Contacts of the helix formed by residues 172 - 188 (chain B) in PDB entry 4BHT
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 GLY 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLY 4.1 0.6 - - - -
171B VAL* 1.3 75.6 - - - +
173B GLY* 1.3 65.9 + - - -
174B ARG 3.2 3.4 - - - -
175B GLU* 2.7 14.6 + - - -
176B VAL* 3.1 25.2 + - - +
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Residues in contact with GLY 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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172B GLY* 1.3 71.3 - - - -
174B ARG* 1.3 62.2 + - - +
176B VAL* 3.8 2.3 - - - +
177B GLY* 2.9 21.7 + - - -
196B GLY 4.4 16.1 - - - +
201B PHE* 5.5 1.7 - - - -
207B ARG* 5.6 5.8 - - - -
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Residues in contact with ARG 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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135B PRO* 6.1 0.8 - - - +
138B LYS 5.3 3.0 + - - -
139B SER 5.1 0.8 - - - -
140B GLU* 3.9 38.9 + - - +
143B VAL* 3.5 24.9 - - - +
172B GLY 3.2 0.6 - - - -
173B GLY* 1.3 77.4 - - - +
175B GLU* 1.3 81.9 + - - +
177B GLY* 3.3 2.1 + - - -
178B PHE* 3.1 57.8 + - + -
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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
----------------------------------------------------------
97B PHE* 4.4 5.4 - - + -
135B PRO* 5.8 2.1 - - - +
143B VAL* 3.4 19.1 - - + +
147B CYS* 4.0 15.7 - - - -
170B GLY 3.9 18.8 - - - +
171B VAL* 3.6 20.2 - - + -
172B GLY* 2.7 31.4 + - - +
174B ARG* 1.3 108.2 + - - +
176B VAL* 1.3 61.6 + - - +
178B PHE* 3.3 3.4 + - - +
179B MET* 3.0 36.4 + - + +
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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
----------------------------------------------------------
166B ALA* 4.2 3.8 - - - -
167B GLY* 3.9 26.0 - - - +
171B VAL* 4.0 10.5 - - + -
172B GLY 3.1 17.3 + - - +
173B GLY 3.8 4.0 - - - +
175B GLU* 1.3 71.6 - - - +
177B GLY* 1.3 61.4 + - - +
179B MET* 3.2 8.5 + - + +
180B ALA* 2.8 34.1 + - - +
194B PHE* 4.1 15.7 - - + -
195B THR 3.5 22.7 - - - +
196B GLY* 3.6 20.9 - - - +
197B LYS* 4.1 8.7 - - + +
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLY 2.9 14.3 + - - -
174B ARG 3.6 4.5 - - - -
176B VAL* 1.3 79.2 - - - +
178B PHE* 1.3 57.8 + - - +
180B ALA* 3.9 1.0 - - - +
181B GLY* 3.0 25.1 + - - -
201B PHE* 3.8 27.0 - - - -
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Residues in contact with PHE 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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140B GLU* 3.9 21.8 - - + -
143B VAL* 4.3 2.0 - - + -
144B MET* 3.4 59.9 - - + +
147B CYS* 3.7 25.5 - - + +
148B GLN* 4.7 8.3 + - + +
174B ARG* 3.1 48.7 + - + -
175B GLU 3.7 3.1 - - - +
176B VAL 3.2 0.4 - - - -
177B GLY* 1.3 74.5 - - - +
179B MET* 1.3 62.5 + - - +
181B GLY* 4.0 0.8 - - - -
182B MET* 3.1 27.2 + - - +
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Residues in contact with MET 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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95B MET* 4.4 15.7 - - + -
97B PHE* 4.2 14.4 - - + -
147B CYS* 4.0 16.2 - - + +
150B LEU* 4.2 21.1 - - - -
151B MET* 3.6 27.4 - - + +
154B LEU* 5.6 0.2 - - - -
166B ALA 4.9 0.7 - - - +
171B VAL* 3.7 27.1 - - + -
175B GLU* 3.0 23.8 + - + +
176B VAL* 3.9 6.1 - - + +
178B PHE* 1.3 75.3 - - - +
180B ALA* 1.3 61.4 + - - +
182B MET 3.3 0.9 + - - -
183B MET* 2.8 28.9 + - - +
194B PHE* 3.7 33.4 - - + -
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Residues in contact with ALA 180 (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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176B VAL 2.8 22.9 + - - +
177B GLY 3.9 2.9 - - - +
179B MET* 1.3 70.0 - - - +
