Contacts of the helix formed by residues 159 - 170 (chain B) in PDB entry 2J2M
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 ASP 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B SER 4.4 0.9 + - - +
150B LYS 5.0 2.0 + - - -
152B ASP* 4.8 6.9 - - + +
157B ILE* 3.5 7.1 + - + +
158B GLN* 1.3 79.4 - - - +
160B PRO* 1.3 64.3 - - - +
161B ASP* 2.9 17.5 + - - +
162B ARG* 2.9 47.9 + - - +
163B TYR* 3.4 10.3 + - - -
449B GLN 4.3 0.9 - - - +
451B ARG* 2.7 44.2 + - - -
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Residues in contact with PRO 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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158B GLN* 4.0 5.6 - - + +
159B ASP* 1.3 88.2 - - - +
161B ASP* 1.3 58.7 + - - +
163B TYR* 3.4 36.7 - - + +
164B TRP* 2.8 42.1 + - + +
446B ASP* 3.9 21.5 - - - +
449B GLN* 3.7 35.4 - - + +
450B VAL* 4.0 2.7 - - + -
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Residues in contact with ASP 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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159B ASP* 2.9 16.4 + - - +
160B PRO* 1.3 78.0 - - - +
162B ARG* 1.3 62.8 + - - +
164B TRP* 4.8 0.3 - - - +
165B ASP* 3.5 7.4 + - - +
449B GLN 4.3 2.5 + - - +
450B VAL* 3.6 10.5 - - - +
451B ARG* 2.7 55.9 + - - +
452B HIS* 2.9 24.8 + - - -
387C ARG* 2.9 51.0 + - - -
388C TYR* 4.5 1.2 + - - -
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Residues in contact with ARG 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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147B HIS 3.0 19.4 + - - -
148B SER* 3.2 20.7 + - - +
150B LYS 3.4 12.7 + - - -
151B PRO 4.5 0.2 + - - -
152B ASP* 3.5 36.1 + - - +
153B PRO* 3.5 8.5 - - - +
159B ASP* 2.9 26.3 + - + +
161B ASP* 1.3 80.8 - - - +
163B TYR* 1.3 63.2 - - - +
165B ASP* 3.2 18.4 + - - +
166B PHE 3.3 5.4 + - - -
451B ARG* 5.7 0.4 - - - +
380C SER* 2.9 23.2 + - - -
382C ASN* 2.5 36.0 + - - +
383C TYR* 3.5 31.9 - - + +
387C ARG* 6.0 0.7 - - - +
388C TYR* 6.1 0.4 - - - +
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Residues in contact with TYR 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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148B SER* 3.3 28.7 + - - +
149B LEU* 3.7 27.6 - - + -
158B GLN* 3.8 34.0 + - + -
159B ASP 3.4 14.9 + - - -
160B PRO* 3.4 24.6 - - + +
162B ARG* 1.3 77.9 - - - +
164B TRP* 1.3 78.0 + + - +
166B PHE* 3.6 2.1 + - - +
167B MET* 2.9 38.9 + - + +
177B LEU* 6.6 0.4 - - + -
181B PHE* 4.5 10.1 - + - -
446B ASP* 2.5 37.8 + - - -
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Residues in contact with TRP 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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160B PRO* 2.8 32.9 + - + +
163B TYR* 1.3 87.1 - + - +
165B ASP* 1.3 56.6 + - - +
167B MET* 4.3 6.3 - - + -
168B THR* 2.7 57.0 + - + +
177B LEU* 3.7 30.5 - - + -
181B PHE* 3.6 22.0 - + - -
443B LEU* 3.9 10.1 - - + -
446B ASP* 3.0 27.6 + - + +
447B LEU* 3.5 20.3 - - + +
450B VAL* 3.5 26.2 - - + -
455B THR* 3.6 10.3 - - + -
459B ALA* 3.8 15.3 - - + -
463B PHE* 3.7 23.3 - + - -
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Residues in contact with ASP 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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161B ASP 3.5 14.1 + - - +
162B ARG 3.2 12.9 + - - +
164B TRP* 1.3 74.4 - - - +
166B PHE* 1.3 63.4 + - - +
168B THR* 2.9 18.4 + - - -
169B LEU* 3.3 24.5 + - - +
455B THR* 3.8 9.7 + - - +
383C TYR* 2.7 28.2 + - - +
386C ASN* 3.3 2.3 - - - +
387C ARG* 2.9 56.8 + - - +
388C TYR* 4.0 0.2 - - - -
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Residues in contact with PHE 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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136B ILE* 4.0 20.9 - - + -
141B LYS* 4.0 8.1 - - + -
144B ASP* 3.7 27.6 - - + -
145B MET* 3.6 33.9 - - + -
148B SER* 3.5 31.9 - - - +
162B ARG 3.3 2.8 + - - -
163B TYR 3.9 1.3 - - - +
165B ASP* 1.3 78.5 - - - +
167B MET* 1.3 77.1 + - - +
169B LEU* 3.3 3.9 + - - +
170B ARG* 3.0 38.8 + - + +
383C TYR* 3.9 7.5 - + + -
384C GLU 3.7 11.0 - - - -
385C PRO* 3.8 32.2 - - + +
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Residues in contact with MET 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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135B PHE* 3.3 34.3 - - + -
145B MET* 3.7 22.7 - - + -
148B SER* 4.9 0.4 - - - +
149B LEU* 4.1 22.2 - - + -
163B TYR* 2.9 33.8 + - + +
164B TRP* 4.1 9.2 - - + +
165B ASP 3.3 0.2 - - - -
166B PHE* 1.3 88.1 - - + +
168B THR* 1.3 62.8 + - - +
170B ARG 2.9 25.2 + - - +
171B PRO* 3.7 1.4 - - - +
173B SER* 3.0 32.2 + - - +
177B LEU* 4.2 20.2 - - + -
462B ASN* 4.7 0.3 + - - -
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Residues in contact with THR 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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164B TRP* 2.7 35.3 + - + +
165B ASP* 2.9 11.8 + - - -
167B MET* 1.3 76.3 - - - +
169B LEU* 1.3 61.1 + - - +
170B ARG 3.2 0.6 + - - -
171B PRO* 3.8 8.8 - - - +
455B THR* 3.6 18.2 + - + +
458B LEU* 3.5 30.6 - - - +
459B ALA* 3.6 36.6 - - + +
462B ASN* 3.2 22.7 + - - +
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Residues in contact with LEU 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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165B ASP* 3.3 35.3 + - - +
166B PHE 3.8 0.7 - - - +
167B MET 3.2 0.4 - - - -
168B THR* 1.3 81.8 + - - +
170B ARG* 1.3 68.5 + - - +
171B PRO* 3.4 9.3 - - - +
454B ASN* 6.0 1.3 - - - +
458B LEU* 3.7 20.4 - - + -
385C PRO* 3.8 21.0 - - + +
386C ASN* 3.5 35.2 - - - +
387C ARG* 4.0 3.1 - - + +
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Residues in contact with ARG 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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20A GLN* 3.7 39.2 + - - +
136B ILE* 4.5 4.7 - - + -
141B LYS* 4.1 20.6 - - - +
166B PHE* 3.0 34.9 + - + +
167B MET* 2.9 10.9 + - - +
169B LEU* 1.3 86.8 + - - +
171B PRO* 1.4 58.8 - - - +
172B GLU* 2.8 61.6 + - - +
173B SER* 2.9 22.1 + - - -
414B GLU* 5.3 9.7 + - - -
385C PRO* 3.7 25.7 - - - +
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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