Contacts of the strand formed by residues 120 - 128 (chain B) in PDB entry 2P9R
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 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASP* 4.5 2.8 - - - +
112B LYS* 5.8 0.2 - - - +
115B TYR* 4.0 9.3 - - - -
118B GLY 5.1 2.2 - - - +
119B GLN* 1.3 76.6 - - - +
121B VAL* 1.3 68.4 + - - +
122B LYS* 3.5 30.3 + - - +
168B SER* 4.1 11.1 - - - -
169B PHE 3.5 3.8 - - - -
170B PRO* 3.7 22.7 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B THR* 4.1 16.8 - - + -
115B TYR* 3.7 33.9 - - + +
120B THR* 1.3 71.3 - - - +
122B LYS* 1.3 63.2 + - - +
123B PHE* 4.3 10.2 + - + -
144B ILE* 4.7 3.1 - - + -
168B SER* 3.0 4.7 - - - -
169B PHE* 2.7 47.9 + - + +
171B LEU* 3.8 32.1 - - + -
196B PHE* 4.0 25.8 - - + -
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 3.1 5.4 - - - -
111B ASP* 2.9 56.8 + - + +
120B THR* 3.5 27.6 + - - +
121B VAL* 1.3 76.3 - - - +
123B PHE* 1.3 61.4 + - - +
166B GLN* 5.8 6.5 - - + +
167B PHE 3.4 6.7 - - - +
168B SER* 4.3 10.4 - - - -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 5.0 1.3 - - + -
109B GLN 2.9 17.5 - - - +
110B THR* 3.6 14.1 - - + -
121B VAL* 4.7 6.5 - - + -
122B LYS* 1.3 76.5 - - - +
124B ARG* 1.3 71.0 + - - +
125B VAL* 4.1 3.6 - - + -
142B VAL* 3.9 15.5 - - + -
143B TYR 5.5 0.2 - - - -
144B ILE* 3.9 29.2 - - + -
155B TRP* 3.8 19.7 - + - -
166B GLN* 3.5 5.2 - - - +
167B PHE* 2.8 75.6 + + + +
168B SER* 5.6 0.4 - - - -
182B VAL* 3.8 33.9 - - + -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B VAL* 3.3 8.3 - - - +
109B GLN* 2.8 66.3 + - + +
123B PHE* 1.3 79.7 - - - +
125B VAL* 1.3 64.4 + - - +
126B VAL* 4.1 16.5 + - + +
164B LEU* 3.9 27.5 - - + +
165B LYS 3.1 13.9 - - - +
166B GLN* 3.8 24.0 - - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 4.1 22.7 - - + -
107B PHE 3.5 3.8 - - - +
108B VAL* 4.9 0.7 - - + -
123B PHE* 4.1 5.4 - - + -
124B ARG* 1.3 76.6 - - - +
126B VAL* 1.3 65.3 + - - +
139B ILE* 4.7 4.3 - - + -
142B VAL* 4.1 22.4 - - + -
158B PHE* 4.4 13.5 - - + -
160B LEU* 4.5 14.9 - - + +
164B LEU* 3.0 28.6 - - - +
165B LYS* 2.8 14.4 + - + +
167B PHE* 4.1 19.5 - - + -
184B VAL* 4.2 17.7 - - + -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU 3.5 0.9 - - - +
106B VAL* 3.1 9.2 - - - +
107B PHE* 2.8 56.7 + - + +
109B GLN* 4.6 9.0 - - - +
124B ARG* 4.1 32.1 - - + +
125B VAL* 1.3 81.2 - - - +
127B SER* 1.3 69.8 + - - +
128B MET* 4.9 10.5 - - + -
163B GLY 3.3 8.1 - - - +
164B LEU* 4.6 5.8 - - + -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B SER* 3.7 4.9 + - - -
105B LEU 3.4 4.3 - - - -
106B VAL* 4.4 6.4 - - - +
126B VAL* 1.3 78.7 - - - +
128B MET* 1.3 56.3 + - - +
134B PRO* 3.6 4.7 - - - +
135B LEU* 2.8 39.2 + - - +
137B GLU* 2.7 27.3 + - - -
160B LEU* 3.4 29.2 - - - -
163B GLY* 2.8 14.6 + - - +
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B SER* 3.5 2.1 - - - -
105B LEU* 2.9 62.3 + - + +
107B PHE* 3.9 18.8 - - + -
126B VAL* 4.9 10.3 - - + -
127B SER* 1.3 76.2 + - - +
129B ASP* 1.3 67.5 + - - +
131B ASN* 4.5 7.2 - - - +
132B PHE* 2.9 37.7 - - - +
133B HIS 3.1 6.1 - - - +
134B PRO* 4.6 0.7 - - + -
135B LEU* 4.0 5.8 - - - +
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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