Contacts of the strand formed by residues 101 - 111 (chain A) in PDB entry 4WNB
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ILE* 1.3 87.7 - - - +
102A VAL* 1.3 58.3 + - - -
166A LYS* 3.3 11.8 + - - -
167A PHE* 3.0 49.8 + - - -
169A PRO* 4.8 3.1 - - - -
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Residues in contact with VAL 102 (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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91A ILE* 4.8 4.3 - - + -
100A ILE 5.1 1.8 - - - +
101A GLY* 1.3 76.3 - - - +
103A VAL* 1.3 78.2 + - - +
164A ILE* 4.1 23.1 - - + -
165A LEU 3.3 8.1 - - - +
166A LYS* 3.7 25.8 - - + +
167A PHE* 3.3 6.4 - - - -
203A 4BN 3.9 53.6 - - + +
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Residues in contact with VAL 103 (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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102A VAL* 1.3 88.1 - - - +
104A ALA* 1.3 65.8 + - - +
105A THR* 4.6 1.8 - - + -
138A LEU* 3.6 31.4 - - + -
164A ILE* 3.3 2.5 - - - +
165A LEU* 2.8 42.8 + - + +
167A PHE* 4.0 9.2 - - + -
203A 4BN 3.6 45.5 - - + +
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Residues in contact with ALA 104 (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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102A VAL* 5.1 0.2 - - - +
103A VAL* 1.3 73.0 - - - +
105A THR* 1.3 60.1 + - - +
106A ASN 5.1 0.9 - - - +
162A TRP* 4.5 12.1 - - + -
163A ARG 3.7 9.2 - - - +
164A ILE* 4.1 11.1 - - + +
203A 4BN 2.8 51.3 + - + +
52B ILE* 3.8 13.2 - - + -
80B LEU* 3.5 18.9 - - + +
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Residues in contact with THR 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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103A VAL* 4.0 9.6 - - + +
104A ALA* 1.3 79.5 - - - +
106A ASN* 1.3 86.3 + - - +
143A PHE* 4.2 4.0 - - + -
163A ARG* 3.0 25.4 + - - +
165A LEU* 4.0 17.3 - - + +
203A 4BN 3.8 45.6 + - + +
79B ARG* 3.7 4.2 - - - +
80B LEU* 3.0 30.9 + - - +
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Residues in contact with ASN 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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104A ALA* 3.9 0.7 - - - +
105A THR* 1.3 105.1 + - - +
107A CYS* 1.3 61.9 + - - +
108A GLU* 4.3 2.0 - - + +
161A ASN 5.5 1.3 - - - +
162A TRP* 3.3 6.8 - - - +
163A ARG* 2.9 55.0 + - + +
203A 4BN 2.8 24.2 + - - -
78B LEU 3.3 13.4 + - - +
79B ARG* 4.1 15.8 - - - +
80B LEU* 4.3 4.1 - - - +
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Residues in contact with CYS 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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70A GLN* 4.9 2.5 - - - -
106A ASN* 1.3 77.2 - - - +
108A GLU* 1.3 55.9 + - - +
109A GLN* 4.3 13.2 - - - -
160A MET* 3.6 31.6 - - - -
161A ASN 3.8 3.1 - - - -
162A TRP* 4.2 6.5 - - + -
52B ILE* 4.4 26.5 - - + -
56B THR* 4.9 7.2 - - - -
76B ILE 3.7 2.4 - - - +
77B GLY* 3.6 1.2 - - - -
78B LEU* 2.7 46.4 + - + +
80B LEU* 5.1 3.8 - - + +
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Residues in contact with GLU 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 ASN* 5.5 1.5 - - + +
107A CYS* 1.3 74.6 - - - +
109A GLN* 1.3 68.5 + - - +
110A THR* 4.8 9.2 + - - +
159A GLU* 3.9 1.0 - - - +
160A MET* 3.2 2.5 - - - -
161A ASN* 2.9 51.8 + - + +
75B SER* 5.5 5.7 + - - -
76B ILE 3.5 3.1 - - - +
77B GLY* 4.0 14.4 - - - +
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Residues in contact with GLN 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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67A ALA* 4.3 4.9 - - - +
69A ILE* 3.9 11.1 - - + +
70A GLN* 3.1 36.6 + - - +
107A CYS* 4.3 9.1 - - - -
108A GLU* 1.3 78.6 - - - +
110A THR* 1.3 62.3 + - - +
111A TYR* 2.6 44.0 + - + +
150A TRP* 4.3 4.6 - - - -
159A GLU 3.2 6.1 - - - +
160A MET* 3.5 21.8 - - + -
53B LEU* 4.5 4.6 - - - +
56B THR* 3.7 15.8 + - + +
75B SER* 3.2 6.4 - - - -
76B ILE 2.8 36.0 + - - +
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Residues in contact with THR 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 GLU* 4.2 10.4 + - - +
109A GLN* 1.3 75.0 + - - +
111A TYR* 1.3 65.7 + - - +
112A HIS* 4.2 25.6 - - + +
158A ALA* 3.1 8.5 - - - +
159A GLU* 2.8 55.0 + - + +
74B LYS 3.7 9.2 - - - +
75B SER* 4.2 8.6 - - - -
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Residues in contact with TYR 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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66A PRO* 3.2 46.9 - - + -
67A ALA* 3.7 9.8 - - - -
69A ILE* 3.8 13.2 - - + -
109A GLN* 2.6 43.1 + - + +
110A THR* 1.3 77.3 - - - +
112A HIS* 1.3 64.3 + - - +
113A ARG* 3.4 11.7 + - - +
114A TYR* 6.0 0.9 - - + -
157A VAL 4.0 4.0 - - - +
158A ALA* 4.4 4.7 - - + -
56B THR* 3.8 9.4 - - - +
73B ILE* 3.7 35.9 - - + +
74B LYS* 2.9 35.8 + - - +
76B ILE* 3.9 20.5 - - + +
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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