Contacts of the helix formed by residues 166 - 178 (chain B) in PDB entry 3J2I
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 SER 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B GLN 3.1 5.8 + - - -
165B THR* 1.3 81.0 - - - +
167B VAL* 1.3 65.1 + - - +
168B GLN* 3.3 10.4 + - - +
169B ASP* 3.0 34.6 + - - -
170B GLN* 3.1 19.6 + - - +
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Residues in contact with VAL 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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165B THR 3.8 0.2 + - - -
166B SER* 1.3 73.7 - - - +
168B GLN* 1.3 57.7 + - - +
170B GLN* 3.3 17.9 + - + +
171B GLU* 2.9 50.7 + - + +
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Residues in contact with GLN 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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166B SER* 3.1 9.8 + - - +
167B VAL* 1.3 80.0 - - - +
169B ASP* 1.3 64.5 + - - +
171B GLU* 3.5 13.5 + - - +
172B GLU* 3.2 33.3 + - - +
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Residues in contact with ASP 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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141B THR 5.6 2.0 - - - +
143B SER* 4.7 13.0 + - - +
165B THR* 3.6 19.4 - - + +
166B SER* 3.0 21.4 + - - +
168B GLN* 1.3 79.0 + - - +
170B GLN* 1.3 56.9 + - - +
172B GLU* 3.6 12.7 - - - +
173B LEU* 2.6 48.8 + - + +
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Residues in contact with GLN 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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161B VAL* 4.3 8.1 - - + -
165B THR* 2.8 37.5 + - + -
166B SER 3.1 16.5 + - - +
167B VAL* 3.4 21.4 - - + +
169B ASP* 1.3 78.2 - - - +
171B GLU* 1.3 58.7 + - + +
173B LEU* 3.9 5.2 - - - +
174B SER* 2.8 34.6 + - - -
181B LEU* 3.7 13.9 - - - +
182B VAL* 3.5 11.3 - - - +
183B ALA* 3.1 35.6 + - - +
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Residues in contact with GLU 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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167B VAL* 2.9 43.5 + - + +
168B GLN* 3.8 11.4 - - - +
169B ASP 3.2 0.4 - - - -
170B GLN* 1.3 77.5 - - + +
172B GLU* 1.3 58.6 + - - +
174B SER* 3.5 7.2 + - - -
175B SER* 3.1 27.9 + - - -
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Residues in contact with GLU 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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140B GLN* 5.7 5.7 + - - +
168B GLN* 3.2 25.4 + - - +
169B ASP* 3.7 13.1 - - - +
171B GLU* 1.3 77.9 - - - +
173B LEU* 1.3 60.8 + - + +
175B SER* 3.3 7.8 + - - -
176B LEU* 2.9 28.6 + - - +
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Residues in contact with LEU 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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116B LEU* 4.3 17.3 - - + -
140B GLN* 3.4 32.5 - - + +
141B THR 5.1 6.1 - - - +
142B ILE* 4.5 21.1 - - + -
161B VAL* 4.7 4.3 - - + -
165B THR* 4.6 10.3 - - + -
169B ASP* 2.6 41.0 + - + +
170B GLN* 3.9 1.6 - - - +
172B GLU* 1.3 70.6 - - + +
174B SER* 1.3 58.9 + - - +
176B LEU* 4.1 11.7 - - + -
177B LEU* 2.8 37.0 + - + +
181B LEU* 3.2 24.0 - - + -
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Residues in contact with SER 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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170B GLN 2.8 22.5 + - - -
171B GLU* 3.6 8.5 - - - -
172B GLU 3.3 0.2 - - - -
173B LEU* 1.3 74.6 - - - +
175B SER* 1.3 52.2 + - - +
178B GLN* 2.7 32.6 + - - -
179B VAL 3.2 22.9 + - - -
180B PRO* 3.8 2.7 - - - +
181B LEU* 3.0 31.7 + - - +
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Residues in contact with SER 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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171B GLU 3.1 13.2 + - - -
172B GLU* 3.5 10.3 - - - -
173B LEU 3.2 0.4 - - - -
174B SER* 1.3 79.2 - - - +
176B LEU* 1.3 61.9 + - - +
178B GLN* 3.4 12.5 + - - +
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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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114B VAL* 3.6 17.4 - - + +
116B LEU* 3.9 24.5 - - + -
138B PHE* 3.5 46.7 - - + -
140B GLN* 3.9 29.2 - - + +
172B GLU 2.9 17.4 + - - +
173B LEU* 3.1 9.2 + - + +
175B SER* 1.3 79.7 - - - +
177B LEU* 1.3 59.4 + - + +
178B GLN* 3.7 0.7 + - - +
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Residues in contact with LEU 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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111B ASN* 4.0 10.7 + - - -
113B TYR* 5.3 1.0 - - - +
114B VAL* 3.5 37.7 - - + +
116B LEU* 3.9 35.0 - - + -
152B CYS* 4.8 4.0 - - - -
154B LEU* 3.6 40.4 - - + -
173B LEU* 2.8 18.9 + - + +
174B SER 4.3 0.2 - - - +
176B LEU* 1.3 74.4 - - + +
178B GLN* 1.3 71.2 + - - +
179B VAL* 3.4 20.9 + - + +
181B LEU* 3.7 23.3 - - + -
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Residues in contact with GLN 178 (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 TYR* 4.4 30.6 - - + +
114B VAL* 5.4 3.8 - - + +
156B ASN 5.0 0.2 - - - +
174B SER 2.7 12.1 + - - -
175B SER* 3.4 7.7 + - - +
176B LEU 3.3 3.9 - - - +
177B LEU* 1.3 79.8 - - - +
179B VAL* 1.3 63.1 + - + +
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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