Contacts of the strand formed by residues 164 - 177 (chain B) in PDB entry 2MPR
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 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B GLY* 4.1 18.2 - - - -
151B GLY 4.3 0.2 - - - +
152B SER 3.1 5.8 - - - +
153B TYR* 3.4 29.8 - - + -
161B TYR* 3.3 27.4 - - + +
162B ASP 5.5 0.2 - - - +
163B GLU* 1.3 78.9 - - - +
165B LYS* 1.3 68.6 + - - +
202B TYR* 4.1 3.8 + - - -
255B SER* 5.3 1.8 - - - +
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Residues in contact with LYS 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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150B GLY* 3.0 26.6 - - - +
152B SER* 2.7 20.7 + - - +
164B VAL* 1.3 77.9 - - - +
166B ASP* 1.3 80.5 + - - +
198B THR* 5.9 0.2 - - - +
199B THR* 2.8 31.4 + - + +
202B TYR* 3.6 37.7 - - + +
19C GLU* 3.1 33.5 + - - -
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Residues in contact with ASP 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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147B THR* 3.7 14.8 - - + -
148B GLU 3.3 12.8 - - - +
149B ALA* 3.4 7.8 - - - +
150B GLY* 2.9 19.7 + - - +
152B SER* 4.2 0.5 + - - -
165B LYS* 1.3 103.9 + - - +
167B THR* 1.3 61.6 + - - +
168B ALA 3.9 1.4 + - - -
19C GLU* 5.1 0.7 - - - -
71C GLN* 4.6 17.3 + - - +
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Residues in contact with THR 167 (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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147B THR* 3.4 3.3 - - - -
148B GLU* 2.9 36.4 + - - -
150B GLY 2.7 22.0 + - - -
151B GLY* 3.3 8.1 - - - -
152B SER* 2.8 24.4 + - - +
166B ASP* 1.3 71.4 - - - +
168B ALA* 1.3 61.6 + - - +
169B ASN* 3.0 11.1 + - - +
196B ALA* 3.8 29.4 - - + -
197B ASN 4.6 2.0 - - - +
198B THR* 4.3 5.8 - - + +
204B LEU* 3.8 11.2 - - + -
250B SER* 3.9 11.9 - - - +
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Residues in contact with ALA 168 (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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145B ARG* 4.0 18.4 - - - +
146B SER 3.7 5.8 - - - -
147B THR* 4.2 6.2 - - + +
166B ASP 3.9 3.6 + - - -
167B THR* 1.3 74.4 - - - +
169B ASN* 1.3 59.8 + - - +
170B ASP* 4.2 0.7 - - - +
196B ALA* 3.4 4.0 - - - -
197B ASN* 2.8 44.5 + - + +
19C GLU* 3.7 34.6 + - + +
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Residues in contact with ASN 169 (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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145B ARG* 3.5 5.5 - - - +
146B SER* 2.8 37.8 + - - +
148B GLU* 2.9 29.9 + - - +
167B THR* 3.0 25.3 + - - +
168B ALA* 1.3 75.8 + - - +
170B ASP* 1.3 63.3 + - - +
171B VAL* 4.1 2.6 + - - +
195B ARG 3.4 4.5 - - - -
196B ALA* 3.7 8.2 - - - -
247B ALA* 3.1 33.3 + - + +
249B GLY* 2.8 29.5 + - - -
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Residues in contact with ASP 170 (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 THR 3.8 4.3 - - - +
145B ARG* 2.8 34.6 + - - +
168B ALA* 5.0 0.2 - - - +
169B ASN* 1.3 74.5 + - - +
171B VAL* 1.3 61.7 + - - +
172B PHE* 3.7 25.9 - - + -
193B TYR 3.9 0.7 - - - +
194B GLY* 3.0 5.4 - - - -
195B ARG* 3.0 36.1 + - + +
197B ASN* 3.1 25.9 + - - +
247B ALA* 4.5 0.2 - - - +
11C ILE* 5.2 0.2 - - - +
13C TRP* 2.8 28.3 + - + -
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Residues in contact with VAL 171 (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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122B ILE* 4.5 6.1 - - + -
