Contacts of the helix formed by residues 172 - 188 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A GLY* 5.6 0.2 - - - -
170A GLY 4.2 0.2 - - - -
171A VAL* 1.3 75.1 - - - +
173A GLY* 1.3 68.9 + - - -
174A ARG 3.1 2.7 - - - -
175A GLU* 2.6 15.8 + - - -
176A VAL* 2.9 26.8 + - - +
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Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY* 1.3 70.7 - - - -
174A ARG* 1.3 63.8 + - - +
176A VAL* 3.3 8.3 + - - +
177A GLY* 2.8 23.6 + - - -
196A GLY 4.4 11.3 - - - +
201A PHE* 5.5 1.7 - - - -
207A ARG* 5.4 8.5 - - - -
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PRO* 5.6 5.5 + - - +
138A LYS 5.0 5.5 + - - -
139A SER 4.8 0.4 - - - -
140A GLU* 3.8 38.2 + - - +
143A VAL* 3.7 27.3 - - - +
172A GLY* 3.1 0.8 - - - -
173A GLY* 1.3 77.5 - - - +
175A GLU* 1.3 88.2 + - - +
177A GLY* 3.3 1.6 + - - -
178A PHE* 3.2 46.4 + - + -
289A ARG* 3.3 39.4 - - - +
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 4.4 5.8 - - + -
135A PRO* 6.0 1.0 - - + +
143A VAL* 3.4 21.5 - - + +
147A CYS* 4.2 14.6 - - - -
170A GLY 4.1 16.1 - - - +
171A VAL* 3.6 20.0 - - + -
172A GLY* 2.6 32.0 + - - -
174A ARG* 1.3 111.1 + - - +
176A VAL* 1.3 60.0 + - - +
178A PHE* 3.2 4.8 + - - +
179A MET* 2.9 36.6 + - + +
289A ARG* 4.3 5.2 + - - -
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA* 4.2 3.6 - - - +
167A GLY* 3.9 29.4 - - - +
171A VAL* 4.3 4.0 - - + -
172A GLY 2.9 20.5 + - - +
173A GLY 3.6 4.5 - - - +
175A GLU* 1.3 72.2 - - - +
177A GLY* 1.3 61.6 + - - +
179A MET* 3.7 8.4 - - + +
180A ALA* 2.8 30.3 + - - +
194A PHE* 4.2 16.4 - - + -
195A THR 3.5 22.2 - - - +
196A GLY* 3.5 22.2 - - - +
197A LYS* 4.1 9.9 - - + +
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Residues in contact with GLY 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLY 2.8 15.9 + - - -
174A ARG* 3.7 2.5 - - - -
176A VAL* 1.3 77.9 - - - +
178A PHE* 1.3 59.4 + - - +
180A ALA* 4.0 0.3 - - - +
181A GLY* 2.9 26.9 + - - -
201A PHE* 3.9 25.2 - - - -
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 4.1 24.2 - - + -
143A VAL* 4.3 12.1 - - + -
144A MET* 3.5 58.1 - - + +
147A CYS* 3.8 17.2 - - + -
148A GLN* 5.0 6.8 + - + +
174A ARG* 3.2 41.6 + - + -
175A GLU 3.2 5.3 + - - +
177A GLY* 1.3 78.2 - - - +
179A MET* 1.3 62.2 + - - +
181A GLY* 3.9 1.1 - - - -
182A MET* 3.1 23.4 + - - +
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Residues in contact with MET 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET* 4.3 17.0 - - + -
97A PHE* 4.4 14.4 - - + -
147A CYS* 4.0 15.5 - - + +
150A LEU* 4.3 21.1 - - - -
151A MET* 3.8 31.1 - - + +
154A LEU* 5.6 0.2 - - - -
166A ALA 4.9 0.7 - - - +
171A VAL* 3.8 27.4 - - + -
175A GLU* 2.9 22.7 + - + +
176A VAL* 3.9 6.1 - - + +
178A PHE* 1.3 75.1 - - - +
180A ALA* 1.3 66.4 + - - +
182A MET 3.3 1.6 + - - -
183A MET* 3.0 22.9 + - - +
194A PHE* 3.9 29.2 - - + -
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A VAL 2.8 22.3 + - - +
