Contacts of the helix formed by residues 232 - 241 (chain K) in PDB entry 1BTH
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 PHE 232 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124K PRO* 3.3 42.8 - - + +
125K ASP* 3.7 2.7 - - - -
126K ARG* 3.3 68.6 - - + -
129K ALA* 3.9 20.6 - - + -
210K MET* 4.4 3.4 + - + -
230K HIS* 3.4 17.7 + + + +
231K VAL* 1.3 77.2 - - - +
233K ARG* 1.3 72.4 + - + +
235K LYS* 3.1 25.3 + - + +
236K LYS 4.8 0.3 + - - -
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Residues in contact with ARG 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K ARG* 5.0 7.3 - - - +
178K ASP* 2.6 66.1 + - - +
179K ASN* 3.8 16.1 - - - +
230K HIS* 3.3 39.0 + - + +
232K PHE* 1.3 85.5 - - + +
234K LEU* 1.3 63.1 + - + +
235K LYS 3.5 0.4 + - - -
236K LYS* 4.9 4.3 + - - +
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Residues in contact with LEU 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K HIS* 4.1 19.3 - - + +
101K ARG* 3.9 28.5 - - + +
103K ILE* 3.7 28.7 - - + -
179K ASN* 3.7 32.3 - - + +
229K THR* 4.1 11.4 - - + -
230K HIS 3.3 15.0 + - - +
231K VAL 2.7 10.3 + - - +
233K ARG* 1.3 83.3 - - + +
235K LYS* 1.3 62.5 + - - +
236K LYS 3.3 3.1 - - - -
237K TRP* 3.2 20.3 + - + +
238K ILE* 3.3 14.3 + - - +
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Residues in contact with LYS 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K LEU* 3.9 37.3 + - + -
124K PRO* 3.4 29.4 + - + +
125K ASP* 4.2 10.5 - - - +
231K VAL* 2.8 10.1 + - + +
232K PHE* 3.1 24.8 + - + +
234K LEU* 1.3 80.2 - - - +
236K LYS* 1.3 58.7 + - + +
238K ILE* 3.2 7.6 + - + +
239K GLN* 2.9 59.5 + - + +
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Residues in contact with LYS 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K PHE 4.8 0.6 + - - -
233K ARG 4.9 4.4 + - - +
234K LEU 3.3 1.0 - - - -
235K LYS* 1.3 79.6 - - + +
237K TRP* 1.3 58.0 + - - +
239K GLN* 3.2 25.7 + - - +
240K LYS* 2.8 29.9 + - - +
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Residues in contact with TRP 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K TYR* 3.6 22.7 - - + -
90K ILE 4.0 5.2 - - - -
91K HIS* 3.5 57.7 - + + +
92K PRO* 3.6 15.3 - - + +
103K ILE* 3.8 27.1 - - + -
104K ALA* 4.2 2.0 - - - -
105K LEU* 4.0 26.7 - - + -
234K LEU* 3.2 15.5 + - + +
236K LYS* 1.3 74.5 - - - +
238K ILE* 1.3 75.5 + - + +
240K LYS* 3.3 17.3 - - + +
241K VAL* 2.7 61.4 + - + +
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Residues in contact with ILE 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K ILE* 4.4 4.5 - - + -
53K LEU* 4.0 17.7 - - + -
103K ILE* 4.0 11.4 - - + -
105K LEU* 3.9 14.8 - - + -
123K LEU* 4.0 22.9 - - + -
231K VAL* 3.9 28.0 - - + -
234K LEU 3.4 14.4 - - - +
235K LYS* 3.2 12.3 + - - +
237K TRP* 1.3 89.4 - - + +
239K GLN* 1.3 62.6 + - + +
241K VAL* 3.2 1.6 + - - +
242K ILE* 2.8 55.5 + - + +
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Residues in contact with GLN 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K LEU* 6.3 0.7 - - + -
235K LYS* 2.9 46.8 + - + +
236K LYS* 3.2 43.6 - - - +
238K ILE* 1.3 79.4 - - + +
240K LYS* 1.3 64.9 + - - +
242K ILE* 3.2 21.3 + - - +
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Residues in contact with LYS 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K LYS 2.8 19.7 + - - +
237K TRP* 3.3 20.2 - - + +
239K GLN* 1.3 77.6 - - - +
241K VAL* 1.3 67.2 + - + +
242K ILE 4.1 3.1 - - - -
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Residues in contact with VAL 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K TRP* 4.1 9.4 - - + -
89K TYR* 3.9 40.7 - - + -
105K LEU* 3.9 18.6 - - + -
237K TRP* 2.7 55.1 + - + +
238K ILE 3.9 2.0 - - - +
240K LYS* 1.3 76.1 - - + +
242K ILE* 1.3 65.7 + - - +
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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