Contacts of the helix formed by residues 203 - 209 (chain B) in PDB entry 3OTC
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 LEU 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B SER* 6.0 2.0 - - - -
201B ASN 5.5 0.9 - - - +
202B GLU* 1.3 83.9 + - - +
204B PRO* 1.3 74.3 - - + +
205B MET* 4.2 12.6 - - + +
206B TYR* 3.2 55.6 + - + +
207B ARG* 3.3 12.1 + - - +
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Residues in contact with PRO 204 (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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202B GLU 4.0 1.6 - - - +
203B LEU* 1.3 85.0 - - + +
205B MET* 1.3 59.9 + - + +
206B TYR 3.3 0.2 - - - -
207B ARG* 3.7 24.9 - - - +
208B LYS* 2.8 37.4 + - + +
209B GLY 3.5 0.5 + - - -
249B HIS* 3.7 27.7 - - + +
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Residues in contact with MET 205 (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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48B SER* 5.3 4.5 - - - -
51B LEU* 4.3 32.3 - - + +
52B GLN* 4.3 31.9 - - + +
55B THR* 5.8 2.5 - - - +
151B CYS* 5.0 0.5 - - - -
203B LEU* 4.7 10.3 - - + -
204B PRO* 1.3 80.1 - - + +
206B TYR* 1.3 72.7 + - + +
209B GLY* 3.1 24.3 + - - -
210B THR* 4.1 9.4 - - + +
249B HIS* 2.9 50.3 - - + +
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Residues in contact with TYR 206 (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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46B ASN* 3.4 50.9 + - + +
48B SER* 3.5 29.4 + - - -
51B LEU* 3.7 24.2 - - + -
151B CYS* 3.8 10.2 - - - -
155B ASN* 3.1 30.0 - - - +
202B GLU* 4.2 14.8 - - + +
203B LEU* 3.2 51.5 + - + +
205B MET* 1.3 91.1 - - + +
207B ARG* 1.3 61.4 + - + +
209B GLY 4.5 0.2 - - - -
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Residues in contact with ARG 207 (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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148B GLN* 4.9 1.0 - - - +
151B CYS* 3.8 9.4 - - - +
152B HIS* 4.0 21.8 + - + +
155B ASN* 4.6 1.6 - - - +
199B TYR* 3.3 60.1 + - + +
200B ASN* 3.8 23.0 + - - +
202B GLU* 3.1 30.3 + - + -
203B LEU 3.3 7.6 + - - +
204B PRO* 3.7 24.6 - - - +
206B TYR* 1.3 82.0 - - - +
208B LYS* 1.3 82.5 + - + +
209B GLY 3.7 0.2 - - - -
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Residues in contact with LYS 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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72B TYR* 2.6 28.2 + - - -
148B GLN* 2.8 32.2 + - - +
151B CYS* 4.1 0.9 - - - -
152B HIS* 5.9 8.0 - - + +
204B PRO* 2.8 22.5 + - + +
207B ARG* 1.3 102.9 - - + +
209B GLY* 1.3 52.2 + - - +
249B HIS 3.9 17.7 - - - +
250B CYS 3.8 7.9 - - - +
251B ASP* 3.0 48.3 + - - +
253B ILE* 5.2 3.2 - - - +
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Residues in contact with GLY 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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72B TYR* 3.7 7.9 - - - -
73B GLY 4.0 5.8 - - - -
74B GLN* 4.8 2.0 - - - -
151B CYS* 3.9 9.5 - - - -
204B PRO 3.5 0.4 + - - -
205B MET 3.1 21.0 + - - -
207B ARG 3.7 1.4 - - - -
208B LYS* 1.3 83.2 - - - +
210B THR* 1.3 64.4 + - - -
211B VAL* 4.9 0.9 - - - +
249B HIS* 3.3 25.6 - - - -
250B CYS 4.7 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
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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