Contacts of the helix formed by residues 171 - 186 (chain B) in PDB entry 2B4J
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 HIS 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLN* 6.2 1.0 - - - -
166B ARG* 3.9 2.2 - - - -
169B ALA* 3.8 3.8 - - - +
170B GLU* 1.3 101.6 - - + +
172B LEU* 1.3 65.6 + - - +
173B LYS* 4.2 30.7 + - + +
174B THR* 3.1 15.5 + - - +
175B ALA* 3.3 8.7 + - - +
403B GOL 2.9 43.6 + - - -
366D ASP* 2.9 30.3 + - - +
367D ASN* 5.8 1.3 - - + -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.5 42.0 - - + +
69B GLU* 3.8 19.3 - - + +
71B LYS* 3.7 24.7 - - + -
73B ILE* 4.4 4.0 - - + -
88B VAL* 4.1 7.0 - - + -
162B ILE* 3.8 29.6 - - + -
166B ARG* 3.4 20.0 - - - +
171B HIS* 1.3 70.8 - - - +
173B LYS* 1.3 58.8 + - - +
175B ALA* 3.0 2.2 + - + -
176B VAL* 2.7 45.9 + - + +
403B GOL 3.2 14.4 + - - +
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLN* 4.4 23.9 + - - +
96A GLU* 5.6 4.5 + - - -
99A TYR* 3.5 36.9 - - + +
71B LYS* 5.7 1.8 - - - +
88B VAL* 3.6 28.8 - - + +
171B HIS* 3.2 25.8 + - + +
172B LEU* 1.3 79.1 - - - +
174B THR* 1.3 66.6 + - - +
176B VAL* 3.7 3.3 + - - +
177B GLN* 3.5 26.0 + - - +
403B GOL 5.0 9.1 + - - -
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLN* 4.5 6.6 + - - -
99A TYR* 4.7 6.9 - - - -
102A LEU* 3.8 22.0 - - + -
169B ALA* 3.6 16.2 - - + -
171B HIS* 3.1 8.4 + - - +
172B LEU 3.1 0.2 - - - -
173B LYS* 1.3 84.1 - - - +
175B ALA* 1.3 60.5 + - - +
176B VAL 3.1 1.8 - - - -
177B GLN* 3.1 7.2 + - - +
178B MET* 2.9 38.2 + - + +
365D ILE* 4.1 9.0 - - + -
366D ASP* 3.0 28.7 + - + +
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Residues in contact with ALA 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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162B ILE* 4.2 7.3 - - + +
165B VAL* 3.9 14.0 - - + +
166B ARG* 3.8 33.4 - - - +
169B ALA* 4.1 5.8 - - + +
171B HIS 3.3 7.9 + - - +
172B LEU* 3.0 7.5 + - - +
174B THR* 1.3 76.0 - - - +
176B VAL* 1.3 66.7 + - - +
178B MET* 3.5 13.7 - - - +
179B ALA* 2.9 24.3 + - - +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.8 26.0 - - + -
86B ALA* 4.1 37.0 - - + +
87B GLU* 4.3 5.8 - - - +
88B VAL* 3.7 19.7 - - + -
158B LEU* 4.6 2.0 - - + +
162B ILE* 3.9 17.5 - - + -
172B LEU* 2.7 26.3 + - + +
173B LYS 3.8 6.5 - - - +
175B ALA* 1.3 77.6 - - - +
177B GLN* 1.3 60.6 + - - +
179B ALA* 3.1 3.5 + - - +
180B VAL* 2.9 29.0 + - + +
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Residues in contact with GLN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR* 3.7 22.3 + - + -
102A LEU* 4.2 28.2 - - + +
103A LYS* 3.4 30.2 - - + +
106A GLY* 5.5 0.2 - - - -
132A TRP* 5.6 0.2 - - - -
86B ALA 2.9 29.1 + - - +
87B GLU* 3.7 23.0 - - - +
173B LYS 3.5 14.1 + - - +
174B THR 3.1 8.3 + - - +
176B VAL* 1.3 77.3 - - - +
178B MET* 1.3 62.4 + - - +
180B VAL* 3.7 11.5 - - - +
181B PHE* 3.0 23.7 + - - +
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Residues in contact with MET 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 5.0 5.2 - - + -
132A TRP* 3.5 51.3 - - + +
165B VAL* 3.9 12.3 - - + +
168B GLN* 3.7 29.4 - - - +
169B ALA* 4.3 3.8 - - - -
174B THR* 2.9 24.5 + - + +
175B ALA* 3.5 17.5 - - - +
177B GLN* 1.3 77.0 - - - +
179B ALA* 1.3 55.3 + - - +
181B PHE* 3.3 4.7 + - - +
182B ILE* 3.0 33.7 + - - +
365D ILE* 3.3 39.3 - - + -
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Residues in contact with ALA 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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158B LEU* 3.7 12.1 - - + +
161B ILE* 3.5 30.6 - - + +
162B ILE* 3.6 27.1 - - + +
