Contacts of the strand formed by residues 152 - 166 (chain B) in PDB entry 2NMY
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 GLY 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.6 7.3 - - - +
51A GLY* 3.9 5.4 - - - -
81A PRO* 6.0 0.2 - - - +
148B GLY* 3.5 0.3 - - - -
149B GLY 2.9 32.3 + - - -
150B ILE 3.6 0.4 + - - -
151B GLY* 1.3 78.3 - - - +
153B PHE* 1.3 71.9 + - - -
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Residues in contact with PHE 153 (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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50A ILE* 4.9 0.2 - - - -
51A GLY* 4.8 2.4 - - - +
146B MET* 3.5 36.8 - - + -
147B ILE* 3.3 10.1 - - - +
148B GLY* 3.6 27.4 - - - -
149B GLY 6.1 0.2 - - - -
152B GLY* 1.3 81.6 - - - -
154B ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 154 (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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50A ILE* 4.2 13.7 - - + +
51A GLY* 4.0 21.1 - - - +
132B VAL* 5.0 0.2 - - + -
146B MET* 3.5 8.6 - - - +
147B ILE* 3.0 53.2 + - + +
153B PHE* 1.3 78.1 - - - +
155B LYS* 1.3 61.7 + - - +
156B VAL* 3.9 19.4 + - + -
179B PRO* 4.0 42.6 - - + +
180B THR* 4.1 10.8 - - - +
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Residues in contact with LYS 155 (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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144B PRO* 6.5 0.7 - - - -
145B LYS 3.7 6.3 - - - +
146B MET* 4.0 26.2 - - + -
154B ILE* 1.3 71.8 - - - +
156B VAL* 1.3 64.7 + - - +
179B PRO* 3.6 19.1 - - - +
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Residues in contact with VAL 156 (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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132B VAL* 4.6 5.4 - - + -
142B TRP* 4.4 3.9 - - - -
144B PRO* 4.1 4.3 - - - +
145B LYS* 3.1 49.8 + - + +
147B ILE* 4.1 16.4 - - + -
154B ILE* 3.9 26.9 - - + -
155B LYS* 1.3 79.0 - - - +
157B ARG* 1.4 61.7 + - - +
176B LEU* 4.0 27.4 - - + -
177B VAL 3.5 16.4 - - - +
178B GLY* 4.2 7.4 - - - +
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Residues in contact with ARG 157 (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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135B GLU* 3.0 40.4 + - - -
136B MET 3.3 19.2 + - - -
137B SER* 5.2 1.4 - - - +
142B TRP* 3.5 52.9 - - + +
156B VAL* 1.4 73.9 - - - +
158B GLN* 1.4 60.4 + - - +
159B TYR* 3.0 34.4 + - + -
175B VAL 3.8 1.7 - - - +
176B LEU* 3.4 4.3 - - - -
177B VAL* 2.9 51.8 + - - +
178B GLY* 5.4 0.8 - - - -
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Residues in contact with GLN 158 (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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141B ARG 4.3 0.5 - - - +
142B TRP* 3.3 6.8 - - - -
143B LYS* 2.9 69.8 + - + +
144B PRO 4.7 1.6 - - - +
145B LYS* 3.6 31.3 + - + +
156B VAL 4.1 1.0 + - - -
157B ARG* 1.4 70.6 - - - +
159B TYR* 1.4 59.5 + - - +
160B ASP* 3.0 22.4 + - - +
174B THR* 3.7 23.2 + - + +
176B LEU* 3.6 15.5 - - + -
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Residues in contact with TYR 159 (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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138B LEU* 3.8 44.8 + - + -
139B PRO 3.7 18.2 - - - -
140B GLY 4.1 9.4 - - - -
141B ARG 4.0 13.5 - - - -
142B TRP* 3.7 22.6 - + + -
157B ARG* 3.0 54.8 + - + -
158B GLN* 1.4 72.0 - - - +
160B ASP* 1.3 61.4 + - - +
162B ILE* 3.8 20.6 - - + +
