Contacts of the helix formed by residues 185 - 193 (chain A) in PDB entry 1ZEB
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 ASP 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A TRP* 3.4 8.5 - - - +
170A SER* 3.2 28.1 - - - +
171A ASP* 3.3 17.2 + - - +
174A VAL* 4.0 12.0 - - + +
183A CYS 3.8 2.4 + - - -
184A GLN* 1.3 75.5 - - - +
186A ILE* 1.3 64.8 + - - +
187A ALA 3.4 4.3 + - - -
188A THR* 2.8 33.5 + - - -
189A GLN* 3.1 15.9 + - - +
227A ARG* 2.9 30.7 + - - -
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Residues in contact with ILE 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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110A ILE* 4.3 8.7 - - + -
152A GLN* 3.5 33.7 - - + +
157A ALA* 4.1 5.4 - - + -
160A TYR* 3.5 27.4 - - + +
161A ALA* 4.6 5.6 - - + -
163A THR* 4.1 30.7 - - + +
165A ASN 4.4 0.7 - - - +
166A ARG* 3.5 28.3 - - - +
168A TRP 2.8 23.3 + - - +
169A TYR* 4.2 1.6 - - - +
184A GLN 5.2 0.2 - - - +
185A ASP* 1.3 72.3 - - - +
187A ALA* 1.3 52.6 + - - +
189A GLN* 3.1 8.5 + - - +
190A LEU* 2.7 32.7 + - - +
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Residues in contact with ALA 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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152A GLN* 3.9 12.1 - - + +
169A TYR 3.0 20.2 + - - +
185A ASP* 3.3 5.8 - - - +
186A ILE* 1.3 76.4 - - - +
188A THR* 1.3 62.5 + - - +
190A LEU* 3.2 18.2 + - - +
191A ILE* 3.5 9.0 + - - +
206A TYR* 3.7 28.0 - - + +
207A MET* 3.8 12.6 - - - +
233A LEU* 3.6 14.4 - - + +
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Residues in contact with THR 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 GLN* 3.5 29.2 - - + +
185A ASP* 2.8 35.4 + - - -
187A ALA* 1.3 76.8 - - - +
189A GLN* 1.3 57.6 + - - +
191A ILE* 3.1 5.8 + - + +
192A SER* 2.9 42.1 + - - +
227A ARG* 3.1 14.2 + - - -
231A LYS* 5.2 11.6 - - - +
233A LEU* 3.6 15.4 - - + +
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Residues in contact with GLN 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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160A TYR* 3.9 4.7 - - - +
161A ALA* 3.2 12.2 - - + +
162A HIS* 2.9 44.6 + - - +
163A THR* 4.0 5.4 - - - -
184A GLN* 2.8 35.6 + - + +
185A ASP 3.1 13.8 + - - +
186A ILE* 3.1 11.3 + - - +
188A THR* 1.3 74.1 - - - +
190A LEU* 1.3 62.5 + - - +
192A SER* 4.7 0.7 - - - -
193A ASN* 2.8 67.2 + - - +
194A MET 4.5 0.3 + - - -
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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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145A VAL* 6.0 1.3 - - + -
151A VAL* 3.6 27.8 - - + +
152A GLN* 4.3 4.7 - - + +
160A TYR* 3.4 37.0 - - + +
186A ILE 2.7 16.6 + - - +
187A ALA* 3.2 9.2 - - - +
189A GLN* 1.3 75.4 - - - +
191A ILE* 1.3 59.6 + - + +
194A MET 4.1 5.5 - - - +
196A ILE* 3.7 19.8 - - + +
199A ILE* 3.9 36.2 - - + +
207A MET* 4.1 28.5 - - + -
237A TRP* 5.1 1.2 + - - -
266A MET* 4.5 4.3 - - + -
268A LEU* 5.6 0.2 - - + -
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Residues in contact with ILE 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 ALA 3.9 6.3 - - - +
188A THR* 3.1 15.8 + - + +
190A LEU* 1.3 77.9 - - + +
192A SER* 1.3 64.1 + - - +
193A ASN 3.9 0.2 - - - -
194A MET 4.6 1.8 - - - -
207A MET* 3.8 28.9 - - + -
233A LEU* 3.5 38.1 - - + +
236A GLU* 3.7 18.6 - - + +
237A TRP* 3.7 34.5 - - + +
240A LYS* 2.8 39.9 + - - +
241A ARG* 3.3 11.3 + - - +
266A MET* 4.2 3.8 - - + -
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Residues in contact with SER 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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184A GLN* 4.6 7.8 + - - -
188A THR* 2.9 31.1 + - - +
191A ILE* 1.3 88.4 - - - +
193A ASN* 1.3 71.7 + - - +
194A MET* 3.3 3.4 + - - -
240A LYS* 3.9 9.6 + - - +
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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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134A ASN* 4.9 3.5 - - - +
160A TYR* 2.8 25.7 - - + +
161A ALA* 3.7 0.2 - - - -
162A HIS* 4.0 10.1 + - + -
184A GLN* 3.9 16.8 - - - +
189A GLN* 2.8 57.2 + - - +
192A SER* 1.3 79.4 - - - +
194A MET* 1.3 65.4 + - + +
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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