Contacts of the strand formed by residues 150 - 159 (chain A) in PDB entry 2GPY
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 VAL 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LEU* 6.5 0.2 - - + -
126A LEU* 4.3 3.4 - - - +
127A PHE* 3.4 13.9 - - + +
128A ASP 4.3 0.9 - - - +
129A VAL 4.8 0.9 - - - -
130A LEU* 3.6 33.7 - - + +
146A TYR 4.0 6.5 - - - +
147A SER 3.0 12.4 + - - +
148A PRO 4.0 2.8 - - - +
149A MSE 1.3 81.8 - - - +
151A ARG* 1.3 74.0 + - - +
152A PRO* 3.9 1.0 - - - +
154A GLY* 3.8 22.9 - - - -
155A LEU 3.8 8.7 - - - +
156A ILE* 3.8 13.9 - - + -
213A LYS* 2.8 31.9 + - + -
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Residues in contact with ARG 151 (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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53A ALA 4.8 10.9 + - - -
54A ALA 5.9 0.4 + - - -
55A PRO* 6.1 0.2 - - - +
126A LEU* 4.0 21.6 - - + +
127A PHE 3.0 20.6 + - - +
128A ASP* 2.7 32.9 + - - +
149A MSE 4.0 0.6 + - - -
150A VAL* 1.3 79.6 - - - +
152A PRO* 1.3 94.7 + - + +
153A GLY* 3.3 23.1 + - - -
154A GLY* 2.9 24.5 + - - -
213A LYS* 3.6 4.7 - - - +
52B MSE 5.8 1.8 + - - -
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Residues in contact with PRO 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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126A LEU* 4.5 10.1 - - + -
150A VAL 4.4 1.8 - - - +
151A ARG* 1.3 105.4 + - + +
153A GLY* 1.3 58.1 + - - +
213A LYS* 4.2 7.8 - - + -
214A ARG 3.8 22.7 - - - +
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Residues in contact with GLY 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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151A ARG* 3.3 18.0 + - - -
152A PRO* 1.3 71.1 - - - +
154A GLY* 1.3 63.6 + - - +
155A LEU* 4.6 4.7 - - - +
212A ILE* 3.9 14.1 - - - +
213A LYS 2.9 21.1 + - - -
214A ARG 4.8 0.6 - - - -
51B LYS 5.3 1.9 - - - +
52B MSE 5.0 5.7 - - - +
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Residues in contact with GLY 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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128A ASP 3.4 12.3 - - - -
150A VAL* 3.8 9.9 - - - -
151A ARG* 2.9 28.2 + - - -
152A PRO 3.1 1.6 + - - -
153A GLY* 1.3 79.9 - - - +
155A LEU* 1.3 62.0 - - - -
212A ILE* 3.5 3.5 - - - -
213A LYS* 2.9 25.3 + - - +
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Residues in contact with LEU 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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49A LEU 5.3 0.9 - - - +
50A LEU* 5.3 2.5 - - + -
53A ALA* 3.7 21.5 - - + -
128A ASP 2.9 12.1 + - - +
129A VAL* 3.2 16.2 - - + +
130A LEU 2.8 24.9 + - - +
150A VAL* 3.8 3.0 - - - +
153A GLY 4.6 2.9 - - - +
154A GLY* 1.3 81.7 - - - +
156A ILE* 1.3 66.0 + - - +
157A LEU* 4.5 20.6 - - + -
210A ILE* 4.4 4.3 - - + -
211A SER 3.3 2.7 - - - +
212A ILE* 3.8 22.2 - - + -
52B MSE 3.3 48.2 - - + +
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Residues in contact with ILE 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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130A LEU* 3.3 23.8 - - + +
132A ILE* 4.4 4.7 - - + -
143A PHE* 3.6 29.6 - - + -
147A SER* 3.5 37.9 - - - -
150A VAL* 3.8 16.2 - - + -
155A LEU* 1.3 78.0 - - - +
157A LEU* 1.3 64.4 + - - +
158A SER* 3.9 13.0 + - - +
197A TYR* 3.6 24.0 - - + -
209A ALA 3.4 3.1 - - - +
210A ILE* 3.8 0.2 - - - -
211A SER* 2.8 44.9 + - - -
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Residues in contact with LEU 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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46A LEU* 3.5 28.7 - - + -
49A LEU* 5.4 7.0 - - + -
50A LEU* 3.8 23.8 - - + -
129A VAL* 4.0 14.6 - - + -
130A LEU 2.8 9.1 + - - +
131A PHE* 3.5 18.6 - - + -
132A ILE* 3.0 27.0 + - - +
155A LEU* 4.5 13.9 - - + -
156A ILE* 1.3 78.4 - - - +
158A SER* 1.3 62.1 + - - +
159A ASP 3.9 0.2 - - - -
208A ILE* 4.0 9.9 - - + -
209A ALA 3.3 2.7 - - - +
210A ILE* 3.9 36.6 - - + -
52B MSE 5.4 1.6 - - - -
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Residues in contact with SER 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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132A ILE* 3.2 6.4 - - - +
139A TYR* 2.6 30.0 + - - -
143A PHE* 4.6 0.7 - - - -
156A ILE* 3.9 16.3 + - - +
157A LEU* 1.3 74.1 - - - +
159A ASP* 1.3 62.9 + - - +
160A ASN 3.7 0.2 + - - -
161A VAL* 3.1 27.7 - - - +
191A LEU* 4.3 4.2 - - - +
208A ILE* 3.4 3.7 - - - +
209A ALA* 2.9 37.5 + - - +
211A SER* 5.1 0.5 + - - -
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Residues in contact with ASP 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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38A MSE 4.3 20.4 - - - +
131A PHE* 3.7 29.3 - - + -
132A ILE 2.8 9.8 + - - +
133A ASP* 4.0 13.0 - - - +
134A ALA* 2.9 27.4 + - - +
157A LEU 3.9 1.2 + - - -
158A SER* 1.3 73.6 - - - +
160A ASN* 1.3 87.0 + - - +
204A VAL 4.8 4.5 - - - +
205A GLY* 5.5 1.6 - - - -
206A ASP 5.0 2.9 + - - -
207A GLY 4.0 6.1 - - - +
208A ILE* 3.9 16.2 - - + +
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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