Contacts of the strand formed by residues 113 - 119 (chain B) in PDB entry 3BPL
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B HIS 4.9 1.4 - - - +
108B THR* 5.7 0.3 - - - -
110B VAL* 3.7 29.7 + - - +
111B SER 4.9 1.3 - - - -
112B ASP* 1.3 88.7 - - + +
114B LEU* 1.3 63.5 + - - +
115B LEU* 4.0 2.1 + - - +
160B ARG* 4.6 25.2 + - + +
161B ILE 3.5 7.0 - - - +
162B ALA* 4.2 17.0 - - + +
163B ALA* 4.8 1.6 - - - -
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Residues in contact with LEU 114 (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 VAL* 3.5 15.5 - - + -
107B HIS 3.4 19.1 - - - +
108B THR* 3.5 23.3 - - + +
112B ASP 4.4 0.2 + - - -
113B THR* 1.3 73.9 - - - +
115B LEU* 1.3 60.1 + - - +
116B LEU* 4.9 5.7 - - + +
159B LEU 3.5 1.6 - - - +
160B ARG* 3.4 6.9 - - - -
161B ILE* 2.8 53.4 + - + +
163B ALA* 4.5 4.0 - - + +
166B LEU* 3.6 21.5 - - + -
196B TRP* 3.4 37.2 - - + +
198B ASN* 5.4 3.8 - - + +
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Residues in contact with LEU 115 (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 VAL* 3.6 3.5 - - - +
107B HIS* 2.7 75.5 + - + +
113B THR 4.0 1.7 + - - +
114B LEU* 1.3 73.2 - - - +
116B LEU* 1.3 68.1 + - - +
117B THR* 4.1 7.2 - - + -
158B SER* 4.5 9.9 - - - -
159B LEU 3.5 17.3 - - - +
160B ARG* 3.8 32.3 - - + +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.2 14.8 - - + -
105B THR 3.6 7.4 - - - +
106B VAL* 3.2 40.2 - - + -
114B LEU* 4.0 6.0 + - + +
115B LEU* 1.3 73.5 - - - +
117B THR* 1.3 64.9 + - - +
118B TRP* 3.6 6.9 - - + -
136B VAL* 3.8 21.5 - - + -
138B ILE* 3.6 31.9 - - + -
158B SER* 3.3 6.6 - - - -
159B LEU* 2.8 55.0 + - + +
161B ILE* 5.0 3.6 - - + -
174B ALA* 4.4 7.2 - - + -
196B TRP* 5.1 1.6 - - + -
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Residues in contact with THR 117 (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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103B ASN 3.2 1.4 + - - +
104B LEU* 3.3 3.1 - - - +
105B THR* 2.8 52.8 + - - -
107B HIS* 3.3 32.1 + - + +
115B LEU* 4.1 11.4 - - + -
116B LEU* 1.3 79.6 - - - +
118B TRP* 1.3 66.0 + - - +
157B PRO 3.5 9.0 - - - -
158B SER* 4.5 9.6 - - - +
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Residues in contact with TRP 118 (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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101B PRO* 3.9 14.4 - - + -
102B GLY 3.4 9.2 - - - +
103B ASN 3.5 9.2 - - - -
104B LEU* 3.8 22.7 - - + -
116B LEU* 3.6 19.1 - - + -
117B THR* 1.3 84.3 - - - +
119B SER* 1.3 73.5 + - - +
134B TYR* 3.2 47.2 - + + -
136B VAL* 3.7 26.0 - - + -
152B VAL* 3.7 8.7 - - + -
157B PRO* 3.2 56.8 + - + +
158B SER 3.6 22.9 - - - -
159B LEU* 3.9 3.8 - - + -
176B VAL* 3.9 15.7 - - + -
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Residues in contact with SER 119 (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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101B PRO* 3.6 8.0 - - - +
102B GLY 2.6 28.9 + - - -
103B ASN* 2.8 37.0 + - - +
118B TRP* 1.3 77.4 - - - +
120B ASN* 1.3 62.6 + - - +
121B PRO* 3.5 4.0 - - - +
157B PRO* 5.2 0.4 - - - -
1D NAG 3.6 18.9 + - - -
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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