165B VAL* 4.3 0.9 - - + +
175B ALA 2.9 18.3 + - - +
176B VAL 3.5 4.3 - - - +
178B MET* 1.3 76.7 - - - +
180B VAL* 1.3 57.6 + - - +
182B ILE* 4.5 0.4 - - - -
183B HIS* 2.9 30.1 + - - +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS 6.0 0.9 - - - +
106A GLY* 4.6 8.3 - - - +
107A ARG* 6.0 1.3 - - + -
84B ILE* 3.6 19.5 - - + +
85B GLU* 4.4 5.4 - - + -
86B ALA* 3.7 40.6 - - + +
158B LEU* 4.3 7.4 - - + -
176B VAL 2.9 20.5 + - - +
177B GLN* 3.7 12.6 - - - +
179B ALA* 1.3 74.1 - - - +
181B PHE* 1.3 65.5 + - - +
183B HIS* 3.3 5.4 + - - +
184B ASN* 2.9 43.2 + - - +
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Residues in contact with PHE 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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102A LEU* 4.9 3.4 - - + +
105A ALA* 3.5 39.5 - - + -
106A GLY* 3.6 19.0 - - - -
132A TRP* 3.6 30.5 - + + -
133A ALA* 3.5 31.0 - - + -
177B GLN 3.0 14.1 + - - +
178B MET 3.3 9.0 - - - +
180B VAL* 1.3 77.9 - - - +
182B ILE* 1.3 63.8 + - + +
184B ASN* 3.8 0.3 - - - +
185B LYS* 2.9 58.2 + - + +
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Residues in contact with ILE 182 (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 TRP* 4.0 17.9 - - + -
161B ILE* 3.8 19.5 - - + -
164B GLN* 5.5 3.1 - - - +
165B VAL* 3.2 34.8 - - + -
178B MET 3.0 17.5 + - - +
179B ALA 3.8 3.1 - - - +
181B PHE* 1.3 81.5 - - + +
183B HIS* 1.3 67.0 + - - +
185B LYS* 4.0 1.7 - - - -
186B LYS* 3.2 48.6 + - + +
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Residues in contact with HIS 183 (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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82B GLY 2.8 30.5 - - - -
84B ILE* 3.5 28.5 - - + +
154B MET* 3.8 20.3 - - - +
157B GLU* 4.5 17.6 - - + +
158B LEU* 5.7 1.6 - - + -
161B ILE* 3.8 15.7 - - + -
179B ALA 2.9 19.5 + - - +
180B VAL 3.7 3.1 - - - +
182B ILE* 1.3 80.5 - - - +
184B ASN* 1.3 79.9 + - - +
185B LYS 3.4 0.2 + - - -
186B LYS* 3.5 17.8 + - - +
196B ALA* 4.3 9.7 - - + +
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Residues in contact with ASN 184 (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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106A GLY 3.0 27.6 + - - +
83B TYR* 3.3 22.6 - - + -
84B ILE* 2.8 44.2 + - - +
180B VAL* 2.9 27.1 + - - +
181B PHE 4.0 1.3 - - - +
183B HIS* 1.3 84.9 + - - +
185B LYS* 1.3 62.6 + - + +
186B LYS 3.4 0.2 - - - -
195B SER* 3.3 8.8 + - - -
196B ALA* 3.6 2.9 + - - -
197B GLY* 2.9 33.7 + - - +
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Residues in contact with LYS 185 (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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105A ALA 3.1 18.6 + - - -
106A GLY* 4.2 9.0 + - - -
107A ARG 4.5 1.0 - - - -
108A TRP* 2.8 38.2 + - - +
109A PRO* 3.9 6.9 - - - +
181B PHE* 2.9 49.4 + - + +
182B ILE* 4.4 2.2 - - - +
184B ASN* 1.3 81.2 - - - +
186B LYS* 1.3 63.3 + - - +
187B ARG* 3.3 13.0 + - - +
195B SER* 3.4 12.3 - - - +
197B GLY* 5.9 5.3 - - - -
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU* 5.3 4.3 - - - -
161B ILE* 4.6 15.1 - - - +
164B GLN* 5.3 5.9 - - - +
182B ILE* 3.2 39.9 + - + +
183B HIS* 3.8 11.0 - - - +
184B ASN 3.4 1.8 - - - -
185B LYS* 1.3 76.2 - - - +
187B ARG* 1.3 68.3 + - - +
195B SER* 3.4 15.9 - - - -
196B ALA 4.3 2.4 + - - -
199B ARG* 5.6 0.2 + - - -
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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
------------------------------------------------------------
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