Contacts of the strand formed by residues 98 - 108 (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 GLU 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ARG* 3.1 27.8 + - - -
96B GLY 4.1 0.6 + - - -
97B ALA* 1.3 70.1 - - - +
99B PRO* 1.3 62.5 - - + +
100B LEU* 2.8 32.7 - - + +
159B GLY* 3.1 1.1 - - - -
160B ILE* 2.7 44.7 + - + +
233B LEU* 4.3 24.8 - - + +
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Residues in contact with PRO 99 (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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31B ARG* 2.9 20.1 + - - -
89B VAL* 3.3 35.9 - - + -
92B ILE* 3.3 11.6 - - + -
93B VAL* 4.7 0.2 - - + -
97B ALA 3.1 11.4 - - - +
98B GLU* 1.3 87.7 - - + +
100B LEU* 1.3 60.1 + - - +
130B ALA 3.9 5.2 - - - +
131B GLY 3.4 6.6 - - - +
132B CYS* 3.9 11.4 - - + -
157B THR* 4.8 4.5 - - + -
158B VAL 3.7 8.3 - - - +
159B GLY* 3.9 3.1 - - - -
229B VAL* 3.3 25.1 - - + -
233B LEU* 4.7 2.7 - - + -
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Residues in contact with LEU 100 (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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57A LEU* 4.7 1.8 - - + -
31B ARG* 3.7 14.9 - - - +
45B PHE* 3.3 40.5 - - + -
47B LEU* 4.3 10.5 - - + -
57B LEU* 4.8 1.3 - - + -
98B GLU* 2.8 42.6 - - + +
99B PRO* 1.3 75.8 - - - +
101B PHE* 1.3 77.1 - - + +
132B CYS* 3.5 5.8 - - - -
133B ALA* 2.9 17.7 + - - +
158B VAL* 2.9 20.0 + - + +
159B GLY 4.3 8.3 - - - +
160B ILE* 3.9 26.9 - - + -
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Residues in contact with PHE 101 (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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57A LEU* 3.9 27.8 - - + -
59A SER* 3.4 29.8 - - - -
156A PHE* 4.2 5.8 - + - -
158A VAL* 4.2 7.6 - - + -
45B PHE* 3.9 20.9 - - + -
100B LEU* 1.3 92.4 - - + +
102B PHE* 1.3 62.6 + - - +
103B LEU* 4.3 10.8 - - + -
132B CYS* 3.7 3.5 - - - +
133B ALA 3.0 13.7 - - - +
135B ILE* 4.1 22.0 - - + -
157B THR* 3.2 23.3 - - - +
158B VAL* 3.3 49.2 + - + -
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Residues in contact with PHE 102 (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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84B ALA* 4.5 2.9 - - + -
85B VAL* 3.7 48.9 - - + -
88B CYS* 3.9 9.6 - - + -
101B PHE* 1.3 75.0 - - - +
103B LEU* 1.3 85.8 + - - +
104B ASP* 4.5 4.5 - - + -
123B ILE* 3.9 25.8 - - + -
127B CYS* 3.5 22.4 - - - -
132B CYS* 4.2 4.0 - - - -
133B ALA 2.5 9.3 + - - +
134B LEU* 3.4 9.2 - - + +
135B ILE 3.2 15.9 + - - -
154B ALA 5.0 0.2 - - - -
155B GLY* 3.8 20.2 - - - -
156B PHE 3.4 10.3 - - - -
157B THR* 3.6 29.2 - - + -
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Residues in contact with LEU 103 (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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59A SER* 4.2 13.9 - - - +
60A GLY* 4.1 8.1 - - - -
61A THR* 3.3 41.1 - - + +
156A PHE* 3.5 26.4 - - + -
101B PHE* 4.3 11.0 - - + -
102B PHE* 1.3 90.3 - - - +
104B ASP* 1.3 60.5 + - - +
135B ILE* 4.1 4.7 - - + -
136B GLY* 3.6 17.9 - - - +
137B GLY 3.6 12.6 - - - +
155B GLY* 3.5 3.5 - - - -
156B PHE* 3.0 43.0 + - + +
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Residues in contact with ASP 104 (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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61A THR* 4.0 4.7 - - - +
41B PHE* 4.5 4.5 - - - -
102B PHE* 4.5 5.1 - - + -
103B LEU* 1.3 74.9 - - - +
105B TYR* 1.3 56.8 + - - +
106B ILE* 4.5 9.0 + - - +
120B VAL* 5.0 12.3 - - - +
123B ILE* 3.5 33.8 - - + +
134B LEU* 3.5 14.7 - - - +
136B GLY 3.2 21.4 + - - +
137B GLY* 2.8 7.3 - - - -
138B GLU 2.6 40.4 + - - +
139B THR* 5.7 0.2 + - - -
153B LEU* 4.5 1.5 - - + +
154B ALA 3.5 7.0 - - - +
156B PHE* 5.1 1.1 - - - -
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Residues in contact with TYR 105 (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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61A THR* 4.6 5.8 - - - +
63A GLY* 3.6 24.5 - - - -
105A TYR* 4.6 10.5 - + - -
152A ASP* 3.1 31.6 + - + -
153A LEU 4.6 0.7 - - - -
154A ALA* 3.3 34.3 - - + +
104B ASP* 1.3 73.9 - - - +
106B ILE* 1.3 59.4 + - - +
107B ALA* 3.7 22.9 - - + -
138B GLU* 3.3 26.2 - - + -
140B ALA* 3.8 19.1 - - + +
142B MET* 4.9 0.9 - - - -
152B ASP* 3.6 2.1 - - - +
153B LEU* 3.7 2.2 - - - -
154B ALA* 2.8 52.6 + - + -
156B PHE* 4.2 13.2 - - + -
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Residues in contact with ILE 106 (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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104B ASP* 4.2 8.2 - - - +
105B TYR* 1.3 73.8 - - - +
107B ALA* 1.3 63.6 + - - +
108B CYS* 3.3 10.5 + - + +
116B ILE* 5.9 3.1 - - - -
119B ILE* 3.3 28.3 - - + -
138B GLU 2.5 15.2 + - - +
139B THR* 4.2 14.8 - - + +
140B ALA 2.7 26.5 + - - -
151B TYR* 3.3 40.6 - - + -
152B ASP 3.3 7.9 - - - +
153B LEU* 4.7 7.0 - - + +
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Residues in contact with ALA 107 (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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107A ALA* 6.1 0.4 - - + -
146A TYR* 3.9 5.6 - - - +
152A ASP* 3.7 11.0 - - - +
105B TYR* 3.7 22.4 + - + +
106B ILE* 1.3 69.3 - - - +
108B CYS* 1.3 60.0 + - - +
140B ALA* 4.0 8.3 - - + -
142B MET* 5.8 0.2 - - + -
146B TYR* 2.8 25.6 + - + +
151B TYR* 3.3 11.6 - - - +
152B ASP* 2.8 41.2 + - + +
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Residues in contact with CYS 108 (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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106B ILE* 3.7 13.5 - - + +
107B ALA* 1.3 76.0 - - - +
109B GLY* 1.3 58.3 + - - +
110B LYS 3.8 3.1 - - - -
111B ALA* 3.3 40.2 - - - +
112B GLU 4.7 1.3 - - - -
116B ILE* 6.3 1.3 - - - -
139B THR* 3.8 9.0 - - + -
140B ALA* 2.5 25.6 + - - +
142B MET* 2.5 36.6 + - - +
146B TYR* 3.6 7.2 - - - -
150B GLU 5.9 0.4 - - - -
151B TYR* 4.8 7.0 - - - -
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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