Contacts of the helix formed by residues 266 - 273 (chain T) in PDB entry 1BGX
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 ARG 266 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264T PRO* 3.4 29.2 + - + +
265T ASP* 1.3 71.6 - - - +
267T GLU* 1.3 62.4 + - + +
268T ARG 3.4 0.9 - - - -
269T LEU* 3.9 23.2 + - + +
270T ARG* 3.0 46.0 + - - +
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Residues in contact with GLU 267 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265T ASP* 3.2 15.6 - - - +
266T ARG* 1.3 80.5 - - + +
268T ARG* 1.3 63.5 + - + +
270T ARG* 4.3 19.8 + - - +
271T ALA* 4.1 9.7 - - - +
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Residues in contact with ARG 268 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105T LEU* 3.8 29.0 - - + +
265T ASP* 3.3 23.9 + - - +
267T GLU* 1.3 79.5 - - + +
269T LEU* 1.3 65.8 + - - +
270T ARG 3.3 2.2 - - - -
271T ALA* 3.1 17.4 + - + +
272T PHE* 3.3 31.5 + - + -
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Residues in contact with LEU 269 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T PHE* 5.5 0.7 - - + -
102T LEU* 3.7 31.1 - - + +
105T LEU* 3.6 29.3 - - + +
106T LEU* 3.9 35.0 - - + -
264T PRO* 5.1 1.8 - - + -
265T ASP 3.6 14.2 + - - +
266T ARG* 4.0 23.6 - - + +
267T GLU 3.6 0.6 - - - -
268T ARG* 1.3 79.5 - - - +
270T ARG* 1.3 58.8 + - + +
273T LEU* 3.6 36.7 + - + +
282T LEU* 5.3 10.3 - - + -
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Residues in contact with ARG 270 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266T ARG* 3.0 40.0 + - - +
267T GLU* 4.3 17.7 + - - +
269T LEU* 1.3 76.6 - - - +
271T ALA* 1.3 65.9 + - - +
272T PHE 3.4 0.7 - - - -
273T LEU* 4.1 7.2 - - - +
274T GLU* 3.4 31.1 + - + +
279T GLY* 5.2 5.3 - - - +
282T LEU* 5.6 10.5 - - + -
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Residues in contact with ALA 271 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267T GLU 4.1 6.1 - - - +
268T ARG* 3.1 22.4 + - + +
270T ARG* 1.3 82.3 - - + +
272T PHE* 1.3 66.6 + - + +
274T GLU* 4.0 8.4 + - - +
275T ARG* 3.9 20.1 + - - +
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Residues in contact with PHE 272 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98T LEU* 4.4 23.7 - - + +
101T GLU* 3.8 40.4 - - + -
102T LEU* 3.9 22.4 - - + -
105T LEU* 4.4 9.2 - - + -
268T ARG* 3.3 31.1 + - + -
269T LEU 4.0 0.2 + - - -
270T ARG 3.4 0.2 - - - -
271T ALA* 1.3 84.8 - - + +
273T LEU* 1.3 61.8 + - - +
274T GLU 3.3 0.6 + - - -
275T ARG* 3.2 42.6 + - - +
276T LEU* 3.6 19.9 + - + +
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Residues in contact with LEU 273 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T VAL 5.9 2.0 - - - +
47T PHE* 6.0 1.3 - - + -
48T ALA* 4.8 17.0 - - + -
99T ILE* 6.3 0.9 - - + -
102T LEU* 3.9 26.7 - - + -
269T LEU* 3.6 26.2 + - + +
270T ARG* 3.8 4.1 + - - +
271T ALA 3.5 0.4 - - - -
272T PHE* 1.3 77.4 - - - +
274T GLU* 1.3 57.4 - - - +
275T ARG 3.3 0.2 - - - -
276T LEU* 3.3 19.6 + - + +
277T GLU 3.2 5.4 + - - -
278T PHE* 2.9 49.7 + - + +
279T GLY* 3.2 7.8 + - - -
282T LEU* 3.8 33.0 - - + -
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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