Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 1B54
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 ILE 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ALA* 4.7 1.6 - - - -
108A LEU* 3.6 33.0 - - + +
109A TYR 3.9 4.7 - - - +
110A SER* 3.7 14.8 - - - -
111A VAL* 3.8 18.2 - - + +
123A LEU* 4.1 22.7 - - + -
127A ARG* 3.3 42.4 - - + +
135A ASN 3.5 0.8 + - - -
136A PRO* 1.3 70.5 - - - +
138A LEU* 1.3 71.3 + - - +
139A CYS* 3.5 4.5 + - - -
174A TYR 3.0 6.3 + - - -
175A ILE* 3.2 11.3 - - + +
176A LYS 2.7 28.6 + - - -
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Residues in contact with LEU 138 (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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109A TYR* 3.0 51.4 + - + +
110A SER* 3.0 13.4 - - - -
111A VAL 2.9 23.7 + - - -
136A PRO 3.2 8.7 + - - +
137A ILE* 1.3 74.6 - - - +
139A CYS* 1.3 58.3 + - - +
176A LYS* 3.4 41.5 - - + +
178A ASN* 4.0 29.2 - - + +
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Residues in contact with CYS 139 (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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110A SER* 5.6 0.2 - - - -
111A VAL* 3.2 13.5 - - - +
114A ILE* 4.0 11.7 - - + -
123A LEU* 3.8 28.5 - - - -
137A ILE* 3.8 9.9 - - - -
138A LEU* 1.3 80.6 - - - +
140A ASN* 1.3 64.1 + - - +
167A PHE* 3.6 21.8 - - + -
175A ILE* 3.9 12.8 - - - -
176A LYS 2.6 14.6 + - - +
177A LEU* 3.6 3.7 - - - +
178A ASN* 2.6 33.6 + - - +
179A GLY 3.3 0.7 + - - +
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Residues in contact with ASN 140 (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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110A SER* 4.9 1.5 + - - -
111A VAL 3.0 5.9 + - - +
112A GLU* 3.2 50.1 - - + +
114A ILE* 3.3 27.1 + - - +
139A CYS* 1.3 76.9 + - - +
141A VAL* 1.3 61.8 + - - +
178A ASN* 3.3 15.1 + - - +
179A GLY* 2.7 44.6 - - - +
180A LEU 3.7 6.9 - - - +
181A MET* 3.9 8.7 - - + -
218A LYS* 4.1 3.6 + - - +
220A SER* 3.8 6.5 - - - -
237A GLU* 4.3 3.6 - - - +
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Residues in contact with VAL 141 (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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114A ILE* 3.4 6.5 - - + +
140A ASN* 1.3 73.6 - - - +
142A GLN* 1.3 61.8 + - - +
143A ILE* 3.5 18.9 + - + +
154A LEU* 3.8 27.1 - - + -
160A ILE* 4.9 7.6 - - + -
163A VAL* 4.1 19.7 - - + -
164A ILE* 3.9 12.8 - - + -
167A PHE* 4.3 5.8 - - + -
177A LEU* 3.8 24.7 - - + -
179A GLY 2.8 13.1 + - - +
180A LEU* 3.4 13.2 - - + +
181A MET 2.8 22.9 + - - -
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Residues in contact with GLN 142 (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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112A GLU 3.9 10.5 - - - +
113A THR* 3.4 34.8 - - - +
114A ILE 2.9 12.7 + - - +
115A ASP* 3.8 11.4 - - + +
140A ASN 3.7 2.6 + - - -
141A VAL* 1.3 72.0 - - - +
143A ILE* 1.3 67.0 + - - +
144A ASN* 6.1 0.4 - - - +
152A SER* 3.6 31.8 + - - -
153A GLY* 3.4 13.5 + - - +
154A LEU* 3.0 21.1 + - - +
181A MET* 3.3 26.5 - - - +
182A THR* 4.7 0.2 - - - -
183A ILE* 4.0 27.7 - - - +
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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