Contacts of the strand formed by residues 138 - 145 (chain A) 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 LEU 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ASN 4.0 1.0 + - - -
137A GLU* 1.3 79.9 - - - +
139A ILE* 1.3 61.7 + - - +
140A PRO* 3.6 10.5 - - + +
157A SER* 3.7 24.2 - - - +
158A PHE 3.2 25.6 - - - +
159A GLN* 4.0 18.6 - - + +
187A LYS* 4.5 11.2 - - + +
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Residues in contact with ILE 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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106A VAL* 4.3 15.5 - - + -
125A VAL* 5.2 2.7 - - + -
137A GLU* 3.7 33.9 - - + +
138A LEU* 1.3 72.5 - - - +
140A PRO* 1.3 67.0 - - - +
141A LEU 3.7 6.5 + - - +
157A SER* 3.3 3.1 + - - -
158A PHE* 2.8 59.1 + - + -
160A LEU* 3.7 30.3 - - + -
184A VAL* 3.7 21.1 - - + -
185A GLN 3.4 15.0 - - - +
186A LYS* 4.8 4.9 - - - -
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Residues in contact with PRO 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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138A LEU* 3.6 7.4 - - + +
139A ILE* 1.3 85.7 - - - +
141A LEU* 1.3 61.4 + - + +
156A GLN* 3.5 9.6 + - - +
157A SER* 3.1 26.1 + - - +
185A GLN* 3.0 25.1 - - + +
186A LYS 4.2 1.3 - - - +
187A LYS* 3.6 33.2 - - + +
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Residues in contact with LEU 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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139A ILE* 3.5 7.7 - - - +
140A PRO* 1.3 83.4 - - + +
142A VAL* 1.3 67.5 + - - +
143A TYR* 3.9 18.4 - - + -
151A ARG* 3.9 22.0 - - - +
154A GLN* 3.4 40.4 - - + +
155A TRP 3.7 7.9 - - - +
156A GLN* 4.2 9.6 - - + +
158A PHE* 4.3 0.7 - - - -
183A VAL 5.3 0.2 - - - +
184A VAL* 3.3 2.1 - - - -
185A GLN* 2.8 58.9 + - + +
191A ARG* 6.2 0.2 - - - +
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Residues in contact with VAL 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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123A PHE* 3.7 24.7 - - + -
125A VAL* 3.9 1.6 - - + -
141A LEU* 1.3 76.1 - - - +
143A TYR* 1.3 66.1 + - - +
154A GLN* 3.4 1.0 - - - +
155A TRP* 2.9 46.5 + - + -
158A PHE* 3.4 29.4 - - + -
167A PHE* 4.0 7.9 - - + -
182A VAL* 3.9 5.6 - - + -
183A VAL 3.0 7.0 - - - +
184A VAL* 3.2 28.5 - - + -
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Residues in contact with TYR 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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141A LEU* 3.9 23.3 - - + -
142A VAL* 1.3 76.7 - - - +
144A ILE* 1.3 68.0 + - - +
145A GLN* 4.1 25.4 + - + -
151A ARG* 3.4 59.6 + - + -
153A ALA 3.0 18.6 - - - +
154A GLN* 3.8 11.4 - - + +
155A TRP* 4.5 3.1 - - - -
181A LYS* 3.6 0.5 - - - +
182A VAL* 3.3 5.3 - - - +
183A VAL* 2.7 65.8 + - + +
191A ARG* 3.5 19.7 + - - -
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Residues in contact with ILE 144 (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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121A VAL* 4.8 10.3 - - + -
123A PHE* 4.0 29.6 - - + -
143A TYR* 1.3 79.3 - - - +
145A GLN* 1.3 62.9 + - - +
151A ARG* 3.4 5.5 - - - -
152A ILE* 3.2 48.8 + - + +
153A ALA* 3.1 7.4 + - + +
155A TRP* 4.2 8.3 - - + -
169A PHE* 3.6 35.9 - - + -
180A TYR* 4.2 3.8 - - + -
181A LYS 3.3 3.4 - - - +
182A VAL* 4.6 7.9 - - + -
196A PHE* 4.0 26.7 - - + -
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Residues in contact with GLN 145 (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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143A TYR* 4.1 25.0 + - + -
144A ILE* 1.3 74.1 - - - +
146A ASP* 1.3 64.2 + - - +
149A GLY* 3.6 32.4 - - - +
150A ASN 3.0 12.3 - - - +
151A ARG* 5.2 2.4 + - - +
180A TYR* 3.1 10.1 - - - +
181A LYS* 2.8 71.5 + - + +
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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