Contacts of the helix formed by residues 204 - 210 (chain A) in PDB entry 3BPT
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 GLY 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ALA* 4.4 2.1 - - - +
160A THR 3.4 20.6 - - - +
161A GLU* 3.7 15.9 - - - -
163A CYS* 2.8 15.7 + - - -
203A LYS* 1.3 72.7 - - - +
205A ARG* 1.3 59.0 + - - -
207A VAL* 2.9 29.4 + - - +
208A TYR 3.9 1.2 + - - -
216A PHE* 3.6 9.0 - - - -
254A ASP* 6.0 0.2 - - - -
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Residues in contact with ARG 205 (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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161A GLU* 4.9 0.2 - - - +
203A LYS 3.4 1.0 + - - -
204A GLY* 1.3 70.7 - - - -
206A ASP* 1.3 57.6 + - - +
208A TYR* 3.1 18.2 + - + +
209A ARG* 2.9 48.3 + - - +
216A PHE* 3.3 43.4 - - + +
248A HIS* 4.1 17.0 + - - -
251A SER* 3.0 41.8 + - - -
253A ILE 2.8 28.9 + - - -
254A ASP* 3.2 38.2 + - + +
255A ARG* 3.6 15.9 + - - +
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Residues in contact with ASP 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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202A LEU* 4.1 6.0 - - + +
203A LYS* 3.1 23.5 + - - +
204A GLY 3.0 1.2 + - - -
205A ARG* 1.3 77.1 - - - +
207A VAL* 1.3 57.2 + - - +
209A ARG* 3.6 6.9 - - - +
210A ALA* 2.9 31.5 + - - +
257A LYS* 5.7 5.8 - - - +
258A SER 3.9 4.2 - - - +
259A PHE* 3.5 17.9 - - + -
260A ILE* 2.9 49.6 + - + +
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Residues in contact with VAL 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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139A ILE* 4.5 2.2 - - + -
159A ALA* 4.5 2.2 - - + -
163A CYS* 3.9 28.0 - - - -
165A PHE* 3.8 15.5 - - + -
202A LEU* 3.4 34.3 - - + +
203A LYS* 4.0 2.9 - - - -
204A GLY 2.9 14.0 + - - +
206A ASP* 1.3 77.1 - - - +
208A TYR* 1.3 59.5 + - - +
210A ALA* 3.7 4.4 + - - +
211A GLY 3.5 2.1 + - - -
212A ILE* 3.1 52.7 + - + +
213A ALA* 3.1 13.7 + - + +
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Residues in contact with TYR 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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159A ALA* 4.9 0.2 - - - +
204A GLY 3.9 0.6 + - - -
205A ARG* 3.1 28.1 + - + +
207A VAL* 1.3 78.0 - - - +
209A ARG* 1.3 86.6 + - + +
210A ALA 3.1 0.2 - - - -
211A GLY* 2.9 15.4 + - - -
213A ALA* 3.6 28.4 - - + +
214A THR* 3.4 26.0 - - - -
215A HIS* 3.9 2.9 - - - -
216A PHE* 4.3 14.6 - - + -
248A HIS* 3.4 35.2 + + - -
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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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188A GLN* 4.8 6.4 + - - -
205A ARG* 2.9 44.4 + - - +
206A ASP* 3.3 3.8 + - - +
208A TYR* 1.3 95.1 - - + +
210A ALA* 1.3 60.4 + - - +
211A GLY* 3.4 1.6 + - - -
254A ASP 3.6 1.2 + - - -
255A ARG 3.1 26.7 + - - -
256A ASP* 4.3 1.2 - - - +
257A LYS* 2.7 24.8 + - - +
258A SER* 3.9 1.7 - - - +
259A PHE* 3.4 56.1 - - + +
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Residues in contact with ALA 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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187A LEU* 3.5 18.2 - - - +
188A GLN* 5.2 2.8 + - - +
191A LEU* 3.9 18.2 - - + +
202A LEU* 3.5 24.0 - - + -
206A ASP 2.9 17.4 + - - +
207A VAL 3.8 6.7 - - - +
209A ARG* 1.3 77.9 - - - +
211A GLY* 1.3 58.9 + - - +
212A ILE* 3.6 9.6 + - + -
259A PHE* 3.8 16.3 - - + -
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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