Contacts of the strand formed by residues 147 - 156 (chain D) in PDB entry 2RFQ
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 TRP 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D ASP* 3.5 29.3 + - + -
104D VAL* 3.7 23.6 + - + +
111D VAL* 3.8 16.2 - - + +
112D ARG 3.6 1.0 + - - -
113D ILE* 3.3 18.8 - - + -
114D SER* 2.9 22.3 + - - -
145D ALA* 3.6 3.3 - - - +
146D SER* 1.3 101.9 + - - +
148D ALA* 1.3 59.5 + - - +
167D LEU* 3.6 27.8 - - + -
168D ILE 3.3 10.8 - - - -
169D PRO* 3.4 46.2 - - + -
173D TYR* 3.2 11.2 + - - -
203D ARG* 3.7 34.8 - - - -
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ILE* 4.1 1.8 - - - -
114D SER* 3.1 18.8 - - - +
115D SER* 5.1 0.2 - - - -
147D TRP* 1.3 74.6 - - - +
149D VAL* 1.3 60.9 + - - +
150D LEU* 4.0 25.5 - - + +
166D PHE 3.3 3.1 - - - +
167D LEU* 3.4 3.5 - - - +
168D ILE* 2.9 31.3 + - - +
173D TYR* 3.5 21.3 + - + +
192D VAL* 4.6 5.8 - - + -
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D HIS* 4.6 5.4 - - + -
92D HIS* 4.0 5.4 - - + +
93D LEU* 5.5 3.8 - - + +
96D PHE* 3.9 26.2 - - + -
113D ILE* 4.1 10.8 - - + -
114D SER 2.8 18.4 + - - +
115D SER* 3.2 10.1 - - - -
116D SER 3.1 23.7 + - - +
117D TYR* 3.5 28.5 - - + +
148D ALA* 1.3 70.8 - - - +
150D LEU* 1.3 61.7 + - - +
165D SER* 4.2 12.3 - - - -
166D PHE 3.3 2.5 - - - -
167D LEU* 3.7 28.0 - - + -
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D SER 4.6 0.9 - - - -
116D SER* 3.4 12.3 - - - +
136D TRP* 3.6 46.2 - - + -
148D ALA* 4.0 20.6 - - + -
149D VAL* 1.3 81.6 - - - +
151D GLY* 1.3 64.6 + - - +
165D SER* 3.3 3.3 - - - -
166D PHE* 2.9 43.8 + - + +
168D ILE* 3.8 19.5 - - + -
173D TYR* 5.3 0.2 - - + -
192D VAL* 4.0 15.3 - - + -
194D VAL* 3.7 30.7 - - + -
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Residues in contact with GLY 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D SER 2.9 12.1 + - - -
117D TYR* 3.6 27.0 - - - +
118D ALA 3.2 7.0 - - - +
119D PRO* 3.6 2.1 - - - +
136D TRP* 2.8 28.6 + - - -
149D VAL 4.3 0.2 - - - -
150D LEU* 1.3 71.6 - - - +
152D GLY* 1.3 58.5 + - - -
163D PHE* 4.2 4.9 - - - -
164D VAL 3.2 10.1 - - - -
165D SER* 4.4 4.5 - - - -
207D PHE* 4.9 0.4 - - - -
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Residues in contact with GLY 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PRO* 4.3 1.6 - - - -
121D GLY 3.6 8.5 - - - -
150D LEU 3.8 1.4 + - - -
151D GLY* 1.3 75.2 - - - -
153D PRO* 1.3 77.6 - - - +
163D PHE* 3.8 15.1 - - - -
164D VAL* 3.0 33.9 + - - +
166D PHE* 4.2 7.9 - - - -
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Residues in contact with PRO 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PRO* 4.2 14.1 - - + -
121D GLY 3.3 14.1 - - - +
122D ALA* 3.5 13.2 - - + +
123D GLY 3.1 23.6 + - - -
152D GLY* 1.3 86.5 - - - +
154D VAL* 1.3 60.3 + - - +
155D ILE* 4.0 17.7 - - + -
160D PRO* 4.1 14.4 - - + -
162D ASP 3.2 12.3 - - - +
163D PHE* 4.0 9.1 - - + -
166D PHE* 3.8 1.4 - - - -
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Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLY 3.4 5.4 - - - +
125D VAL* 3.5 30.1 - - + -
130D TYR* 3.7 27.6 - - + +
152D GLY 3.9 0.2 + - - -
153D PRO* 1.3 70.8 - - - +
155D ILE* 1.3 62.0 + - - +
160D PRO* 3.3 5.2 - - - +
161D VAL* 3.0 40.1 + - + +
162D ASP* 3.0 21.5 + - + +
164D VAL* 3.7 37.5 - - + -
166D PHE* 4.3 1.8 - - + -
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ALA* 4.1 20.2 - - + -
123D GLY 2.8 14.0 + - - +
124D GLN* 3.5 24.2 + - + +
125D VAL* 3.0 27.2 + - - +
153D PRO* 4.0 22.2 - - + -
154D VAL* 1.3 77.4 - - - +
156D LYS* 1.3 64.5 + - - +
158D GLY* 4.0 24.7 - - - +
159D ARG 3.6 2.9 - - - +
160D PRO* 4.1 16.8 - - + -
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Residues in contact with LYS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLN* 4.6 3.8 - - - +
125D VAL* 4.2 29.7 - - + +
154D VAL 4.0 0.4 + - - -
155D ILE* 1.3 76.0 - - - +
157D ASP* 1.3 89.5 + - - +
158D GLY 3.1 0.7 - - - -
159D ARG* 2.9 24.1 + - - +
161D VAL* 3.8 30.5 - - + +
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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