Contacts of the helix formed by residues 167 - 181 (chain B) in PDB entry 3ZQI
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 PRO 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A TYR* 3.7 30.3 - - + +
111A GLU* 4.8 2.5 - - - +
114A GLU* 3.5 37.0 - - + +
165B SER 3.8 4.3 - - - +
166B MET* 1.4 95.1 - - + +
168B PRO* 1.3 71.5 - - + +
169B LEU 3.5 1.6 - - - -
170B LEU* 3.4 5.2 + - + -
171B ARG* 2.9 24.8 + - - +
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Residues in contact with PRO 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 3.6 8.1 - - - +
166B MET 3.9 1.3 - - - +
167B PRO* 1.3 87.6 - - + +
169B LEU* 1.4 64.3 + - + +
171B ARG* 3.5 25.7 + - - +
172B GLN* 3.0 43.0 + - - +
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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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114A GLU* 2.8 28.3 + - + +
117A LEU* 3.6 18.1 - - + +
118A ALA* 3.7 38.6 - - + +
121A THR* 4.5 9.0 - - + +
127A LEU* 4.1 14.8 - - + +
168B PRO* 1.4 75.1 - - + +
170B LEU* 1.3 56.3 + - - +
172B GLN* 3.4 24.5 + - - +
173B ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 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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110A TYR* 3.8 49.4 - - + +
113A LEU* 3.9 19.3 - - + -
114A GLU* 2.7 22.8 + - - +
117A LEU* 3.8 8.0 - - + +
166B MET* 3.9 12.8 - - + -
167B PRO* 3.7 6.5 - - + +
169B LEU* 1.3 72.1 - - - +
171B ARG* 1.4 66.5 + - - +
173B ALA* 3.2 1.0 + - - +
174B ILE* 3.0 31.4 + - + +
13C MET* 3.8 13.0 - - + -
14C TRP* 3.6 29.8 - - + -
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Residues in contact with ARG 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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166B MET* 3.7 25.4 + - + +
167B PRO 2.9 16.7 + - - +
168B PRO* 3.8 28.2 + - - +
170B LEU* 1.4 76.9 - - - +
172B GLN* 1.3 80.8 + - - +
174B ILE* 3.6 1.5 - - - +
175B GLU* 3.0 52.3 + - - +
8C ARG* 3.4 39.0 - - - +
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Residues in contact with GLN 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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127A LEU* 3.2 28.7 - - + +
168B PRO* 3.0 38.4 + - - +
169B LEU* 3.7 15.6 - - - +
171B ARG* 1.3 90.0 - - - +
173B ALA* 1.3 57.8 + - - +
175B GLU* 3.5 7.6 + - - +
176B LEU* 2.9 30.7 + - - +
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Residues in contact with ALA 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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117A LEU* 4.0 18.8 - - + -
127A LEU* 4.1 13.9 - - + +
131A LEU* 3.6 16.3 - - + +
169B LEU 2.9 17.8 + - - +
170B LEU 3.6 4.3 - - - +
172B GLN* 1.3 77.8 - - - +
174B ILE* 1.3 58.9 + - - +
176B LEU* 3.2 6.6 + - - +
177B PHE* 2.9 28.9 + - - +
14C TRP* 4.0 15.3 - - + -
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Residues in contact with ILE 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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104A ARG* 4.2 4.0 - - - +
166B MET* 3.6 28.3 - - + -
170B LEU* 3.0 30.0 + - + +
171B ARG* 3.6 7.4 - - - +
173B ALA* 1.3 74.7 - - - +
175B GLU* 1.3 67.0 + - + +
177B PHE* 3.8 4.4 - - - +
178B ASP* 3.0 24.1 + - - +
8C ARG* 3.8 29.6 - - + +
11C MET* 4.1 12.6 - - + +
12C TRP 3.5 23.7 - - - +
13C MET* 3.8 27.4 - - + -
14C TRP* 4.1 8.5 - - + -
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Residues in contact with GLU 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 ARG* 3.0 40.7 + - + +
172B GLN* 3.9 5.1 - - - +
174B ILE* 1.3 80.0 - - + +
176B LEU* 1.4 55.8 + - - +
178B ASP* 3.4 2.1 + - - +
179B HIS* 3.0 29.5 + - - +
4C VAL* 5.4 0.3 - - - +
8C ARG* 3.1 35.7 + - - +
11C MET* 3.8 27.8 - - + +
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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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127A LEU* 5.0 9.0 - - + -
128A GLU* 3.6 41.7 - - + +
131A LEU* 4.2 10.3 - - + -
172B GLN 2.9 21.6 + - - +
173B ALA* 3.6 4.3 - - - +
175B GLU* 1.4 68.9 - - - +
177B PHE* 1.3 68.6 + - - +
179B HIS* 3.2 8.6 + - + +
180B GLN* 2.9 59.4 + - + +
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Residues in contact with PHE 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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131A LEU* 3.9 22.8 - - + +
132A TYR* 4.1 16.2 - + - -
135A SER* 3.8 10.3 - - - -
139A HIS* 5.0 5.8 - + - -
173B ALA 2.9 20.4 + - - +
174B ILE* 3.8 7.4 - - - +
176B LEU* 1.3 73.0 - - - +
178B ASP* 1.3 60.9 + - - +
180B GLN* 3.8 0.5 - - - +
181B GLY* 2.8 27.9 + - - +
182B ALA* 3.9 29.2 - - + -
185B ALA* 3.5 30.1 - - + -
12C TRP* 3.6 57.2 - + + +
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Residues in contact with ASP 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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174B ILE 3.0 17.3 + - - +
175B GLU 3.7 3.8 - - - +
177B PHE* 1.3 83.0 - - - +
179B HIS* 1.3 65.5 + - - +
181B GLY* 3.5 8.8 + - - -
11C MET* 3.7 44.6 - - + +
12C TRP 4.9 3.1 + - - +
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Residues in contact with HIS 179 (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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175B GLU 3.0 18.1 + - - +
176B LEU* 3.7 10.5 - - + +
178B ASP* 1.3 81.0 - - - +
180B GLN* 1.3 74.3 + - + +
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Residues in contact with GLN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 2.9 28.0 + - - +
132A TYR* 2.8 30.5 + - - +
176B LEU* 2.9 37.4 + - + +
177B PHE 4.4 0.2 - - - +
179B HIS* 1.3 87.4 - - + +
181B GLY* 1.3 60.4 + - - +
184B PRO* 3.2 30.2 - - + +
188B HIS* 5.6 0.7 + - - -
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Residues in contact with GLY 181 (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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132A TYR* 4.8 2.1 + - - -
177B PHE* 2.8 20.8 + - - +
178B ASP* 4.0 6.7 - - - -
179B HIS 3.4 2.0 - - - -
180B GLN* 1.3 78.9 - - - +
182B ALA* 1.3 67.9 + - - -
183B GLU 3.2 2.2 - - - -
184B PRO* 3.2 12.9 - - - +
185B ALA* 3.3 12.5 + - - +
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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