Contacts of the helix formed by residues 185 - 193 (chain A) in PDB entry 1ZG3
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 MET 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO 2.9 29.6 - - - +
117A THR* 4.3 4.3 - - - +
118A CYS 3.7 20.2 - - - +
119A LEU* 3.7 25.1 - - + -
122A ILE* 5.4 0.4 - - + -
181A SER* 3.1 26.7 - - - +
182A ASP* 3.2 17.3 - - - +
184A ARG* 1.3 86.7 - - - +
186A PHE* 1.3 63.9 + - - +
187A LYS 3.1 0.7 - - - -
188A LEU* 3.0 34.6 + - + +
189A VAL* 3.2 13.5 + - - +
354A SER* 4.8 11.6 + - - +
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Residues in contact with PHE 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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182A ASP 3.8 2.1 + - - +
183A SER* 3.1 20.1 + - - +
184A ARG 3.0 1.4 - - - -
185A MET* 1.3 79.4 - - - +
187A LYS* 1.3 60.9 + - - +
189A VAL* 3.0 36.4 + - + +
190A LEU* 3.0 46.8 + - + +
197A PHE* 4.9 3.1 - + - -
213A VAL* 3.8 25.8 - - + -
216A LEU* 4.4 10.5 - - + -
217A ILE* 4.3 4.9 - - + -
262A LEU* 4.8 6.5 - - + -
264A LYS* 3.6 27.8 - - + -
265A TRP* 5.6 2.9 - + + -
298A ILE* 3.1 39.3 - - + -
353A ILE* 5.9 0.2 - - + -
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Residues in contact with LYS 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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116A PRO* 6.4 2.7 - - + -
183A SER 4.4 0.4 + - - -
184A ARG* 3.0 16.4 + - + +
186A PHE* 1.3 80.0 - - - +
188A LEU* 1.3 62.4 + - + +
190A LEU* 3.1 12.9 + - - +
191A GLN* 3.0 53.6 + - - +
216A LEU* 4.5 14.2 - - + +
219A GLU* 3.0 30.1 + - - +
220A ILE* 4.0 19.5 - - + -
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Residues in contact with LEU 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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116A PRO* 4.4 12.6 - - + +
117A THR* 3.7 31.6 - - + -
184A ARG 5.4 0.7 - - - +
185A MET* 3.0 35.0 + - + +
187A LYS* 1.3 80.8 - - + +
189A VAL* 1.3 57.7 + - + +
191A GLN* 3.4 22.3 + - + +
192A GLU* 2.9 42.2 + - - +
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Residues in contact with VAL 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 MET 3.2 9.6 + - - +
186A PHE* 3.0 34.9 + - + +
188A LEU* 1.3 78.4 - - + +
190A LEU* 1.3 62.6 + - + +
192A GLU* 3.4 2.1 + - - -
193A ASN* 2.9 34.9 + - + +
197A PHE* 6.0 0.4 - - + -
353A ILE* 4.1 36.8 - - + -
354A SER* 3.5 26.5 - - - +
359A LEU* 4.3 14.1 - - + -
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Residues in contact with LEU 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 PHE* 3.0 46.7 + - + +
187A LYS* 3.1 6.9 + - - +
189A VAL* 1.3 75.0 - - + +
191A GLN* 1.3 66.7 + - - +
193A ASN 3.1 11.3 + - - -
194A LYS* 3.2 17.3 + - - +
197A PHE* 3.6 40.6 - - + -
216A LEU* 3.8 13.7 - - + +
217A ILE* 3.8 33.7 - - + +
220A ILE* 4.1 19.7 - - + -
221A PHE* 4.5 8.8 - - + -
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Residues in contact with GLN 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 LYS* 3.0 57.4 + - - +
188A LEU* 3.8 21.5 - - + +
190A LEU* 1.3 77.5 - - - +
192A GLU* 1.3 62.3 + - - +
193A ASN 3.6 0.5 + - - -
194A LYS* 3.7 31.9 + - - +
220A ILE* 4.1 15.5 - - + +
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Residues in contact with GLU 192 (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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188A LEU* 2.9 28.1 + - - +
189A VAL* 3.8 1.6 - - - +
190A LEU 3.1 0.2 - - - -
191A GLN* 1.3 81.1 - - - +
193A ASN* 1.3 73.7 + - - +
194A LYS 3.8 0.7 - - - -
195A ARG* 5.9 0.5 + - - -
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Residues in contact with ASN 193 (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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189A VAL* 2.9 27.0 + - - +
190A LEU 3.1 4.7 + - - -
192A GLU* 1.3 92.1 + - - +
194A LYS* 1.3 64.7 + - - +
195A ARG* 3.1 11.7 - - + +
196A VAL* 3.0 35.5 + - + +
197A PHE* 3.8 7.4 - - + -
351A THR* 3.3 32.7 + - - +
352A PRO 5.4 0.2 + - - -
353A ILE* 4.2 16.1 - - - +
359A LEU* 5.0 7.1 - - + +
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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