Contacts of the strand formed by residues 114 - 123 (chain A) in PDB entry 3WJG
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 SER 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TYR* 4.4 0.9 + - - -
108A TYR* 3.2 4.5 - - - +
109A ASN* 2.9 40.8 + - - +
112A GLU* 2.9 30.9 + - - +
113A GLN* 1.3 77.4 - - - +
115A ILE* 1.3 67.5 + - - +
116A LYS* 4.7 14.4 - - - +
135A PHE 3.2 12.8 - - - -
136A GLU* 4.5 8.7 - - - -
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Residues in contact with ILE 115 (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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23A LEU* 4.2 13.0 - - + -
25A TYR* 3.8 17.9 - - - +
26A LEU* 3.9 26.5 - - + -
82A PHE* 4.5 12.8 - - + -
90A ILE* 4.3 13.0 - - + -
107A THR 3.5 9.4 - - - +
108A TYR* 4.0 10.1 - - + -
114A SER* 1.3 79.7 - - - +
116A LYS* 1.3 66.1 + - - +
117A LEU* 4.0 29.8 - - + -
133A ARG 3.9 0.3 - - - +
134A GLU* 3.3 3.3 - - - -
135A PHE* 2.8 50.7 + - + +
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Residues in contact with LYS 116 (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 GLY* 3.2 4.2 - - - -
107A THR* 2.9 43.6 + - - +
112A GLU* 4.7 16.0 + - - -
114A SER* 4.7 10.3 - - - +
115A ILE* 1.3 80.4 - - - +
117A LEU* 1.3 60.5 + - - +
118A LYS* 5.9 0.4 - - - -
133A ARG 3.9 2.0 - - - -
134A GLU* 4.1 34.4 + - + +
135A PHE 5.4 0.4 - - - +
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Residues in contact with LEU 117 (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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82A PHE* 4.8 0.4 - - + -
90A ILE* 3.8 31.0 - - + +
92A VAL* 3.7 36.6 - - + -
104A GLN* 3.3 22.4 - - + +
105A LYS* 3.5 4.9 - - - -
106A GLY 3.9 10.5 - - - +
115A ILE* 4.0 14.4 - - + -
116A LYS* 1.3 77.3 - - - +
118A LYS* 1.3 63.4 + - - +
132A SER* 3.2 8.7 - - - -
133A ARG* 2.9 44.9 + - + +
134A GLU* 4.5 2.9 + - - +
135A PHE* 4.3 16.8 - - + -
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Residues in contact with LYS 118 (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 GLN* 2.8 7.6 + - - -
105A LYS* 2.9 31.0 + - - +
116A LYS 5.9 0.2 - - - -
117A LEU* 1.3 78.0 - - - +
119A SER* 1.4 66.4 + - - +
120A ASP* 3.4 1.2 + - - +
131A ILE 3.8 4.5 - - - +
132A SER* 4.3 10.1 - - - +
134A GLU* 5.9 2.0 - - - +
155A LEU* 5.9 7.9 - - + -
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Residues in contact with SER 119 (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 GLU* 5.4 0.4 - - - -
103A VAL 3.2 11.9 - - - -
104A GLN* 3.6 10.1 - - - -
118A LYS* 1.4 75.3 - - - +
120A ASP* 1.3 61.1 + - - +
121A LEU 3.9 14.9 + - - -
122A VAL* 3.7 9.4 - - - +
129A LYS 4.4 0.3 + - - -
130A GLU* 3.4 20.4 - - - +
131A ILE 2.9 37.4 + - - -
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Residues in contact with ASP 120 (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* 2.8 24.1 + - + +
105A LYS* 3.3 41.3 + - + +
118A LYS 3.4 2.9 + - - +
119A SER* 1.3 74.7 - - - +
121A LEU* 1.3 61.6 + - + +
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Residues in contact with LEU 121 (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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101A VAL* 4.3 11.9 - - + +
102A GLU* 3.5 2.9 - - - -
103A VAL* 2.9 52.1 + - + +
119A SER* 3.4 2.6 - - - -
120A ASP* 1.3 84.0 - - + +
122A VAL* 1.3 72.8 + - - +
123A GLY* 3.6 20.6 - - - +
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Residues in contact with VAL 122 (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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100A LEU* 4.4 4.9 - - + -
101A VAL 3.4 8.7 - - - +
102A GLU* 4.9 1.3 - - + -
119A SER* 3.7 16.4 - - - +
121A LEU* 1.3 84.1 - - - +
123A GLY* 1.3 60.7 + - - +
124A ASN 4.2 0.3 + - - -
125A ALA* 4.0 27.6 + - + +
128A VAL* 4.1 12.3 - - + +
129A LYS 3.6 25.1 + - - +
131A ILE* 3.9 34.1 - - + +
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Residues in contact with GLY 123 (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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100A LEU* 3.3 7.6 - - - +
101A VAL* 2.8 44.8 + - - -
121A LEU* 3.6 7.3 - - - +
122A VAL* 1.3 73.1 - - - +
124A ASN* 1.3 70.4 - - - +
125A ALA 3.2 3.1 - - - -
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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