Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 4BPW
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 LEU 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LYS 3.6 1.0 + - - -
105A GLU* 1.3 70.7 - - - +
107A VAL* 1.3 61.5 + - - +
108A PHE* 3.9 30.6 - - + -
152A PHE* 3.8 22.4 - - + -
167A CYS 3.5 2.9 - - - +
168A TRP* 3.7 0.7 - - - -
169A VAL* 2.9 37.4 + - + +
174A VAL* 3.5 20.5 - - + +
177A LEU* 4.9 1.8 - - + -
182A ARG* 3.8 40.1 - - + +
185A ILE* 3.7 26.0 - - + -
310A SER* 4.2 15.0 - - - +
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Residues in contact with VAL 107 (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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104A LYS* 3.5 31.2 - - - +
105A GLU 3.6 5.6 - - - +
106A LEU* 1.3 81.2 - - - +
108A PHE* 1.3 59.5 + - - +
167A CYS 3.3 2.7 - - - -
168A TRP* 3.5 35.9 - - + -
309A VAL* 3.3 30.0 - - + +
310A SER* 2.5 33.6 + - - +
312A GLY 5.7 0.4 - - - +
315A HIS* 4.9 2.0 - - + -
317A LEU* 3.8 16.2 - - + -
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Residues in contact with PHE 108 (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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106A LEU* 3.9 32.1 - - + -
107A VAL* 1.3 76.4 - - - +
109A ASP* 1.3 61.0 + - - +
110A ILE* 4.2 6.3 - - + -
142A ILE* 4.9 5.2 - - + -
146A LEU* 3.8 32.8 - - + -
157A TRP* 5.4 1.6 - - + -
165A VAL 4.0 0.4 - - - +
166A HIS* 3.1 11.1 - - - +
167A CYS* 3.0 48.6 + - + +
169A VAL* 4.3 1.8 - - + -
185A ILE* 4.2 5.2 - - + -
186A VAL* 4.3 10.8 - - + -
189A LEU* 3.8 29.2 - - + -
305A LEU* 4.3 26.7 - - + -
309A VAL* 4.5 1.6 - - - -
310A SER* 3.4 22.4 - - - -
317A LEU* 4.5 1.2 - - - +
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Residues in contact with ASP 109 (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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108A PHE* 1.3 74.7 - - - +
110A ILE* 1.3 64.4 + - - +
111A ASP* 2.9 21.5 + - - +
165A VAL 4.0 1.3 - - - -
166A HIS* 2.9 19.4 + - + -
304A ARG 4.5 0.2 - - - +
305A LEU* 4.3 4.2 - - - +
306A ASP* 3.9 22.2 + - - +
309A VAL* 3.8 29.0 - - + +
310A SER* 4.9 0.4 + - - -
317A LEU* 4.5 3.8 - - + -
1412A MG 2.9 20.6 - - - -
1413A MG 2.8 5.4 - - - -
1414A UTP 2.7 33.9 + - - -
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Residues in contact with ILE 110 (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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108A PHE* 5.0 4.5 - - + -
109A ASP* 1.3 78.9 - - - +
111A ASP* 1.3 64.7 + - - +
115A TYR* 4.0 15.5 - - + +
135A MET* 3.5 25.5 - - + +
138A ALA* 4.0 15.9 - - + -
142A ILE* 3.7 28.0 - - + -
157A TRP* 4.0 24.2 - - + -
164A GLY* 3.3 24.8 - - - -
165A VAL* 3.2 17.8 + - + +
303A PRO* 5.0 0.2 - - + -
304A ARG 3.9 14.6 - - - +
305A LEU* 3.5 16.6 - - + -
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Residues in contact with ASP 111 (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 ASP* 2.9 12.3 + - - +
110A ILE* 1.3 73.5 - - - +
112A MET* 1.3 64.5 + - - +
113A THR 4.1 4.0 - - - +
114A ASP* 3.1 37.0 + - - +
115A TYR* 3.4 11.3 - - - -
135A MET* 3.7 3.4 - - - -
163A ARG* 3.3 28.1 + - - +
304A ARG 4.7 1.8 + - - -
306A ASP* 5.2 1.9 - - - +
1412A MG 3.1 21.7 - - - -
1413A MG 2.4 31.6 - - - -
1414A UTP 3.1 2.7 + - - -
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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