Contacts of the strand formed by residues 206 - 213 (chain B) in PDB entry 4ZDH
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 HIS 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B TRP 3.6 0.9 + - - +
160B VAL* 3.3 7.3 - - - +
161B ASN* 2.8 47.2 + - - +
162B GLY 4.9 5.9 + - - -
205B ASN* 1.3 73.7 - - - +
207B PHE* 1.3 66.8 + - - +
208B ARG* 3.4 43.1 + - + +
237B GLU* 2.9 32.6 + - + +
238B ALA 3.9 6.1 - - - -
239B TRP* 3.3 49.9 + + + -
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Residues in contact with PHE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.7 4.4 - - - +
142B LEU* 3.8 22.2 - - + -
158B TRP* 4.6 6.5 - - + -
159B TRP 3.6 3.4 - - - -
160B VAL* 4.1 8.3 - - + -
193B LEU* 3.8 20.6 - - + -
195B VAL* 4.0 17.3 - - + -
199B PHE* 3.5 45.1 - + - -
200B TRP* 3.8 33.7 - + - -
205B ASN* 3.6 24.7 - - + -
206B HIS* 1.3 75.1 - - - +
208B ARG* 1.3 59.5 + - - +
237B GLU* 3.3 5.3 - - - -
238B ALA 3.0 40.0 + - - +
240B GLY* 4.1 4.0 - - - -
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B TRP* 3.3 10.2 - - - -
159B TRP* 2.7 77.2 + - + +
162B GLY* 4.5 13.1 + - - -
206B HIS* 3.4 33.8 + - + +
207B PHE* 1.3 74.1 - - - +
209B CYS* 1.3 69.3 + - - +
210B GLN* 3.5 21.7 + - - +
235B SER* 4.3 13.5 - - - -
236B ALA 3.6 11.0 - - - +
237B GLU* 4.5 7.1 + - + -
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Residues in contact with CYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 4.4 1.0 - - + +
126B LEU* 3.8 17.5 - - + +
144B CYS* 2.0 54.3 - - + -
156B LEU* 3.9 21.8 - - - -
157B SER 3.6 3.6 - - - -
158B TRP* 4.1 6.3 - - + -
208B ARG* 1.3 73.2 - - - +
210B GLN* 1.3 62.1 + - - +
211B VAL* 4.4 5.2 - - - -
235B SER* 3.2 7.1 - - - -
236B ALA 3.0 30.8 + - - +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU 3.7 1.2 - - - +
156B LEU* 3.3 4.5 - - - +
157B SER* 2.8 39.8 + - - +
159B TRP* 3.6 40.4 + - + +
208B ARG* 3.5 24.6 + - - +
209B CYS* 1.3 73.9 - - - +
211B VAL* 1.3 62.1 + - - +
212B GLN* 4.0 2.3 + - + +
233B ILE* 3.4 38.8 - - + +
235B SER* 3.7 8.3 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 4.0 18.2 - - + -
124B VAL* 3.6 31.2 - - + -
146B ALA* 4.2 10.5 - - + -
154B VAL* 4.0 28.3 - - + -
155B GLU 3.5 5.2 - - - +
156B LEU* 4.0 25.4 - - + -
189B LEU* 5.9 0.7 - - + -
209B CYS* 4.4 1.3 - - - -
210B GLN* 1.3 77.9 - - - +
212B GLN* 1.3 61.5 + - - +
213B PHE* 3.6 1.7 + - - +
232B GLN 3.8 0.2 - - - +
233B ILE* 3.3 5.0 - - - -
234B VAL* 2.8 44.5 + - - +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B HIS 3.8 0.2 - - - +
154B VAL* 3.1 7.6 - - - +
155B GLU* 2.8 47.0 + - + +
210B GLN* 4.0 2.9 - - + +
211B VAL* 1.3 72.1 - - - +
213B PHE* 1.3 69.3 + - - +
214B TYR* 3.3 33.5 + - + +
231B THR* 3.6 16.8 - - - +
232B GLN* 3.3 26.1 + - - +
233B ILE* 3.7 23.9 - - + +
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Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 4.0 2.7 - - + -
120B PHE 3.2 24.2 - - - -
121B PRO* 3.7 20.2 - - + -
122B PRO* 3.6 29.8 - - + -
149B PHE* 4.3 0.7 - - + -
150B TYR 3.4 18.2 - - - -
151B PRO* 3.8 13.9 - - + -
153B HIS 3.6 8.5 - - - -
154B VAL* 4.0 10.1 - - + -
211B VAL 3.6 1.1 + - - +
212B GLN* 1.3 74.4 + - - +
214B TYR* 1.3 76.8 + - - +
215B GLY* 3.8 15.3 - - - -
229B PRO 3.9 6.7 - - - -
230B VAL 3.6 24.0 - - - -
231B THR* 3.2 7.4 - - - +
232B GLN* 2.8 41.1 + - + +
234B VAL* 5.6 0.2 - - + -
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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
------------------------------------------------------------
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