181B GLY* 1.3 56.7 + - - +
183B MET* 3.2 3.0 + - - +
184B LYS* 2.8 36.9 + - - +
194B PHE* 3.7 29.0 - - + +
197B LYS* 4.7 7.4 - - + -
201B PHE* 4.3 17.9 - - + -
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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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177B GLY 3.0 18.1 + - - -
178B PHE* 4.0 1.1 - - - -
180B ALA* 1.3 77.3 - - - +
182B MET* 1.3 56.8 + - - +
184B LYS* 3.3 9.1 + - - +
185B LYS* 2.9 29.3 + - - +
201B PHE* 5.7 0.6 - - - -
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Residues in contact with MET 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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152A THR* 3.7 25.6 - - + +
182A MET* 5.1 2.5 - - + -
148B GLN* 4.1 37.2 - - + +
151B MET* 3.8 26.9 - - + -
152B THR* 3.9 19.3 - - - +
178B PHE 3.1 17.8 + - - +
179B MET 3.3 0.6 + - - +
181B GLY* 1.3 72.3 - - - +
183B MET* 1.3 66.1 + - - +
185B LYS* 3.7 10.7 - - - +
186B LEU* 3.0 51.3 + - + +
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Residues in contact with MET 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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151B MET* 3.7 14.0 - - + +
155B TYR* 3.3 48.2 - - + +
158B LEU* 4.0 15.3 - - + +
159B GLY* 4.6 1.3 - - - +
179B MET 2.8 14.5 + - - +
180B ALA* 3.3 9.9 - - - +
182B MET* 1.3 77.2 - - - +
184B LYS* 1.3 62.7 + - - +
186B LEU* 4.0 0.9 - - - +
187B SER* 3.0 48.4 + - - +
189B ASN 5.8 0.4 - - - +
193B VAL* 3.6 44.0 - - + -
194B PHE* 4.0 4.9 - - + -
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Residues in contact with LYS 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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180B ALA 2.8 20.9 + - - +
181B GLY* 3.6 7.6 - - - +
183B MET* 1.3 75.4 - - - +
185B LYS* 1.3 64.0 + - - +
188B ASN* 2.9 23.8 + - - -
189B ASN 3.5 20.5 + - - +
190B THR* 3.8 38.8 + - + +
201B PHE* 5.1 18.3 + - - +
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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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64A ARG 5.0 8.2 + - - -
65A VAL* 6.3 0.4 - - - +
149A ALA 4.5 4.8 + - - -
152A THR* 3.2 37.4 - - + +
153A GLU* 3.9 32.0 - - - +
156A ARG* 2.9 20.1 + - - -
181B GLY 2.9 18.0 + - - +
182B MET* 3.2 13.9 + - - +
184B LYS* 1.3 80.3 - - - +
186B LEU* 1.3 59.9 + - - +
188B ASN* 3.4 5.7 + - - -
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Residues in contact with LEU 186 (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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152A THR* 4.0 16.8 - - + +
155A TYR* 2.6 26.6 + - + +
156A ARG* 3.0 15.0 + - - +
186A LEU* 3.7 31.4 - - + -
151B MET 3.6 23.6 - - - +
152B THR* 3.9 13.0 - - - -
155B TYR* 3.7 29.8 - - + -
182B MET* 3.0 46.1 + - + +
183B MET 4.1 0.9 - - - +
185B LYS* 1.3 78.0 - - - +
187B SER* 1.3 57.2 + - - +
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Residues in contact with SER 187 (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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156A ARG* 4.1 1.2 + - - -
155B TYR* 4.7 9.0 - - - -
183B MET* 3.0 37.6 + - - +
186B LEU* 1.3 76.5 - - - +
188B ASN* 1.3 70.1 + - - +
189B ASN* 3.2 30.1 + - - +
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Residues in contact with ASN 188 (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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153A GLU* 6.1 0.2 - - - -
156A ARG* 3.4 33.2 - - - +
184B LYS* 2.9 12.2 + - - -
185B LYS 3.4 3.7 + - - +
186B LEU 3.3 2.2 - - - -
187B SER* 1.3 80.1 - - - +
189B ASN* 1.3 58.7 + - - +
190B THR* 5.7 1.1 - - - -
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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