Contacts of the helix formed by residues 225 - 230 (chain B) in PDB entry 1B0P
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 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ALA* 3.5 8.0 - - + +
116A ILE 2.8 22.1 + - - -
118A ALA 5.5 0.2 - - - -
119A HIS* 3.4 20.7 - + - -
120A ALA 3.4 23.6 - - - -
122A SER* 3.6 21.8 - - - +
126A ASP* 3.9 10.3 - - - -
128A GLN* 3.0 24.8 + - - -
365A LEU* 4.0 8.1 - - + -
366A GLY* 3.8 21.1 - - - +
220B GLN* 3.4 21.8 - - + +
221B ASN 3.0 18.6 + - - +
222B PRO* 4.1 1.0 + - + -
223B ASP 4.0 0.2 - - - -
224B ILE* 1.3 77.6 - - - +
226B PHE* 1.3 59.0 + - - +
228B GLY 3.2 1.2 + - - -
229B ARG* 2.9 45.3 + - - +
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Residues in contact with PHE 226 (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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362A ARG* 3.8 21.8 - - + -
363A TYR* 3.9 14.8 - - - -
365A LEU* 3.3 53.9 + - + +
368A LYS* 3.8 30.3 - - + -
391A THR* 4.0 17.0 - - - -
392A VAL 3.7 20.2 - - - -
394A ILE* 3.8 18.4 - - + -
222B PRO 4.8 1.6 + - - -
224B ILE 3.4 0.8 - - - -
225B TYR* 1.3 77.8 - - - +
227B GLN* 1.3 61.6 + - - +
229B ARG* 3.3 2.6 + - - +
230B GLU* 3.2 43.6 + - + +
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Residues in contact with GLN 227 (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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368A LYS* 2.9 32.5 + - - +
394A ILE* 3.6 19.5 - - + +
651A GLY 3.5 6.2 - - - +
652A ASP* 4.2 3.3 - - - -
654A LEU 2.8 28.6 - - - +
655A PRO* 4.2 6.5 - - + +
656A VAL* 3.7 23.2 - - + +
659A PHE* 3.6 22.1 - - + -
223B ASP 3.0 19.7 + - - +
224B ILE* 3.3 13.2 + - - +
226B PHE* 1.3 70.0 - - - +
228B GLY* 1.3 66.7 + - - +
230B GLU* 3.3 2.6 + - - +
231B ALA* 3.2 18.7 + - - +
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Residues in contact with GLY 228 (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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119A HIS* 3.6 30.3 - - - +
659A PHE* 4.4 15.6 - - - -
660A GLU 4.6 2.9 - - - +
661A ALA 4.5 7.3 - - - +
220B GLN* 4.7 1.6 - - - -
224B ILE 3.0 13.2 + - - -
225B TYR 3.2 0.2 + - - -
227B GLN* 1.3 76.4 - - - +
229B ARG* 1.3 60.5 + - - +
231B ALA* 3.3 19.9 + - - +
232B ALA* 4.5 0.5 + - - +
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Residues in contact with ARG 229 (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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118A ALA* 3.6 23.6 - - - +
119A HIS* 3.3 17.0 + - + +
128A GLN* 3.0 33.8 - - - +
331A LYS* 3.1 48.1 + - + +
333A PRO* 4.4 18.3 - - - +
365A LEU* 3.8 24.2 - - + -
98B TYR* 4.2 19.6 - - - -
102B GLY* 5.2 4.8 - - - -
136B THR 5.9 0.6 + - - -
225B TYR* 2.9 31.1 + - + +
226B PHE 3.4 11.0 - - - +
227B GLN 3.2 0.2 - - - -
228B GLY* 1.3 74.6 - - - +
230B GLU* 1.3 59.6 + - - +
231B ALA 3.3 0.6 + - - -
232B ALA* 4.3 8.8 + - - +
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Residues in contact with GLU 230 (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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331A LYS* 3.3 16.8 - - - +
362A ARG* 2.9 33.4 + - - -
365A LEU* 4.8 0.2 - - - +
391A THR* 3.9 15.6 - - - +
394A ILE* 3.7 15.5 - - + -
396A ASP* 4.5 2.6 - - - +
398A VAL* 4.7 0.3 - - - +
399A THR* 4.6 1.4 + - - -
401A THR* 4.2 5.5 + - - +
656A VAL* 4.6 12.4 - - + +
226B PHE* 3.2 33.2 + - + +
227B GLN 3.8 4.9 - - - +
228B GLY 3.2 0.6 - - - -
229B ARG* 1.3 75.5 - - + +
231B ALA* 1.3 60.6 + - - +
232B ALA 3.2 2.9 - - - -
233B ASN* 2.7 57.3 + - - +
234B PRO* 4.6 0.5 - - - +
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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