Contacts of the helix formed by residues 205 - 213 (chain A) in PDB entry 3C2B
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 THR 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLY 2.7 29.1 + - - +
153A TYR* 3.0 19.8 + - - -
154A LEU 3.7 16.8 - - - +
155A ARG* 3.8 21.1 - - + +
204A GLY* 1.3 74.3 - - - -
206A GLU* 1.3 66.6 + - - +
207A LYS* 3.4 9.8 + - - -
208A VAL* 3.1 20.8 + - - +
209A HIS* 3.4 7.2 + - - -
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Residues in contact with GLU 206 (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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205A THR* 1.3 73.0 - - - +
207A LYS* 1.3 56.5 + - - +
209A HIS* 3.4 7.6 + - - +
210A SER* 3.0 39.6 + - - +
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Residues in contact with LYS 207 (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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81A ARG* 4.1 12.1 - - - +
151A SER 2.8 22.9 + - - +
152A GLY* 3.8 13.9 - - - +
153A TYR* 3.7 26.1 + - + -
205A THR* 3.1 11.9 + - - +
206A GLU* 1.3 77.9 - - - +
208A VAL* 1.3 60.8 + - - +
210A SER* 3.7 5.9 + - - -
211A GLU* 3.0 35.0 + - + +
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Residues in contact with VAL 208 (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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84A ALA* 3.9 12.3 - - + +
87A LEU* 4.4 11.7 - - + -
153A TYR* 3.5 50.6 - - + +
200A LEU* 4.7 9.6 - - + -
204A GLY* 3.6 15.5 - - - -
205A THR* 3.1 18.7 + - - +
207A LYS* 1.3 78.4 - - - +
209A HIS* 1.3 71.5 - - + +
211A GLU* 4.0 0.7 - - - +
212A LEU* 2.9 48.6 + - + +
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Residues in contact with HIS 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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200A LEU* 3.0 46.0 + - + -
201A THR* 4.2 8.8 + - - -
204A GLY* 3.7 11.1 + - - -
205A THR 3.4 20.0 + - - -
206A GLU* 4.0 7.4 - - - +
207A LYS 3.3 0.6 - - - -
208A VAL* 1.3 80.2 - - + +
210A SER* 1.3 60.3 + - - +
212A LEU* 3.6 9.0 + - - +
213A GLY* 2.9 24.9 + - - -
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Residues in contact with SER 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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206A GLU* 3.0 26.5 + - - +
207A LYS* 3.7 6.8 + - - -
209A HIS* 1.3 76.7 - - - +
211A GLU* 1.3 61.2 + - - +
213A GLY* 3.5 6.7 + - - +
214A GLY 3.5 19.4 + - - +
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Residues in contact with GLU 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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83A SER* 4.1 5.0 - - - -
84A ALA* 3.2 26.2 + - + +
85A PRO* 3.7 11.9 - - + +
153A TYR* 2.9 33.7 + - - -
207A LYS* 3.0 26.4 + - + +
210A SER* 1.3 74.4 + - - +
212A LEU* 1.3 61.0 + - - +
213A GLY 3.0 5.2 - - - -
214A GLY* 3.1 15.1 + - - -
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Residues in contact with LEU 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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84A ALA* 3.6 33.0 - - + +
85A PRO* 3.6 14.1 - - + -
88A ALA* 4.2 12.1 - - + -
200A LEU* 3.9 27.8 - - + -
208A VAL* 2.9 35.1 + - + +
209A HIS* 4.0 9.0 - - - +
211A GLU* 1.3 75.0 - - - +
213A GLY* 1.3 56.7 + - - +
214A GLY 3.2 3.3 + - - -
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Residues in contact with GLY 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 HIS 2.9 16.9 + - - -
210A SER* 3.7 5.8 - - - -
211A GLU 3.0 0.8 - - - -
212A LEU* 1.3 77.5 - - - +
214A GLY* 1.3 63.6 + - - +
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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