177A GLY 4.0 2.5 - - - +
179A MET* 1.3 72.5 - - - +
181A GLY* 1.3 61.7 + - - +
183A MET* 3.2 4.1 + - - +
184A LYS* 3.0 26.3 + - - +
194A PHE* 3.7 31.2 - - + +
197A LYS* 4.5 7.0 - - + -
201A PHE* 4.2 21.1 - - + -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLY 2.9 18.2 + - - -
178A PHE 3.9 1.6 - - - -
180A ALA* 1.3 77.6 - - - +
182A MET* 1.3 62.4 + - - +
184A LYS* 3.2 9.2 + - - +
185A LYS* 3.1 21.8 + - - +
201A PHE* 5.8 0.4 - - - -
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Residues in contact with MET 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLN* 4.1 39.7 - - + +
151A MET* 3.8 28.7 - - + -
152A THR* 4.0 17.9 - - - +
178A PHE 3.1 17.3 + - - +
179A MET 3.3 0.8 + - - +
181A GLY* 1.3 77.0 - - - +
183A MET* 1.3 63.3 + - - +
185A LYS* 3.8 10.0 - - - +
186A LEU* 3.0 44.2 + - + +
152B THR* 3.7 26.7 - - + +
182B MET* 5.1 2.5 - - + -
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Residues in contact with MET 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A MET* 3.9 13.2 - - + +
155A TYR* 3.4 46.0 - - + +
158A LEU* 4.1 14.6 - - + +
159A GLY* 4.8 0.9 - - - -
179A MET 3.0 13.5 + - - +
180A ALA* 3.2 9.8 + - - +
182A MET* 1.3 75.4 - - - +
184A LYS* 1.3 57.6 + - - +
186A LEU* 4.1 0.5 - - - +
187A SER* 2.8 54.6 + - - +
189A ASN 5.7 0.9 - - - +
193A VAL* 3.5 46.9 - - + -
194A PHE* 4.1 4.9 - - + -
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ALA 3.0 13.4 + - - +
181A GLY* 3.6 11.7 - - - +
183A MET* 1.3 77.1 - - - +
185A LYS* 1.3 53.9 + - - +
188A ASN* 2.6 38.0 + - - -
189A ASN 3.5 21.7 + - - +
190A THR* 3.6 39.0 + - + +
201A PHE* 5.1 17.1 + - - +
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLY 3.1 16.3 + - - +
182A MET* 3.3 12.8 + - - +
184A LYS* 1.3 77.8 - - - +
186A LEU* 1.3 53.4 + - - +
188A ASN* 3.5 4.0 + - - +
64B ARG* 5.0 10.5 + - - +
65B VAL* 6.2 0.2 - - - +
149B ALA 4.5 4.6 + - - -
152B THR* 3.2 38.4 - - + +
153B GLU* 3.9 33.8 - - - +
156B ARG* 2.5 31.0 + - - -
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A MET 3.9 11.9 - - - +
152A THR* 3.9 6.1 - - - -
155A TYR* 3.8 38.9 - - + -
182A MET* 3.0 34.9 + - + +
183A MET 4.3 0.4 - - - +
185A LYS* 1.3 80.5 - - + +
187A SER* 1.3 59.7 + - - +
152B THR* 3.8 31.6 - - + +
155B TYR* 2.5 28.2 + - + -
156B ARG* 3.2 10.2 + - - +
186B LEU* 3.7 35.0 - - + -
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A TYR* 4.7 9.9 - - - -
183A MET* 2.8 42.9 + - - +
186A LEU* 1.3 77.4 - - - +
188A ASN* 1.3 70.6 + - - +
189A ASN* 3.3 30.0 + - - +
156B ARG* 4.0 1.6 + - - -
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Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LYS* 2.6 19.9 + - - -
185A LYS* 3.5 2.8 + - - +
186A LEU 3.3 2.4 - - - -
187A SER* 1.3 76.2 - - - +
189A ASN* 1.3 57.2 + - - +
190A THR* 5.8 1.1 - - - -
153B GLU* 6.1 0.4 - - - -
156B ARG* 3.2 31.5 - - - +
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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