Contacts of the helix formed by residues 170 - 185 (chain A) in PDB entry 4B92
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 ARG 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A MET* 5.0 11.4 - - + +
169A LEU* 1.3 75.5 - - - +
171A ASP* 1.3 61.7 + - - +
172A SER* 3.3 18.3 + - - +
173A GLU* 2.9 40.0 + - + +
174A LEU* 2.9 26.1 + - - +
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Residues in contact with ASP 171 (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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169A LEU 5.1 0.2 - - - +
170A ARG* 1.3 74.1 - - - +
172A SER* 1.3 63.3 + - - +
174A LEU* 3.5 9.0 + - - +
175A TYR* 3.0 24.8 + - - +
231A ARG* 2.4 47.7 + - - +
235A ILE* 3.9 21.2 - - + +
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Residues in contact with SER 172 (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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170A ARG* 4.1 18.1 + - - +
171A ASP* 1.3 78.5 - - - +
173A GLU* 1.3 72.5 + - - +
175A TYR* 3.7 6.5 - - - +
176A GLN* 3.3 27.9 + - - +
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Residues in contact with GLU 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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136A TRP* 5.2 0.9 - - - +
137A TRP* 3.8 40.8 + - + +
168A MET 4.5 1.9 - - - +
169A LEU* 3.5 25.2 - - + +
170A ARG* 2.9 61.5 + - + +
172A SER* 1.3 88.4 + - - +
174A LEU* 1.3 55.9 + - - +
176A GLN* 3.0 4.2 + - - +
177A VAL* 2.7 39.8 + - - +
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Residues in contact with LEU 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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159A MET* 4.2 18.8 - - + -
160A PHE 5.4 0.4 - - - +
161A MET* 4.0 35.2 - - + -
169A LEU* 4.1 30.2 - - + +
170A ARG 2.9 15.6 + - - +
171A ASP* 3.8 12.3 - - - +
173A GLU* 1.3 76.7 - - - +
175A TYR* 1.3 55.3 + - - +
177A VAL* 3.0 4.2 + - + +
178A LEU* 2.7 46.6 + - + +
190A VAL* 4.9 4.0 - - + -
232A VAL* 4.5 12.8 - - + -
235A ILE* 4.0 26.7 - - + -
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Residues in contact with TYR 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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171A ASP 3.0 18.6 + - - +
172A SER* 3.7 8.1 - - - +
174A LEU* 1.3 75.7 - - - +
176A GLN* 1.3 78.4 + - - +
179A HIS* 3.0 33.3 + + + +
235A ILE* 3.8 21.9 - - + +
238A ARG* 4.3 22.2 + - + +
239A THR* 3.3 30.6 - - + +
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Residues in contact with GLN 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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137A TRP* 3.2 37.6 - - + +
142A LYS* 5.9 0.7 + - - -
172A SER 3.3 15.0 + - - +
173A GLU 3.0 4.4 + - - +
175A TYR* 1.3 94.3 - - - +
177A VAL* 1.3 61.4 + - - +
179A HIS* 3.6 11.0 - - - +
180A ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 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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134A ILE* 3.8 31.0 - - + -
137A TRP* 3.5 29.4 - - + -
145A MET* 4.1 0.8 - - + +
159A MET* 3.8 27.8 - - + -
169A LEU* 3.9 19.5 - - + -
173A GLU 2.7 24.9 + - - +
174A LEU* 3.6 6.5 - - - +
176A GLN* 1.3 70.6 - - - +
178A LEU* 1.3 66.5 + - + +
180A ALA* 3.1 8.8 + - - +
181A CYS* 2.9 23.5 + - - -
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Residues in contact with LEU 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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159A MET* 3.8 15.3 - - + -
174A LEU* 2.7 28.0 + - + +
175A TYR 4.1 1.1 - - - +
177A VAL* 1.3 73.4 - - + +
179A HIS* 1.3 64.7 + - - +