174B THR* 3.4 4.2 - - - +
175B VAL 3.0 37.6 + - - +
177B VAL* 3.9 15.0 - - + -
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Residues in contact with ASP 160 (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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141B ARG 5.2 2.4 + - - -
143B LYS* 4.2 13.5 + - - +
158B GLN* 3.0 28.4 + - - -
159B TYR* 1.3 73.3 - - - +
161B GLN* 1.3 74.8 + - + +
162B ILE* 3.4 10.6 + - - +
174B THR* 2.9 25.2 + - - +
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Residues in contact with GLN 161 (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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160B ASP* 1.3 79.2 - - + +
162B ILE* 1.3 62.9 + - - +
163B ILE* 4.0 3.3 + - - +
172B ILE* 3.8 24.8 - - + +
173B GLY* 3.5 14.7 + - - +
174B THR* 4.8 0.4 + - - -
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Residues in contact with ILE 162 (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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115B ILE* 4.0 25.8 - - + -
138B LEU* 4.4 19.3 - - + -
139B PRO* 4.5 25.4 - - + +
159B TYR* 3.8 35.9 - - + +
160B ASP 3.9 10.8 - - - +
161B GLN* 1.3 77.4 - - - +
163B ILE* 1.3 72.3 + - - +
164B ILE* 3.6 5.8 + - + +
172B ILE* 3.3 5.1 - - - -
173B GLY 2.9 30.5 + - - +
175B VAL* 4.1 11.0 - - + -
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Residues in contact with ILE 163 (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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114B LYS 4.3 1.9 - - - +
115B ILE* 4.1 11.1 - - - +
116B GLY 4.8 2.4 + - - -
161B GLN 5.0 2.5 - - - +
162B ILE* 1.3 80.9 - - - +
164B ILE* 1.4 64.0 + - - +
170B LYS* 4.0 29.6 - - + -
171B ALA 3.7 4.7 - - - +
172B ILE* 4.2 23.6 - - + -
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Residues in contact with ILE 164 (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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113B ILE* 4.2 23.3 - - + -
114B LYS 3.5 12.3 - - - +
115B ILE* 4.4 20.9 - - + -
131B THR* 5.1 2.2 - - + -
133B ILE* 5.2 2.2 - - + -
162B ILE* 3.9 11.0 - - + +
163B ILE* 1.4 79.0 - - - +
165B GLU* 1.4 68.7 + - - +
166B ILE* 4.2 8.0 - - + +
169B HIS 4.0 0.2 - - - +
170B LYS* 4.1 1.7 - - - -
171B ALA* 3.0 43.7 + - + +
173B GLY 5.1 0.2 - - - +
175B VAL* 4.7 10.1 - - + -
185B ILE* 4.4 16.8 - - + -
189B LEU* 3.9 28.0 - - + -
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Residues in contact with GLU 165 (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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112B THR 4.9 0.2 - - - -
113B ILE* 3.1 10.3 - - - +
114B LYS* 2.9 65.6 + - + +
119B LEU* 6.0 0.3 - - - +
164B ILE* 1.4 72.6 - - - +
166B ILE* 1.4 62.8 + - - +
167B ALA 4.2 0.2 - - - -
168B GLY* 3.9 30.4 + - - +
169B HIS 3.4 12.6 - - - +
170B LYS* 4.6 7.4 - - + +
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Residues in contact with ILE 166 (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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111B VAL* 4.3 8.1 - - + -
112B THR 4.2 2.0 - - - -
113B ILE* 4.2 11.0 - - + -
124B LEU* 4.1 22.0 - - + -
164B ILE* 4.2 13.5 - - + +
165B GLU* 1.4 75.4 - - - +
167B ALA* 1.4 72.4 + - + +
169B HIS* 2.9 31.1 + - - +
171B ALA* 4.4 15.5 - - + -
185B ILE* 4.0 14.1 - - + -
189B LEU* 3.9 37.0 - - + +
193B ILE* 4.0 29.2 - - + +
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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