Contacts of the strand formed by residues 121 - 127 (chain A) in PDB entry 2BPI
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 GLY 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A HIS* 4.0 4.9 - - - -
119A GLY 3.9 1.8 + - - -
120A SER* 1.3 74.6 - - - +
122A TRP* 1.3 64.3 + - - -
138A THR 3.2 12.8 - - - -
140A ASP 3.7 6.5 - - - -
158A ILE* 2.8 40.9 + - - +
159A TRP* 3.3 13.7 - - - -
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Residues in contact with TRP 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLN* 3.0 22.6 + - - -
72A ASN* 3.5 45.3 - - + +
73A HIS* 3.5 29.6 - + - -
76A TYR* 3.8 9.9 - - + -
117A HIS* 5.0 2.7 + - - -
121A GLY* 1.3 75.7 - - - -
123A GLY* 1.3 58.8 + - - +
124A TRP* 3.4 23.9 - + + +
137A GLN* 3.4 7.3 - - - +
138A THR* 3.0 37.6 + - - +
140A ASP 2.9 28.6 + - - -
142A GLY 4.1 0.7 - - - -
155A THR* 3.6 16.6 - - + +
156A CYS 3.6 4.5 - - - -
157A ASP* 3.4 47.1 - - + -
158A ILE* 4.3 3.7 - - - +
159A TRP* 3.5 4.2 - - - +
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PHE* 3.9 8.1 - - - -
113A ILE* 4.5 5.4 - - - -
114A LEU* 3.3 25.8 - - - +
122A TRP* 1.3 73.2 - - - +
124A TRP* 1.3 58.7 + - - -
136A LEU 3.6 5.2 - - - -
155A THR* 2.7 27.2 + - - -
156A CYS 2.9 21.6 + - - -
158A ILE* 5.1 0.4 - - - +
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Residues in contact with TRP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TRP* 4.0 8.5 - + - -
72A ASN* 3.5 26.7 - - + -
75A PHE* 4.0 6.3 - + - -
110A PHE* 3.4 12.0 - - - -
122A TRP* 3.4 15.5 - - + +
123A GLY* 1.3 73.3 - - - -
125A LEU* 1.3 64.7 + - - +
126A ALA* 4.9 1.3 - - + -
135A ILE* 3.3 7.1 - - - -
136A LEU* 2.8 54.9 + - + +
138A THR* 2.8 28.1 + - + +
142A GLY 3.9 5.6 - - - -
143A ASN* 3.6 20.9 - - + -
144A PRO* 3.6 22.9 - - + -
152A PRO* 3.7 31.6 - - + -
154A LEU 3.5 6.5 - - - -
155A THR* 3.4 41.3 - - + -
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ILE* 4.2 11.2 - - + -
96A ILE* 4.5 7.4 - - + -
100A PHE* 4.3 3.4 - - + -
106A PHE* 3.7 39.5 - - + -
110A PHE* 4.1 4.0 - - + -
124A TRP* 1.3 72.3 - - - +
126A ALA* 1.3 57.0 + - - +
133A LEU* 4.0 27.4 - - + -
134A VAL 3.6 17.7 - - - +
152A PRO* 3.7 2.6 - - - +
153A ILE* 2.7 63.8 + - + -
154A LEU* 2.8 28.4 + - + +
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TRP* 4.9 4.3 - - + -
125A LEU* 1.3 75.7 - - - +
127A LEU* 1.3 58.5 + - - +
128A ASN 3.7 0.4 + - - -
132A LYS 3.5 0.5 - - - +
133A LEU* 3.2 9.6 - - - +
134A VAL* 2.9 38.6 + - + +
136A LEU* 4.1 26.9 - - + -
144A PRO* 5.1 1.3 - - + -
150A GLY* 4.3 3.1 - - - -
151A ILE 3.2 22.7 - - - +
152A PRO* 4.4 2.2 - - + -
153A ILE* 4.1 5.2 - - - -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LYS* 3.9 11.9 - - - -
126A ALA* 1.3 71.4 - - - +
128A ASN* 1.3 71.1 + - - +
129A ASN* 5.1 1.0 + - - -
131A ASN* 3.3 33.0 - - - +
132A LYS 3.4 25.4 - - - +
133A LEU* 3.9 9.6 - - + +
150A GLY* 3.2 2.5 - - - -
151A ILE* 2.8 46.1 + - + +
153A ILE* 3.9 7.2 - - + +
191A LEU* 4.4 3.8 - - + -
194A ALA* 4.1 19.5 - - + +
195A MET* 3.7 32.3 - - + +
197A LYS* 5.8 2.9 - - + -
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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