Contacts of the strand formed by residues 96 - 100 (chain T) in PDB entry 2BTO
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 THR 96 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T VAL 3.1 4.0 - - - +
45T ASP* 3.6 0.7 - - - -
46T PHE* 3.0 39.2 + - + -
91T ILE* 3.8 24.6 - - + +
92T ARG 4.9 1.9 + - - -
93T GLY 2.8 25.1 + - - -
94T ILE* 3.8 1.0 - - - +
95T PRO* 1.3 73.7 + - - +
97T LEU* 1.3 65.1 + - - +
98T LEU* 3.5 28.3 - - + -
108T THR* 4.2 8.5 - - + -
109T LYS 3.4 5.4 - - - +
110T VAL* 3.9 13.6 - - + +
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Residues in contact with LEU 97 (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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43T LEU* 3.8 20.0 - - + -
44T VAL 3.2 2.2 - - - +
45T ASP* 3.6 37.9 - - + +
57T ILE* 4.5 10.8 - - + -
61T LEU* 4.0 15.7 - - + -
95T PRO 5.7 1.1 - - - -
96T THR* 1.3 72.5 - - - +
98T LEU* 1.3 67.1 + - - +
99T LEU 4.2 0.2 - - - -
107T ALA 4.1 0.2 - - - +
108T THR* 3.4 1.9 - - - -
109T LYS* 2.7 53.8 + - + +
111T GLY 5.6 2.0 - - - +
113T LEU* 4.2 15.5 - - + -
118T LEU* 3.7 32.5 - - + -
121T PHE* 5.1 1.2 - - + -
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Residues in contact with LEU 98 (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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42T ILE 3.4 2.3 - - - +
43T LEU* 3.2 6.4 - - - -
44T VAL* 2.7 37.9 + - + +
46T PHE* 3.4 29.6 - - + -
89T TYR* 4.0 26.5 - - + +
91T ILE* 4.0 4.0 - - + -
96T THR* 3.5 20.6 + - + -
97T LEU* 1.3 82.0 - - - +
99T LEU* 1.3 60.0 + - - +
100T PHE* 3.6 25.5 + - + -
105T VAL* 3.9 17.9 - - + -
107T ALA 3.7 0.7 - - - -
108T THR* 3.5 23.6 - - + +
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Residues in contact with LEU 99 (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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41T ALA* 4.7 7.0 - - + -
42T ILE 3.4 8.5 - - - +
43T LEU* 4.0 10.4 - - + +
72T LEU* 3.8 28.9 - - + -
98T LEU* 1.3 70.6 - - - +
100T PHE* 1.3 59.4 + - - +
101T LYS* 5.1 4.5 - - + -
105T VAL* 3.3 4.7 - - - -
106T ALA* 2.5 52.5 + - + -
107T ALA* 3.0 23.8 + - + +
121T PHE* 4.7 6.5 - - + +
122T LEU* 4.2 19.7 - - + +
125T ASN* 4.0 32.3 - - + +
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Residues in contact with PHE 100 (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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31T PHE* 3.8 18.2 - + - -
35T VAL* 3.5 17.5 - - + -
36T LEU* 3.9 16.4 - - + -
41T ALA* 3.3 5.2 - - - +
42T ILE* 2.6 54.9 + - + +
44T VAL* 3.8 19.3 - - + -
89T TYR* 3.8 17.7 - + - -
98T LEU* 3.6 36.1 - - + -
99T LEU* 1.3 75.3 - - - +
101T LYS* 1.3 62.8 + - - +
102T ASN 4.2 4.5 - - - +
103T GLY 4.3 1.1 - - - -
104T GLU 3.1 24.9 - - - -
105T VAL* 3.7 24.7 - - + -
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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