Contacts of the helix formed by residues 182 - 191 (chain A) in PDB entry 4WB7
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 GLU 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LEU 5.3 0.3 - - - +
181A GLY* 1.3 71.5 - - - -
183A MET* 1.3 64.6 + - - +
184A PHE* 3.2 27.2 + - + +
185A SER* 3.3 17.6 + - - +
186A HIS* 3.2 18.6 - - - -
224A PRO 3.9 6.3 - - - +
225A GLU* 3.7 16.3 - - - +
227A LEU 3.3 6.7 - - - +
228A LEU* 4.0 4.5 - - + -
229A ILE* 4.6 0.2 - - - -
381A ASN 4.6 0.6 + - - -
382A PHE* 4.4 5.5 - - + -
385A TYR* 4.4 2.1 + - - -
501A ATP 2.6 31.1 + - - +
18I ARG* 2.9 41.6 + - - -
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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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181A GLY 3.8 0.8 + - - -
182A GLU* 1.3 71.2 - - - +
184A PHE* 1.3 63.0 - - - +
186A HIS* 3.2 6.3 + - - +
187A LEU* 2.8 23.8 + - + +
193A PHE* 3.9 17.5 - - + -
201A TYR* 3.6 29.2 - - + -
205A ILE* 6.2 0.2 - - + -
224A PRO* 3.7 20.4 - - + +
227A LEU* 2.8 40.4 + - + +
229A ILE* 4.3 19.3 - - + +
235A ILE* 3.6 21.3 - - + -
282A LEU* 4.3 2.2 - - + -
286A MET* 3.7 30.1 - - - +
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Residues in contact with PHE 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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182A GLU* 3.5 15.3 - - - +
183A MET* 1.3 78.7 - - - +
185A SER* 1.3 71.8 + - - +
187A LEU* 3.3 3.4 + - - +
188A ARG* 3.0 60.1 + - + +
224A PRO* 3.2 27.0 + - + +
225A GLU* 3.3 33.4 - - + +
16I THR 3.3 13.0 - - - -
17I GLY* 3.3 28.3 - - - -
18I ARG* 3.4 24.7 - - + -
19I ARG* 3.9 5.8 - - - -
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Residues in contact with SER 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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182A GLU* 3.3 19.5 + - - +
183A MET 3.3 0.4 - - - -
184A PHE* 1.3 89.5 - - - +
186A HIS* 1.3 68.9 + - - +
188A ARG* 3.9 4.1 - - - +
189A ARG* 3.0 29.9 + - - +
381A ASN 3.9 17.4 + - - -
383A ASP* 4.9 16.4 - - - -
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Residues in contact with HIS 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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180A GLY 2.8 27.4 + - - -
181A GLY* 4.6 0.8 - - - -
182A GLU 3.2 25.6 - - - -
183A MET* 3.2 6.2 + - - +
185A SER* 1.3 83.1 + - - +
187A LEU* 1.3 56.6 + - - +
189A ARG* 3.0 37.3 + - - +
190A ILE* 2.9 43.6 + - + +
193A PHE* 4.7 6.5 - - + -
229A ILE* 4.3 8.5 - - + -
369A PHE* 3.3 34.7 - + + -
371A PRO* 5.3 1.6 - - + -
381A ASN* 3.9 19.4 + - + +
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Residues in contact with LEU 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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183A MET* 2.8 18.3 + - + +
184A PHE* 3.7 4.9 - - + +
186A HIS* 1.3 77.6 - - - +
188A ARG* 1.3 70.8 + - - +
190A ILE* 4.8 0.2 - - - -
191A GLY 2.8 49.7 + - - +
192A ARG* 3.8 14.8 - - - -
193A PHE* 3.8 25.1 - - + +
224A PRO* 4.4 17.5 - - + -
285A GLU* 3.9 32.5 - - + +
286A MET* 3.8 26.5 - - + +
289A GLY* 4.7 0.4 - - - -
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Residues in contact with ARG 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 PHE* 3.0 50.9 + - + +
185A SER* 3.9 5.2 - - - +
187A LEU* 1.3 93.0 - - - +
189A ARG* 1.3 64.0 + - - +
191A GLY* 3.6 8.5 + - - -
285A GLU* 2.6 31.3 + - - -
289A GLY 3.8 17.3 + - - -
7I TYR* 4.4 6.8 + - - -
10I PHE* 3.6 28.7 - - - -
11I ILE* 6.2 2.5 - - - -
15I ARG 4.7 2.0 + - - -
16I THR* 3.0 25.6 + - - +
19I ARG* 3.5 16.0 - - - +
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Residues in contact with ARG 189 (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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185A SER* 3.0 22.6 + - - +
186A HIS* 3.0 48.8 + - - +
188A ARG* 1.3 78.6 - - - +
190A ILE* 1.3 76.8 + - - +
191A GLY* 4.5 0.5 - - - -
369A PHE* 4.2 9.3 - - - -
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Residues in contact with ILE 190 (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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186A HIS* 2.9 26.8 + - + +
187A LEU 4.2 1.6 - - - +
189A ARG* 1.3 97.2 - - - +
191A GLY* 1.3 57.5 + - - +
192A ARG 3.4 24.6 + - - +
193A PHE* 4.0 21.5 - - + -
197A HIS* 5.3 4.5 - - + -
369A PHE* 4.9 15.0 - - + -
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Residues in contact with GLY 191 (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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187A LEU* 2.8 20.7 + - - +
188A ARG* 4.1 4.1 + - - -
189A ARG 3.3 2.6 - - - -
190A ILE* 1.3 75.6 - - - +
192A ARG* 1.3 59.2 + - - -
289A GLY* 3.1 24.2 - - - +
7I TYR* 3.7 27.6 - - - -
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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