5 38.2 - - + +
150A TYR 2.8 25.5 + - - +
208A VAL* 3.5 35.0 - - + +
210A VAL* 4.0 17.9 - - + -
216A PHE* 4.6 6.7 - - + -
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Residues in contact with THR 119 (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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118A LEU* 1.3 74.1 - - - +
120A VAL* 1.3 71.3 + - - +
121A PHE* 5.0 8.8 - - - -
150A TYR* 3.4 16.4 - - + -
152A PHE* 4.3 9.2 - - + -
200A PHE* 3.9 28.9 - - + -
207A LEU* 4.1 18.2 - - + -
208A VAL 2.9 8.9 + - - +
209A CYS* 3.5 27.2 - - - +
210A VAL* 3.2 19.9 + - - +
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Residues in contact with VAL 120 (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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118A LEU* 4.7 4.9 - - + +
119A THR* 1.3 82.2 - - - +
121A PHE* 1.3 67.4 + - - +
122A ALA 4.0 0.2 + - - -
130A LEU* 4.4 12.1 - - + -
133A PHE* 3.3 41.7 - - + -
134A LEU* 5.8 0.2 - - + -
149A TYR* 6.4 0.7 - - + -
150A TYR 3.1 6.0 + - - +
151A VAL* 3.8 31.2 - - + -
152A PHE* 2.9 26.9 + - - +
210A VAL* 3.6 17.7 - - + +
211A ASP 4.7 1.1 - - - +
212A VAL* 4.5 9.9 - - + -
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Residues in contact with PHE 121 (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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119A THR* 5.0 10.1 - - - -
120A VAL* 1.3 80.0 - - - +
122A ALA* 1.3 61.3 + - - +
123A ILE* 3.9 16.1 + - + -
126A TYR* 5.0 1.6 - - - +
152A PHE* 3.4 47.1 - + + -
175A VAL* 5.1 7.0 - - + -
210A VAL 4.6 4.5 + - - -
211A ASP* 5.8 0.6 - - - +
212A VAL* 3.7 19.7 + - - +
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Residues in contact with ALA 122 (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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120A VAL 4.0 0.6 + - - -
121A PHE* 1.3 72.8 - - - +
123A ILE* 1.3 61.0 + - - +
126A TYR* 4.1 18.8 - - - +
127A VAL* 3.5 7.3 - - - +
130A LEU* 3.9 40.4 - - + -
151A VAL* 4.6 2.9 - - + -
152A PHE 2.8 10.7 + - - +
153A THR* 2.7 33.6 + - - -
212A VAL* 4.5 4.3 - - + -
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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