Contacts of the helix formed by residues 200 - 204 (chain A) in PDB entry 3CQ6
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 TYR 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASN* 2.7 27.7 + - + +
168A THR* 5.3 0.2 - - + -
170A PRO* 3.7 41.2 + - + +
172A ASN* 3.6 13.9 + - + -
198A GLU* 3.1 0.8 - - - +
199A ALA* 1.3 80.3 - - + +
201A ALA* 1.3 65.1 + - - +
202A GLU* 3.2 3.4 - - - -
203A PHE* 2.8 36.1 + + + +
228A LLP 2.6 72.0 + + + -
307A SER* 4.1 4.5 - - - -
308A ASN* 3.4 26.5 - - - -
309A PHE* 3.7 15.0 - + - -
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN* 5.3 1.2 + - - -
169A THR 5.0 0.4 - - - +
170A PRO* 3.9 11.3 - - - +
198A GLU* 3.1 33.9 + - + +
199A ALA 3.5 0.2 - - - -
200A TYR* 1.3 76.2 - - - +
202A GLU* 1.3 62.5 + - - +
203A PHE 3.0 1.7 + - - -
204A SER* 3.1 23.7 + - - +
206A SER 5.1 1.7 - - - +
208A SER* 5.5 3.1 - - - -
224A ARG* 3.6 28.5 - - - +
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Residues in contact with GLU 202 (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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78A TYR* 2.6 34.7 + - - +
82A GLN* 3.8 20.8 + - - +
198A GLU 4.5 1.0 - - - +
199A ALA 4.1 10.4 - - - +
200A TYR 3.1 0.6 + - - -
201A ALA* 1.3 82.1 + - - +
203A PHE* 1.3 60.5 + - - +
204A SER 3.3 4.9 + - - +
224A ARG* 2.8 27.0 + - - -
225A THR 4.7 10.0 + - - +
229A ALA* 3.6 25.6 + - + +
230A PHE* 4.5 6.7 - - - -
239A TYR* 4.3 2.6 + - - -
278A LEU* 4.3 15.3 - - + -
281A VAL* 3.6 16.9 - - + +
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Residues in contact with PHE 203 (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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37A ASN* 5.3 0.7 - - + -
200A TYR* 2.8 27.8 + + + +
202A GLU* 1.3 77.7 - - - +
204A SER* 1.3 58.0 + - - +
205A PRO* 4.3 3.8 - - - +
228A LLP 4.2 8.7 - - + -
229A ALA* 3.5 38.8 - - + -
281A VAL* 3.9 28.4 - - + +
284A LEU* 3.8 24.9 - - + -
285A SER* 4.0 19.8 + - - +
288A ARG* 4.2 6.1 + - - -
306A GLU 3.3 8.8 - - - +
307A SER* 3.8 18.2 - - - -
308A ASN* 3.5 50.5 - - + -
323E GLN* 5.5 1.7 - - - +
327E ASP* 4.9 0.2 - - - +
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Residues in contact with SER 204 (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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82A GLN* 5.9 0.3 + - - -
170A PRO* 4.5 7.2 - - - -
177A VAL* 3.7 20.9 - - - +
200A TYR 4.0 0.2 + - - -
201A ALA* 3.1 18.7 + - - +
202A GLU 4.2 3.7 - - - +
203A PHE* 1.3 80.3 - - - +
205A PRO* 1.3 71.5 - - - +
206A SER* 3.2 30.3 + - - +
306A GLU* 4.0 16.1 + - - +
327E ASP* 4.9 0.4 - - - -
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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