Contacts of the helix formed by residues 183 - 191 (chain A) in PDB entry 2ZXI
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A GLU* 3.7 6.5 + - - -
127A VAL* 3.4 27.4 - - - +
182A GLU* 1.3 78.8 - - - +
184A LEU* 1.3 63.2 + - - +
186A ASP* 2.9 34.2 + - - +
187A PHE 4.0 0.3 + - - -
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Residues in contact with LEU 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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13A ILE* 4.4 11.4 - - + -
125A GLU* 4.9 0.2 + - - -
126A VAL* 3.9 18.5 + - + +
127A VAL* 3.4 10.7 + - - +
128A ASP* 3.9 21.3 - - - +
129A ILE* 4.0 26.5 - - + -
154A VAL* 4.0 16.8 - - + -
156A THR* 4.0 26.5 - - + -
160A LEU* 3.9 15.3 - - + -
182A GLU 3.2 2.0 + - - +
183A GLY* 1.3 74.3 - - - +
185A SER* 1.3 62.1 + - - +
187A PHE* 3.0 25.4 + - + +
188A TYR* 3.5 19.2 + - + -
618A FAD 4.7 3.4 - - - +
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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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160A LEU* 4.0 11.6 - - - +
161A ASN* 3.1 28.3 + - - -
182A GLU 2.9 17.8 + - - -
183A GLY 2.9 0.6 + - - -
184A LEU* 1.3 77.7 - - - +
186A ASP* 1.3 64.4 + - - +
188A TYR* 3.3 9.4 + - - +
189A ARG* 2.8 50.5 + - - +
195A LEU* 4.1 4.2 - - - +
353A ASP* 3.7 9.2 - - - -
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Residues in contact with ASP 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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127A VAL 5.7 0.2 - - - +
182A GLU 5.0 0.2 - - - +
183A GLY* 2.9 22.7 + - - +
185A SER* 1.3 77.6 + - - +
187A PHE* 1.3 60.7 + - - +
189A ARG* 3.3 21.5 + - - +
190A ARG* 2.9 41.6 + - - +
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Residues in contact with PHE 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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127A VAL 4.9 0.8 + - - +
128A ASP* 3.4 25.6 - - - +
129A ILE* 3.5 43.3 - - + -
131A VAL* 3.9 5.4 - - + -
183A GLY 4.0 1.0 + - - -
184A LEU* 3.0 18.2 + - + +
186A ASP* 1.3 79.4 - - - +
188A TYR* 1.3 104.1 + + - +
190A ARG* 3.4 14.6 + - - +
191A PHE* 3.2 50.0 + + - -
193A PHE* 4.6 1.6 - + - -
369A ILE* 3.8 23.6 - - + -
372A LEU* 4.1 6.1 - - + -
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Residues in contact with TYR 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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129A ILE* 4.2 0.7 - - - +
154A VAL* 3.3 19.9 - - - +
160A LEU* 5.0 2.9 - - + -
184A LEU* 3.5 31.3 + - + -
185A SER* 3.3 8.8 + - - +
187A PHE* 1.3 97.2 - + - +
189A ARG* 1.3 64.0 + - - +
191A PHE 3.4 1.2 + - - -
192A ASP 3.2 3.1 + - - -
193A PHE* 2.8 67.9 + + + +
195A LEU* 4.3 15.0 - - + -
355A VAL* 4.1 6.5 - - + -
372A LEU* 4.1 5.1 - - + +
374A HIS* 2.8 40.0 + + - -
378A PHE* 3.6 22.1 - + - -
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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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161A ASN* 4.2 8.1 - - - +
185A SER* 2.8 55.9 + - - +
186A ASP* 3.3 20.0 + - - +
188A TYR* 1.3 76.1 - - - +
190A ARG* 1.3 56.2 + - - +
192A ASP* 2.7 30.1 + - - +
193A PHE 4.8 5.4 - - - +
195A LEU* 3.8 17.8 - - + +
353A ASP* 4.3 4.6 + - - -
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Residues in contact with ARG 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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128A ASP* 2.6 39.5 + - - -
129A ILE 4.4 3.0 + - - -
186A ASP* 2.9 27.4 + - - +
187A PHE* 3.5 36.7 - - - +
188A TYR 3.2 0.2 - - - -
189A ARG* 1.3 77.7 - - - +
191A PHE* 1.3 70.6 + - + +
192A ASP* 3.3 1.8 + - - +
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Residues in contact with PHE 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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129A ILE 5.1 0.9 - - - -
131A VAL* 3.9 29.2 - - + -
134A ASN* 5.2 7.4 - - - -
187A PHE* 3.2 42.6 + + - +
188A TYR 3.4 0.2 + - - -
189A ARG 3.1 0.8 - - - -
190A ARG* 1.3 95.6 - - + +
192A ASP* 1.3 71.7 + - - +
193A PHE* 3.4 23.0 + - + -
368A LYS* 3.7 16.5 - - + +
369A ILE* 3.8 23.6 - - + -
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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