181A CYS* 3.2 2.2 + - - -
182A LYS* 3.0 19.6 + - - +
188A ALA* 3.4 30.7 - - + -
190A VAL* 4.8 2.5 - - + -
232A VAL* 4.4 7.2 - - + +
235A ILE* 3.8 12.1 - - + -
236A ALA* 3.6 38.6 - - + +
239A THR* 3.4 12.6 - - + +
241A CYS* 3.4 19.5 - - + +
243A ILE* 4.0 12.3 - - + -
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Residues in contact with HIS 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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142A LYS* 4.9 10.8 - - - -
175A TYR* 3.0 28.5 + + + +
176A GLN* 3.6 15.0 - - - +
178A LEU* 1.3 76.1 - - - +
180A ALA* 1.3 64.9 + - - +
182A LYS* 3.5 20.9 + - - +
183A ASP* 3.2 28.7 + - - -
239A THR* 4.1 18.2 + - + +
1483A ZN 2.2 36.1 - - - -
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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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137A TRP* 4.0 11.7 - - + -
142A LYS* 4.6 17.3 - - + +
145A MET* 3.8 23.8 - - + -
176A GLN 2.9 14.0 + - - +
177A VAL 3.2 10.5 - - - +
179A HIS* 1.3 81.1 - - - +
181A CYS* 1.3 61.1 + - - +
183A ASP* 3.4 8.4 + - - +
184A ILE* 3.3 25.9 + - + +
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Residues in contact with CYS 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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145A MET* 3.8 16.5 - - - +
157A PHE* 3.9 17.9 - - - -
159A MET* 4.4 11.7 - - - -
177A VAL* 2.9 17.4 + - - -
178A LEU 3.5 8.3 - - - +
180A ALA* 1.3 77.0 - - - +
182A LYS* 1.3 57.8 + - - +
184A ILE* 3.3 9.3 + - - +
185A GLY 2.9 10.2 + - - -
186A ALA* 2.8 38.1 + - + +
188A ALA* 4.2 20.0 - - + -
241A CYS* 3.9 11.9 - - - -
472A TYR* 4.2 0.7 - - - -
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Residues in contact with LYS 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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178A LEU 3.0 15.0 + - - +
179A HIS* 3.8 20.4 - - - +
181A CYS* 1.3 76.2 - - - +
183A ASP* 1.3 82.6 + - - +
185A GLY* 3.4 10.7 + - - -
239A THR 3.1 24.9 - - - +
240A HIS* 3.8 15.0 - - - +
241A CYS* 4.0 15.7 - - - -
242A PRO* 4.8 0.2 - - + -
467A PHE* 4.1 5.9 - - - -
472A TYR* 3.6 23.7 - - + +
479A GLU* 3.1 36.2 + - - +
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Residues in contact with ASP 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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142A LYS* 5.1 6.2 + - - +
179A HIS* 3.1 21.5 + - - +
180A ALA* 3.7 7.1 - - - +
181A CYS 3.2 0.4 - - - -
182A LYS* 1.3 105.3 + - - +
184A ILE* 1.3 61.2 + - + +
467A PHE* 3.9 10.6 - - - -
1483A ZN 2.0 37.1 - - - -
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Residues in contact with ILE 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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145A MET* 3.9 31.9 - - + +
146A GLU* 3.8 28.5 - - + +
149A VAL* 3.4 50.3 - - + +
157A PHE* 4.0 8.3 - - + -
180A ALA* 3.3 17.7 + - + +
181A CYS* 3.4 8.5 - - - +
183A ASP* 1.3 80.2 - - + +
185A GLY* 1.3 59.9 + - - +
186A ALA* 4.2 3.6 - - + -
466A SER* 3.5 6.8 - - - -
467A PHE* 3.9 7.5 - - - -
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Residues in contact with GLY 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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155A ASN 4.6 0.2 - - - +
181A CYS 2.9 4.5 + - - -
182A LYS 3.4 3.8 + - - -
183A ASP 3.4 0.6 - - - -
184A ILE* 1.3 79.1 - - - +
186A ALA* 1.3 61.1 + - - +
466A SER* 3.7 4.2 - - - -
467A PHE* 2.7 53.7 + - - -
468A PRO* 3.4 10.9 - - - +
472A TYR* 3.5 8.5 - - - -
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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