Contacts of the helix formed by residues 208 - 217 (chain A) in PDB entry 4Z07
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PRO* 4.8 5.0 - - - +
133A CYS 5.6 0.5 + - - +
135A TYR* 4.6 7.9 - - + -
154A LEU* 3.5 17.9 - - + +
206A ALA 4.3 0.2 - - - -
207A ILE* 1.3 79.4 - - - +
209A ARG* 1.3 58.8 + - - +
210A GLN* 2.9 20.7 + - - +
211A CYS* 2.9 46.0 + - - +
212A PHE* 3.0 25.2 + - - +
135E TYR* 4.3 8.2 + - - +
153E SER* 5.0 0.7 - - - +
154E LEU* 3.9 35.4 - - + +
208E ASP* 4.3 1.6 - - - +
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Residues in contact with ARG 209 (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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151A VAL* 4.4 7.3 - - - +
152A GLY* 2.6 42.5 + - - +
153A SER* 3.2 20.5 + - - +
154A LEU* 4.6 0.2 - - - +
185A ALA 3.7 17.2 + - - -
186A ILE* 3.9 31.6 + - + +
189A ASN* 3.1 31.0 + - - +
190A CYS 5.4 1.4 + - - -
208A ASP* 1.3 72.4 - - - +
210A GLN* 1.3 65.6 + - - +
212A PHE* 4.3 5.4 - - - -
213A GLN* 3.0 31.2 + - + +
151E VAL* 6.3 3.4 - - - -
153E SER* 4.3 14.3 + - - +
208E ASP* 5.3 0.4 + - - -
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Residues in contact with GLN 210 (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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96A LEU* 5.2 1.1 - - - -
208A ASP* 2.9 9.4 + - - +
209A ARG* 1.3 79.2 - - - +
211A CYS* 1.3 58.8 + - - +
213A GLN* 3.9 5.6 - - - +
214A THR* 3.0 28.3 + - - -
145E ILE 5.0 7.1 + - - -
146E ILE* 6.0 1.4 - - - +
151E VAL 4.0 14.1 - - - +
152E GLY* 3.4 3.1 - - - -
153E SER* 2.8 39.7 + - - +
154E LEU* 3.3 14.9 + - - +
156E TYR* 3.6 20.4 + - - -
192E ARG* 2.9 21.7 + - - +
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Residues in contact with CYS 211 (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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96A LEU* 3.9 17.3 - - + -
97A PRO* 3.6 33.2 - - - -
133A CYS* 3.8 28.3 - - - -
207A ILE* 3.8 4.0 - - + -
208A ASP* 2.9 35.6 + - - +
210A GLN* 1.3 76.6 - - - +
212A PHE* 1.3 60.8 + - - +
214A THR* 3.2 1.9 + - - -
215A ILE* 2.8 35.9 + - + +
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Residues in contact with PHE 212 (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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119A MET* 3.5 28.9 - - + -
130A ILE* 4.4 4.5 - - + -
155A VAL* 4.0 23.8 - - + -
183A GLU* 5.5 0.4 - - + -
186A ILE* 3.6 28.0 - - + -
187A LEU* 3.8 30.1 - - + -
207A ILE* 4.0 23.1 - - + +
208A ASP 3.0 17.0 + - - +
209A ARG* 4.0 8.3 - - - +
211A CYS* 1.3 76.8 - - - +
213A GLN* 1.3 59.4 + - - +
215A ILE* 3.3 4.0 + - - +
216A MET* 2.9 70.8 + - + +
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Residues in contact with GLN 213 (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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209A ARG* 3.0 22.2 + - + +
210A GLN* 3.9 5.3 - - - +
212A PHE* 1.3 74.2 - - - +
214A THR* 1.3 79.0 + - - +
216A MET* 3.5 14.3 + - - +
217A MET* 3.6 17.8 + - - +
188C TYR 2.9 28.8 + - - +
189C ASN* 3.4 25.5 + - + +
190C CYS* 4.2 9.9 - - - +
150E ASP* 5.6 4.5 - - - +
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Residues in contact with THR 214 (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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94A VAL* 4.3 14.5 - - + +
96A LEU* 3.9 19.3 - - + +
210A GLN 3.0 13.7 + - - -
211A CYS 3.2 8.4 + - - -
213A GLN* 1.3 89.5 + - - +
215A ILE* 1.3 63.7 + - - +
217A MET* 3.2 14.3 + - - +
218A ARG* 3.4 47.8 + - + +
150E ASP* 5.7 1.0 + - - -
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Residues in contact with ILE 215 (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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96A LEU* 3.6 19.5 - - + -
126A GLN* 3.0 47.7 + - + +
129A GLU* 3.6 22.0 - - + +
130A ILE* 3.6 39.7 - - + +
133A CYS* 3.9 14.4 - - - -
207A ILE* 4.0 2.9 - - + -
211A CYS 2.8 23.7 + - - +
212A PHE* 3.9 4.3 - - - +
214A THR* 1.3 73.1 - - - +
216A MET* 1.3 63.9 + - + +
217A MET 3.0 0.2 - - - -
218A ARG* 2.9 25.5 + - - +
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Residues in contact with MET 216 (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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122A LEU* 3.7 38.8 - - + -
126A GLN* 3.5 11.4 + - - +
130A ILE* 4.4 2.2 - - + -
187A LEU* 4.5 9.4 - - + -
212A PHE* 2.9 68.2 + - + +
213A GLN* 3.8 9.4 - - - +
214A THR 3.3 0.4 - - - -
215A ILE* 1.3 91.0 - - + +
217A MET* 1.3 58.1 + - - +
219A THR* 3.8 4.2 - - - +
188C TYR* 3.3 25.2 - - + -
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Residues in contact with MET 217 (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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213A GLN* 3.6 14.5 + - - +
214A THR* 3.2 10.6 + - - +
215A ILE 3.0 0.6 - - - -
216A MET* 1.3 76.8 - - - +
218A ARG* 1.3 60.9 + - - +
219A THR* 3.1 8.7 + - - -
222A ILE* 3.3 44.4 - - + +
184C LEU* 5.5 2.5 - - + -
188C TYR* 3.8 35.4 - - + -
190C CYS* 3.7 31.6 - - - -
193C THR* 4.4 14.4 - - + -
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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