Contacts of the strand formed by residues 148 - 155 (chain B) in PDB entry 3BN3
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 ALA 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B CYS 4.1 0.2 - - - +
113B VAL* 2.9 36.2 + - + +
114B PRO* 5.0 0.2 - - - +
119B ARG* 4.5 0.9 - - + -
122B LEU* 3.8 18.6 - - + -
124B LEU* 3.9 10.8 - - + -
138B PHE* 3.8 31.6 - - + -
147B GLY* 1.3 76.0 - - - +
149B VAL* 1.3 66.6 + - - +
204B GOL 3.7 9.3 + - - -
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Residues in contact with VAL 149 (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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110B SER* 3.7 9.4 - - - +
111B CYS 3.3 10.3 - - - +
112B ARG* 3.9 24.0 - - + +
124B LEU* 4.0 2.9 - - - -
136B ARG* 3.7 8.5 + - - -
138B PHE* 3.5 10.7 - - - -
148B ALA* 1.3 79.4 - - - +
150B LEU* 1.3 63.5 + - - +
151B THR* 3.6 20.9 - - - +
204B GOL 2.9 32.4 + - - +
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Residues in contact with LEU 150 (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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109B LEU 3.8 1.2 - - - +
110B SER* 3.4 1.0 - - - -
111B CYS* 2.9 37.9 + - + +
124B LEU* 3.3 49.8 - - + +
125B THR 4.1 0.7 - - - +
126B LEU* 4.0 26.6 - - + +
134B ILE* 4.1 23.3 - - + +
136B ARG* 3.9 33.2 - - + +
138B PHE* 4.8 2.0 - - + -
149B VAL* 1.3 74.7 - - - +
151B THR* 1.3 72.4 + - - +
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Residues in contact with THR 151 (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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108B THR* 3.2 33.9 - - + -
109B LEU 3.2 4.3 - - - +
110B SER* 3.0 20.3 + - - -
136B ARG* 5.7 0.4 - - - +
149B VAL* 3.6 11.3 - - - +
150B LEU* 1.3 82.2 - - - +
152B ALA* 1.3 63.6 + - - +
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Residues in contact with ALA 152 (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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108B THR* 3.5 3.8 - - - +
109B LEU* 2.8 33.5 + - - +
126B LEU* 3.7 21.7 - - + +
134B ILE* 4.1 22.9 - - + -
151B THR* 1.3 80.3 - - - +
153B THR* 1.3 66.3 + - - +
154B VAL* 4.0 6.9 + - + -
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Residues in contact with THR 153 (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 ASN* 3.3 43.7 - - + +
107B PHE 3.4 7.4 - - - +
108B THR* 4.7 6.7 + - - +
152B ALA* 1.3 77.2 - - - +
154B VAL* 1.3 63.4 + - - +
200B NAG 3.8 17.2 + - - +
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Residues in contact with VAL 154 (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 ASN* 3.3 3.9 - - - -
107B PHE* 2.9 62.0 + - + +
109B LEU* 4.0 29.4 - - + -
128B ARG* 4.6 12.6 - - - +
133B LEU* 4.5 11.4 - - + -
134B ILE* 6.4 0.7 - - + -
152B ALA* 4.3 10.1 - - + +
153B THR* 1.3 81.6 - - - +
155B LEU* 1.3 69.8 - - - +
160B ASP* 5.3 0.7 - - - +
165B PHE* 4.6 10.5 - - + -
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Residues in contact with LEU 155 (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 GLY* 3.3 35.9 - - - +
105B GLU 3.8 4.0 - - - -
106B ASN* 3.5 19.7 + - - +
128B ARG* 5.3 1.0 + - - -
154B VAL* 1.3 81.4 - - - +
156B ALA* 1.3 70.2 + - - +
157B ARG* 3.6 17.1 + - + +
160B ASP* 3.9 3.6 - - - +
200B NAG 4.1 13.0 - - + +
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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