142B ALA 3.9 0.2 - - - +
143B ALA* 3.1 8.1 - - - +
144B THR* 3.1 44.8 + - - +
145B ARG* 5.8 0.9 - - - -
146B SER* 5.6 2.0 - - - +
169B ASN 4.8 3.4 - - - +
170B ASP* 1.3 79.0 - - - +
172B PHE* 1.3 69.8 + - - +
173B ASP* 4.6 3.1 - - + +
192B ASP* 3.6 23.3 - - + +
193B TYR 3.5 7.4 - - - +
194B GLY* 4.6 1.1 - - - -
239B MET* 4.5 2.0 - - + -
245B GLY 3.3 27.8 - - - +
246B GLN* 4.0 7.2 - - + -
247B ALA* 3.9 21.1 - - + +
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Residues in contact with PHE 172 (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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142B ALA 3.5 3.8 - - - +
143B ALA* 4.2 17.5 - - + -
170B ASP* 3.7 37.9 - - + -
171B VAL* 1.3 76.7 - - - +
173B ASP* 1.3 60.9 + - - +
174B VAL* 5.2 4.2 - - + +
191B VAL 3.8 1.0 - - - +
192B ASP* 3.5 3.3 - - - -
193B TYR* 2.9 64.5 + + + +
195B ARG* 4.9 9.9 - - + -
13C TRP* 4.7 11.9 - + - -
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Residues in contact with ASP 173 (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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107B TYR* 3.8 8.7 + - - -
120B TRP* 3.9 1.9 + - - -
122B ILE* 3.6 21.8 - - + +
140B SER 4.7 0.7 - - - +
141B LEU* 3.4 5.4 - - - -
142B ALA* 2.8 40.6 + - + +
171B VAL* 4.7 1.1 - - + -
172B PHE* 1.3 73.1 - - - +
174B VAL* 1.3 67.0 + - - +
175B ARG* 2.8 50.9 + - - -
191B VAL 3.6 3.4 - - - +
192B ASP* 2.6 28.5 - - - +
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Residues in contact with VAL 174 (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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139B LEU* 4.0 15.7 - - + -
140B SER 3.4 3.1 - - - -
141B LEU* 3.7 26.2 - - + -
172B PHE* 5.2 3.6 - - + +
173B ASP* 1.3 81.2 - - - +
175B ARG* 1.3 67.3 + - - +
190B GLY* 3.2 3.1 - - - -
191B VAL* 2.9 44.3 + - + +
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Residues in contact with ARG 175 (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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107B TYR* 3.9 19.7 + - - -
108B GLN* 2.7 55.7 + - - +
110B HIS* 3.8 4.8 + - - -
120B TRP* 3.4 63.5 + - + +
122B ILE* 4.1 7.5 - - - +
138B LYS 3.5 0.7 - - - +
139B LEU* 3.3 11.1 - - - +
140B SER* 3.0 39.3 + - - +
173B ASP* 2.8 50.3 + - - +
174B VAL* 1.3 76.5 - - - +
176B LEU* 1.3 59.0 + - - +
177B ALA* 4.0 1.1 - - + +
188B GLU* 4.0 11.8 + - - +
189B LEU 3.3 4.7 - - - +
190B GLY* 4.1 0.2 - - - -
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Residues in contact with LEU 176 (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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134B LEU* 3.7 28.5 - - + -
136B PHE* 4.1 14.1 - - + -
137B GLY* 4.3 3.8 - - - -
138B LYS 3.3 22.2 - - - +
139B LEU* 4.4 8.7 - - + +
175B ARG* 1.3 73.4 - - - +
177B ALA* 1.3 60.2 + - - +
179B LEU* 4.1 29.8 - - + +
187B LEU 4.1 1.6 - - - +
188B GLU* 3.3 2.6 - - - -
189B LEU* 2.8 46.5 + - + +
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Residues in contact with ALA 177 (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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137B GLY* 3.3 6.8 - - - -
138B LYS* 2.8 42.8 + - + +
175B ARG* 4.0 0.9 - - + -
176B LEU* 1.3 75.0 - - - +
178B GLY* 1.3 62.6 + - - +
179B LEU* 3.4 3.3 - - - +
187B LEU 4.0 3.6 - - - -
188B GLU* 3.8 27.4 - - + +
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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