Contacts of the strand formed by residues 151 - 156 (chain A) in PDB entry 1R2J
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 HIS 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PHE* 4.8 16.9 - + + -
100A GLU* 2.8 36.2 + - + +
101A LEU* 4.4 17.7 - - + -
106A LEU 3.0 10.4 + - - -
107A ALA* 3.1 14.8 - - + +
108A ALA 3.1 23.9 + - - -
149A ALA* 3.4 5.0 - - - +
150A ASP* 1.3 90.5 + - + +
152A LEU* 1.3 64.0 + - - +
153A VAL* 4.0 1.8 - - + -
167A VAL* 4.0 24.0 - - + +
168A VAL 3.7 1.8 - - - -
169A PRO* 4.7 14.0 - - + +
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Residues in contact with LEU 152 (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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108A ALA* 3.9 21.8 - - + +
110A GLY 6.2 0.2 - - - +
143A THR* 4.9 0.9 - - + -
146A ALA* 4.2 7.9 - - + +
149A ALA* 4.2 8.7 - - + -
151A HIS* 1.3 83.0 - - - +
153A VAL* 1.3 61.2 + - - +
154A VAL* 3.3 15.7 + - + +
166A VAL 3.1 4.9 - - - +
167A VAL* 4.4 0.9 - - - -
168A VAL* 2.7 45.5 + - + +
170A ALA* 3.4 39.7 - - + -
175A VAL* 5.5 7.4 - - + -
177A VAL* 6.4 1.1 - - + -
194A LEU* 4.0 33.0 - - + -
196A LEU* 6.3 1.1 - - + -
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Residues in contact with VAL 153 (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 ALA* 3.8 24.9 - - + +
84A THR* 4.2 17.7 - - + -
85A VAL* 5.0 3.8 - - + -
107A ALA* 4.7 7.0 - - + -
108A ALA 2.9 18.7 + - - +
109A VAL* 3.5 16.3 - - + +
110A GLY 3.0 26.8 + - - +
151A HIS* 5.1 0.9 - - + -
152A LEU* 1.3 70.0 - - - +
154A VAL* 1.3 58.3 + - - +
155A PHE* 4.1 1.4 + - + -
165A VAL* 3.6 26.0 - - + -
166A VAL 3.6 4.0 - - - +
167A VAL* 4.4 22.0 - - + +
207A LEU* 5.1 1.3 - - + -
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Residues in contact with VAL 154 (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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110A GLY 3.7 3.4 - - - +
125A THR* 4.5 1.8 - - - +
127A VAL* 5.2 1.0 - - + +
136A VAL* 4.4 11.2 - - + -
140A LYS* 3.9 12.8 - - + -
152A LEU* 3.7 22.9 - - + +
153A VAL* 1.3 76.5 - - - +
155A PHE* 1.3 77.1 + - - +
164A ALA 3.8 0.2 - - - +
165A VAL* 3.2 3.3 - - - -
166A VAL* 2.7 45.6 + - + +
168A VAL* 4.3 10.8 - - + -
194A LEU* 4.5 13.7 - - + -
196A LEU* 3.9 32.5 - - + -
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Residues in contact with PHE 155 (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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84A THR* 4.2 8.1 - - + -
88A LEU* 5.0 0.9 - - + -
109A VAL* 3.9 24.2 - - + -
110A GLY 3.2 8.3 + - - +
111A PHE* 3.8 35.0 - + + -
123A MET* 3.9 9.2 - - + -
125A THR* 2.9 19.0 - - - +
127A VAL* 5.3 0.4 - - - -
140A LYS* 2.9 11.3 + - - -
153A VAL 4.5 0.9 - - - -
154A VAL* 1.3 82.1 - - - +
156A GLY* 1.3 59.0 + - - +
164A ALA 3.5 4.5 - - - -
165A VAL* 3.4 34.8 - - + -
217A LEU* 3.9 7.9 - - + -
218A VAL* 3.2 46.2 - - + -
221A SER* 3.8 19.3 - - - -
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Residues in contact with GLY 156 (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 MET* 3.8 7.1 - - - +
125A THR* 3.3 20.0 - - - -
127A VAL* 4.5 10.0 - - - +
155A PHE* 1.3 77.0 - - - +
157A LEU* 1.3 62.5 + - - +
163A GLY* 3.1 5.9 - - - -
164A ALA 2.7 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