Contacts of the strand formed by residues 151 - 159 (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 ARG 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LEU* 3.9 16.4 - - - +
143A TYR* 3.4 57.0 + - + -
144A ILE 3.4 7.9 - - - +
145A GLN* 5.2 4.2 + - - +
149A GLY 4.1 2.4 + - - +
150A ASN* 1.3 71.7 - - - +
152A ILE* 1.3 62.6 + - - +
153A ALA 3.2 6.9 + - - +
154A GLN* 3.4 28.8 + - + +
191A ARG* 5.0 4.0 - - - +
156B GLN* 3.0 42.5 + - - +
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Residues in contact with ILE 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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144A ILE* 3.2 27.6 + - + +
146A ASP* 3.3 31.2 - - + +
150A ASN* 3.9 6.5 - - + +
151A ARG* 1.3 73.8 - - - +
153A ALA* 1.3 59.4 + - - +
169A PHE* 3.4 43.4 - - + -
171A LEU* 5.4 0.2 - - + -
180A TYR* 3.7 28.7 - - + -
155B TRP* 3.5 6.8 - - - +
156B GLN 3.4 32.4 + - - +
157B SER* 5.1 4.9 - - - +
158B PHE* 6.1 0.3 - - - +
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Residues in contact with ALA 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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143A TYR* 3.0 21.1 - - - +
144A ILE* 3.1 16.7 + - + +
151A ARG 3.2 3.5 - - - -
152A ILE* 1.3 83.5 + - - +
154A GLN* 1.3 61.8 + - - +
155A TRP* 3.4 28.0 - - + -
169A PHE* 3.7 22.0 - - + -
154B GLN 3.3 9.4 - - - -
155B TRP* 4.0 5.6 - - + -
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Residues in contact with GLN 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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141A LEU* 3.4 28.1 - - + +
142A VAL 3.4 6.1 - - - -
143A TYR* 3.8 6.5 - - + -
151A ARG* 3.4 33.2 + - + +
153A ALA* 1.3 79.4 - - - +
155A TRP* 1.3 68.8 + - - +
156A GLN* 3.0 36.3 - - + +
151B ARG* 6.2 0.2 - - - +
153B ALA* 3.2 3.3 - - - -
154B GLN* 2.7 70.8 + - + +
156B GLN* 5.5 0.3 + - - -
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Residues in contact with TRP 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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123A PHE* 3.8 26.5 - + - -
141A LEU* 3.7 4.3 - - - +
142A VAL* 2.9 51.2 + - + -
143A TYR* 4.5 1.1 - - - -
144A ILE* 4.2 11.4 - - + -
153A ALA* 3.4 34.8 - - + -
154A GLN* 1.3 79.1 - - - +
156A GLN* 1.3 63.5 + - - +
158A PHE* 3.8 8.6 - - + -
167A PHE* 3.4 39.3 - + + -
168A SER 3.9 22.2 - - - -
169A PHE* 4.6 0.9 - - + -
152B ILE 3.4 4.9 - - - +
153B ALA* 4.1 9.9 - - + +
155B TRP* 4.5 17.2 - + - -
168B SER 5.5 1.6 + - - -
169B PHE* 3.8 33.5 - + + -
170B PRO* 6.0 1.8 - - - +
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Residues in contact with GLN 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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140A PRO 3.5 7.8 + - - +
141A LEU* 4.2 12.1 - - + +
154A GLN* 3.0 32.0 - - + +
155A TRP* 1.3 78.6 - - - +
157A SER* 1.3 76.6 + - - +
158A PHE* 3.2 7.9 + - - +
150B ASN* 5.6 1.7 - - + +
151B ARG* 2.8 42.3 + - - +
152B ILE* 3.1 23.6 + - - +
154B GLN* 6.1 0.4 - - + -
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Residues in contact with SER 157 (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* 3.7 16.7 - - - +
139A ILE 3.3 9.8 + - - -
140A PRO* 3.1 16.9 + - - +
156A GLN* 1.3 77.8 - - - +
158A PHE* 1.3 59.1 + - - +
159A GLN 4.4 0.2 + - - -
150B ASN* 5.5 11.2 + - - +
152B ILE* 5.6 5.9 - - - +
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Residues in contact with PHE 158 (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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125A VAL* 3.5 28.9 - - + -
138A LEU* 3.2 3.3 - - - +
139A ILE* 2.8 61.5 + - + -
141A LEU 4.3 0.4 - - - -
142A VAL* 3.4 39.7 - - + -
155A TRP* 3.8 19.1 - - + -
156A GLN 4.1 6.1 - - - +
157A SER* 1.3 75.1 - - - +
159A GLN* 1.3 59.9 + - - +
160A LEU* 3.6 11.7 - - + -
165A LYS* 3.5 32.8 - - + -
167A PHE* 3.5 13.7 - + + -
169B PHE* 6.6 0.4 - - + -
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Residues in contact with GLN 159 (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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136A ASN* 3.9 22.8 + - - +
137A GLU 3.4 12.1 - - - +
138A LEU* 4.0 17.5 - - + +
158A PHE* 1.3 75.8 - - - +
160A LEU* 1.3 79.7 + - - +
161A GLU* 3.7 14.6 + - + +
165A LYS* 4.3 10.6 + - - +
174B GLU* 5.2 7.7 + - - +
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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