Contacts of the strand formed by residues 104 - 110 (chain A) in PDB entry 1WBP
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 LYS 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ARG* 5.4 1.2 - - - +
98A TRP* 3.6 10.5 - - - -
99A ASP* 2.8 49.2 + - + +
102A GLY* 2.7 22.9 + - - +
103A LYS* 1.3 73.8 - - - +
105A PHE* 1.3 69.4 + - - +
106A VAL* 4.0 12.3 - - + -
148A LEU* 4.0 24.4 - - - +
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Residues in contact with PHE 105 (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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83A ILE* 4.1 17.3 - - + -
96A LEU* 3.9 15.3 - - + -
97A SER 3.8 14.8 - - - -
98A TRP* 3.7 33.2 - + + -
104A LYS* 1.3 76.7 - - - +
106A VAL* 1.3 70.4 + - - +
166A GLU* 5.0 1.7 - - - -
167A VAL* 3.8 11.8 + - + +
228A ILE* 3.6 32.5 - - + +
229A ARG* 4.5 19.5 - - + -
232A ALA* 3.6 30.7 - - + -
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Residues in contact with VAL 106 (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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80A TYR* 4.0 15.5 - - + -
96A LEU* 3.6 10.0 - - - +
97A SER* 3.0 49.9 + - - +
99A ASP* 4.1 12.3 - - + +
104A LYS* 4.0 20.0 - - + -
105A PHE* 1.3 83.0 - - - +
107A ALA* 1.3 61.9 + - - +
108A MET* 4.8 0.9 - - + +
148A LEU* 4.0 18.6 - - + -
164A VAL* 3.7 20.9 - - + -
165A PHE 3.6 9.4 - - - +
167A VAL* 4.0 9.0 - - - +
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Residues in contact with ALA 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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86A LEU* 4.1 6.5 - - + -
94A VAL* 3.9 11.9 - - + -
95A TRP 3.3 5.4 - - - -
106A VAL* 1.3 74.3 - - - +
108A MET* 1.3 61.8 + - - +
109A LYS 3.7 1.0 + - - -
163A MET 3.7 1.0 - - - +
164A VAL* 3.6 2.1 - - - -
165A PHE* 2.7 43.6 + - + +
166A GLU 3.8 2.9 - - - +
167A VAL* 4.4 2.9 - - - +
950A ADP 3.7 35.7 - - + +
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Residues in contact with MET 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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70A VAL* 4.6 0.9 - - + -
76A PHE* 4.1 16.6 - - + -
80A TYR* 4.3 16.4 - - + -
82A VAL* 3.4 33.2 - - + -
93A THR 3.6 0.5 - - - +
94A VAL* 3.4 3.1 - - - -
95A TRP* 2.7 57.0 + - + +
97A SER* 3.6 16.4 - - - +
106A VAL* 4.0 1.5 - - + -
107A ALA* 1.3 70.3 - - - +
109A LYS* 1.3 63.5 + - - +
110A VAL* 3.5 17.4 + - + -
151A PHE* 4.0 27.1 - - + -
153A ILE* 6.6 0.2 - - - -
162A CYS* 4.8 2.2 - - + -
163A MET 3.6 6.1 - - - +
164A VAL* 4.7 9.9 - - + +
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Residues in contact with LYS 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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92A SER* 3.6 24.7 - - - +
93A THR 3.5 4.3 - - - -
94A VAL* 4.1 15.0 - - + +
107A ALA 3.7 2.0 + - - -
108A MET* 1.3 69.9 - - - +
110A VAL* 1.3 60.9 + - - +
111A VAL* 4.8 4.3 - - + +
124A GLU* 3.5 31.3 + - - -
161A ILE 3.8 1.0 - - - +
162A CYS* 3.1 6.9 - - - +
163A MET* 2.8 61.5 + - + +
165A PHE* 4.1 24.0 - - + -
497A ASP* 5.4 7.5 + - - -
950A ADP 3.2 23.7 + - - +
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Residues in contact with VAL 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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69A LEU* 4.8 0.4 - - + -
70A VAL* 4.3 15.3 - - + -
92A SER* 3.7 1.4 - - - -
93A THR* 2.7 34.7 + - - +
95A TRP* 3.9 27.1 - - + +
108A MET* 4.0 18.4 - - + +
109A LYS* 1.3 75.7 - - - +
111A VAL* 1.3 69.1 + - - +
112A LYS* 3.6 1.7 + - - +
153A ILE* 4.1 22.4 - - + -
160A HIS* 4.1 14.1 - - + +
161A ILE 3.7 2.9 - - - -
162A CYS* 4.2 10.3 - - - -
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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