Contacts of the strand formed by residues 55 - 62 (chain B) in PDB entry 2BTU
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 PRO 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ASP* 3.3 3.6 - - - +
47A LEU* 2.6 71.2 + - + +
48A SER* 4.1 4.3 - - - -
47B LEU* 6.1 1.1 - - + -
53B GLU 2.8 30.5 - - - +
54B GLU* 1.3 75.9 - - - +
56B VAL* 1.3 55.3 + - - +
160B ILE* 4.0 23.1 - - + -
161B VAL 4.0 4.0 - - - +
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Residues in contact with VAL 56 (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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35A LEU* 4.4 9.9 - - + -
44A MET* 3.6 23.3 - - + -
45A PHE 3.7 2.9 - - - +
46A ASP* 3.9 20.0 - - - +
54B GLU 3.5 0.2 + - - -
55B PRO* 1.3 72.9 - - - +
57B LEU* 1.3 71.6 + - - +
160B ILE* 3.4 3.8 - - - +
161B VAL* 2.8 63.7 + - + +
163B LYS* 3.7 38.8 - - + +
166B ILE* 4.6 1.1 - - + -
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Residues in contact with LEU 57 (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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43A GLY 3.6 0.3 - - - +
44A MET* 3.0 11.3 - - - +
45A PHE* 2.9 42.5 + - + +
47A LEU* 3.3 39.5 - - + -
57A LEU* 4.2 29.8 - - + -
100A LEU* 5.0 2.5 - - + -
101A PHE* 4.0 27.4 - - + -
47B LEU* 5.0 0.2 - - + -
56B VAL* 1.3 72.7 - - - +
58B VAL* 1.3 60.5 + - - +
59B SER* 4.2 0.4 - - - -
100B LEU* 4.8 2.2 - - + -
158B VAL* 4.2 14.6 - - + -
159B GLY 3.4 13.5 - - - +
160B ILE* 4.1 17.3 - - + -
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Residues in contact with VAL 58 (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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42A GLY 3.2 11.4 - - - +
43A GLY 3.4 3.1 - - - -
44A MET* 3.4 13.5 - - + -
57B LEU* 1.3 73.3 - - - +
59B SER* 1.3 61.3 + - - +
92B ILE* 4.1 16.2 - - + +
95B GLN* 3.2 32.1 - - - +
97B ALA* 3.5 23.6 - - + -
158B VAL* 3.4 2.5 - - - +
159B GLY* 2.6 38.5 + - - +
161B VAL* 3.3 33.7 - - + -
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Residues in contact with SER 59 (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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42A GLY* 2.8 28.6 - - - -
43A GLY* 3.1 13.3 + - - -
101A PHE* 3.5 35.6 - - - -
103A LEU* 3.5 21.3 - - - +
135A ILE* 5.7 3.1 - - - -
156A PHE* 4.2 4.3 - - - -
57B LEU 4.2 0.9 - - - -
58B VAL* 1.3 75.4 - - - +
60B GLY* 1.3 58.0 + - - +
92B ILE* 4.5 4.0 - - - -
157B THR 2.9 17.1 + - - -
158B VAL* 4.2 1.5 - - - +
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Residues in contact with GLY 60 (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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41A PHE 4.9 4.3 - - - -
42A GLY* 4.8 4.0 - - - -
103A LEU* 3.9 9.9 - - - +
59B SER* 1.3 76.9 + - - +
61B THR* 1.3 58.5 + - - -
88B CYS* 4.8 6.3 - - - -
92B ILE* 4.6 7.7 - - - +
156B PHE* 3.4 2.5 - - - +
157B THR* 2.7 39.8 + - - +
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Residues in contact with THR 61 (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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103A LEU* 4.1 6.7 - - + +
104A ASP 4.2 4.0 - - - +
105A TYR* 4.6 5.2 - - + +
137A GLY* 3.9 17.0 - - - +
138A GLU* 3.8 33.5 - - + +
60B GLY* 1.3 74.4 - - - -
62B ASP* 1.3 66.8 + - - +
88B CYS* 4.0 3.8 - - - +
154B ALA* 5.4 0.3 - - - +
155B GLY 2.7 20.9 + - - -
156B PHE* 3.1 28.0 - - - -
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Residues in contact with ASP 62 (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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138A GLU* 3.1 18.8 - - - +
61B THR* 1.3 79.5 + - - +
63B GLY* 1.3 69.8 + - - +
84B ALA* 5.0 8.0 - - - +
87B MET* 3.0 44.6 - - + +
88B CYS* 3.6 16.3 - - - -
91B ASP* 4.5 5.0 - - - +
153B LEU 4.2 1.0 - - - +
154B ALA* 3.9 2.2 - - - -
155B GLY* 3.0 28.8 + - - -
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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