Contacts of the helix formed by residues 98 - 105 (chain D) in PDB entry 2BHT
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 GLU 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287C LEU* 3.0 22.7 - - - +
74D ILE* 5.5 1.1 - - - -
99D ARG* 1.3 117.4 + - + +
102D ALA* 3.4 16.7 + - - +
285D ARG* 2.2 70.9 - - + +
286D TYR* 3.8 0.5 - - - -
288D SER* 3.7 11.8 - - - -
289D THR* 3.3 28.9 - - - +
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Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLN* 4.7 1.0 + - - -
98C GLU* 4.5 9.1 + - - +
284C ASP 5.5 0.2 + - - -
287C LEU* 4.2 26.2 - - - +
288C SER* 4.1 21.0 - - - +
98D GLU* 1.3 112.3 + - + +
100D ARG* 1.3 76.0 + - + +
101D ALA* 3.9 10.1 - - + +
102D ALA* 3.1 15.8 + - - +
103D MET* 3.7 10.1 + - - +
284D ASP 5.3 1.2 + - - -
285D ARG* 4.6 3.8 + - - +
288D SER* 1.9 43.8 + - - +
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LYS* 4.3 12.6 - - - +
93D ASP* 3.3 46.1 + - - +
99D ARG* 1.3 78.6 - - + +
101D ALA* 1.3 50.6 + - - +
103D MET* 2.7 24.1 + - + +
104D ARG* 2.5 59.6 + - + +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C LEU* 3.7 24.9 - - + +
290C GLY* 5.8 4.0 - - - -
292C PHE* 4.0 19.5 - - + +
98D GLU 4.5 2.5 - - - +
99D ARG* 3.1 6.6 - - + +
100D ARG* 1.3 75.1 - - - +
102D ALA* 1.3 61.5 + - - +
104D ARG* 3.5 13.7 - - - +
105D ALA* 2.6 35.4 + - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C PHE* 5.2 5.4 - - + -
287C LEU* 3.6 8.4 - - + +
74D ILE* 3.6 33.0 - - + +
98D GLU 3.4 25.1 + - - +
99D ARG 3.1 13.0 + - - +
101D ALA* 1.3 79.2 - - - +
103D MET* 1.3 57.8 + - - +
105D ALA* 4.3 1.4 - - - +
106D TYR* 2.9 32.6 - - - -
285D ARG* 4.5 2.0 - - - -
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Residues in contact with MET 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D THR* 4.4 9.9 - - + -
70D GLY* 3.4 16.6 - - - +
73D GLY* 3.3 43.7 - - - +
74D ILE* 3.7 8.1 - - - +
77D ALA* 4.0 0.8 - - - +
89D LEU* 4.0 17.9 - - + -
99D ARG 3.7 14.8 + - - +
100D ARG* 2.7 20.8 + - + +
102D ALA* 1.3 74.5 - - - +
104D ARG* 1.3 63.3 - - - +
106D TYR* 3.2 23.1 + - - +
107D GLY 3.7 3.1 + - - -
108D ALA* 3.7 14.8 - - + +
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Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C VAL* 5.4 0.5 - - - +
292C PHE 4.4 16.4 - - - +
100D ARG* 2.5 40.3 + - + +
101D ALA* 3.5 10.8 - - - +
103D MET* 1.3 68.2 - - - +
105D ALA* 1.3 65.7 + - - +
106D TYR 3.0 2.5 - - - -
107D GLY* 2.9 16.3 + - - +
108D ALA 4.5 12.1 - - - +
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ARG* 4.3 2.9 - - - +
245C ALA* 3.1 21.2 - - + +
246C VAL* 3.8 11.1 + - - +
251C PHE* 4.0 17.9 - - + -
292C PHE* 3.4 45.2 + - + -
101D ALA 2.6 23.7 + - - +
102D ALA 4.3 3.6 - - - +
104D ARG* 1.3 73.2 - - - +
106D TYR* 1.3 59.4 + - + +
107D GLY 3.6 0.3 + - - -
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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