Contacts of the strand formed by residues 161 - 171 (chain B) in PDB entry 2CMG
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 LEU 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B LYS* 3.0 21.9 + - - -
140B TYR 3.2 17.0 - - - +
141B ASP 4.2 0.9 - - - +
143B ILE* 3.7 18.8 - - + -
157B LEU 3.4 6.6 + - - +
158B LYS* 3.6 16.8 - - - +
159B ARG 3.3 2.3 - - - +
160B MET* 1.3 80.0 - - - +
162B LYS* 1.3 76.4 + - - +
165B GLY* 3.4 23.3 - - - +
166B VAL 3.6 31.9 - - - +
167B PHE* 4.3 4.0 - - + +
192B PHE* 4.0 25.6 - - + -
213B ALA 5.0 0.4 - - - +
214B SER* 5.2 0.4 - - - -
215B PHE* 4.2 10.6 - - + -
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Residues in contact with LYS 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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74B LYS* 5.9 0.6 - - - +
75B GLU* 4.2 9.1 - - - +
139B LYS* 2.7 47.9 + - + +
140B TYR* 2.9 15.0 + - - +
141B ASP* 3.1 42.2 + - - +
161B LEU* 1.3 82.0 - - - +
163B GLU* 1.3 70.2 + - - +
164B ASP* 3.8 17.0 - - - +
165B GLY* 2.7 25.9 + - - +
215B PHE* 3.7 7.3 - - - -
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Residues in contact with GLU 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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139B LYS* 4.9 9.1 + - - +
161B LEU 4.2 0.2 + - - -
162B LYS* 1.3 83.1 - - - +
164B ASP* 1.3 67.3 + - + +
165B GLY 3.6 0.9 + - - -
215B PHE* 3.3 36.7 + - - +
216B LYS* 4.8 3.1 + - - +
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Residues in contact with ASP 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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70B LYS* 3.3 38.6 + - - +
141B ASP* 4.5 8.0 - - - +
162B LYS* 3.8 15.0 - - - +
163B GLU* 1.3 86.2 - - + +
165B GLY* 1.3 62.2 + - - +
216B LYS* 6.2 1.6 - - - -
217B THR* 3.9 13.0 - - - +
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Residues in contact with GLY 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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140B TYR 4.4 0.2 - - - -
141B ASP* 3.3 16.8 - - - -
161B LEU* 3.4 20.0 - - - +
162B LYS* 2.7 20.4 + - - +
163B GLU 3.3 0.4 - - - -
164B ASP* 1.3 82.5 - - - +
166B VAL* 1.3 59.7 + - - -
214B SER* 3.6 9.7 - - - -
215B PHE 4.2 2.6 + - - -
217B THR* 3.5 12.6 - - - +
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Residues in contact with VAL 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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69B THR* 4.9 0.9 - - - +
70B LYS* 3.9 22.9 - - + -
141B ASP 3.1 4.8 + - - -
142B LEU* 3.2 22.7 - - + +
143B ILE 3.0 23.9 + - - +
161B LEU* 3.6 4.9 - - - +
165B GLY* 1.3 77.9 - - - -
167B PHE* 1.3 62.8 + - - +
168B ILE* 4.1 10.9 + - + -
212B TYR* 3.6 46.4 - - + +
213B ALA 3.6 8.3 - - - +
217B THR* 3.4 22.0 - - + -
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Residues in contact with PHE 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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143B ILE* 3.4 26.2 - - + +
145B CYS* 3.5 39.5 - - + -
149B PRO* 4.4 9.2 - - + -
154B ILE* 4.9 11.2 - - - -
157B LEU* 3.6 31.6 - - + -
158B LYS* 6.3 0.2 - - - -
161B LEU* 4.3 7.6 - - + +
166B VAL* 1.3 72.0 - - - +
168B ILE* 1.3 63.2 + - - +
169B SER* 3.9 6.3 - - - -
188B MET* 3.5 36.8 - - + +
192B PHE* 3.8 27.8 - + + -
211B ILE 3.6 1.9 - - - +
213B ALA* 2.9 38.9 + - - +
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Residues in contact with ILE 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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62B LEU* 3.7 37.5 - - + +
65B MET* 4.1 19.5 - - + -
66B GLY* 4.1 12.6 - - - +
142B LEU* 4.9 2.0 - - + -
143B ILE 2.9 6.7 + - - -
144B PHE* 3.2 39.3 - - + +
145B CYS 2.7 31.0 + - - +
166B VAL* 4.3 15.7 - - + +
167B PHE* 1.3 76.5 - - - +
169B SER* 1.3 61.6 + - - +
198B PHE* 4.2 7.4 - - + -
210B TYR* 5.6 0.2 - - + -
211B ILE 3.4 11.7 - - - +
212B TYR* 4.6 7.0 - - + -
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Residues in contact with SER 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 CYS* 3.3 25.6 - - - -
149B PRO* 4.0 15.9 - - - +
167B PHE* 3.9 12.0 + - - -
168B ILE* 1.3 77.1 - - - +
170B VAL* 1.3 63.0 + - - +
188B MET* 3.5 19.8 - - - +
210B TYR* 3.2 9.4 - - - +
211B ILE* 3.0 38.5 + - - +
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Residues in contact with VAL 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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62B LEU* 5.7 3.8 - - + -
145B CYS 3.2 10.5 + - - +
146B LEU* 3.6 27.8 - - + +
147B GLN* 4.8 1.2 - - - -
148B GLU* 3.2 39.2 - - + +
149B PRO* 4.1 3.1 - - - +
169B SER* 1.3 78.7 + - - +
171B ALA* 1.3 77.0 + - - +
208B LYS* 3.4 37.7 - - + +
209B GLY 3.6 4.5 - - - +
210B TYR* 4.2 8.3 - - + -
211B ILE* 4.2 0.9 - - - +
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Residues in contact with ALA 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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148B GLU* 3.7 15.3 - - - +
170B VAL* 1.3 80.3 - - - +
172B LYS* 1.3 63.8 + - - +
180B SER 5.7 0.2 - - - +
181B MET* 3.4 20.4 - - + -
184B ALA* 4.0 12.1 - - + -
207B ASN 4.9 0.5 - - - +
208B LYS* 3.9 3.5 - - - +
209B GLY 2.7 21.4 + - - +
211B ILE* 3.1 30.1 - - + -
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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