Contacts of the strand formed by residues 119 - 126 (chain A) in PDB entry 1LWS
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLN* 3.8 35.2 - - + +
112A LYS 4.1 6.3 - - - +
113A LYS* 4.4 23.1 - - + +
117A GLY 2.8 26.0 - - - +
118A ARG* 1.3 73.6 - - - +
120A VAL* 1.3 62.4 + - - +
121A GLU 4.1 0.7 + - - -
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Residues in contact with VAL 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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111A GLN* 3.6 4.3 - - - +
112A LYS 3.5 33.5 + - - +
114A ALA* 4.6 2.0 - - + -
118A ARG* 3.8 23.3 - - + +
119A ILE* 1.3 77.0 - - - +
121A GLU* 1.3 63.9 + - - +
122A LEU* 3.6 23.5 - - + +
159A ILE* 6.4 0.7 - - + -
163A ASP* 3.3 33.2 - - + +
166A LEU* 3.7 17.5 - - + -
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Residues in contact with GLU 121 (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 MSE 4.0 23.0 - - + +
110A GLY 3.4 9.0 - - - +
111A GLN* 4.7 11.0 - - + +
119A ILE 4.1 1.6 + - - -
120A VAL* 1.3 74.1 - - - +
122A LEU* 1.3 73.8 + - - +
157A TRP* 4.4 10.2 + - + -
158A THR 4.8 3.3 - - - +
159A ILE* 5.3 3.3 - - - +
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Residues in contact with LEU 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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109A MSE 2.9 17.3 - - - +
110A GLY 2.7 42.4 + - - +
111A GLN 4.4 4.9 - - - -
112A LYS* 4.4 6.3 - - + -
120A VAL* 3.6 27.8 - - + +
121A GLU* 1.3 76.6 - - - +
123A VAL* 1.3 64.4 + - - +
124A LYS* 3.7 27.4 - - + -
157A TRP* 3.9 17.7 - - + +
159A ILE* 4.8 14.1 - - + -
166A LEU* 4.5 24.5 - - + +
167A LEU* 4.7 9.4 - - + -
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Residues in contact with VAL 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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85A THR* 4.4 2.9 - - + -
107A PHE* 3.9 16.6 - - + -
108A GLU 2.9 32.3 - - - +
109A MSE 4.3 8.3 - - - -
122A LEU* 1.3 81.6 - - - +
124A LYS* 1.3 67.8 + - - +
155A PHE* 4.2 13.0 - - + -
157A TRP* 3.3 44.1 - - + -
167A LEU* 3.8 15.1 - - - +
168A GLY 4.8 2.4 + - - -
171A VAL* 3.6 21.9 - - + +
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Residues in contact with LYS 124 (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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107A PHE* 3.7 0.6 - - - -
108A GLU* 2.9 31.7 + - - +
110A GLY* 5.1 4.3 - - - -
111A GLN 3.3 25.8 + - - +
112A LYS* 3.2 32.3 - - + +
122A LEU* 3.7 13.0 - - + +
123A VAL* 1.3 81.8 - - - +
125A GLU* 1.3 66.6 + - - +
126A VAL* 3.5 9.3 + - + +
166A LEU 6.1 1.3 - - - +
171A VAL* 4.0 7.6 - - - -
8C C 3.1 33.2 + - - -
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Residues in contact with GLU 125 (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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90A ARG* 3.8 2.7 + - - +
105A ILE* 2.8 42.6 - - + +
106A THR 3.4 7.0 - - - +
107A PHE* 4.6 7.6 - - + -
124A LYS* 1.3 74.2 - - - +
126A VAL* 1.3 61.3 + - - +
127A SER* 4.1 3.7 + - - -
170A HIS* 2.9 40.1 + - + +
171A VAL* 3.8 16.3 - - + +
7C T 4.7 11.4 + - - +
8C C 4.6 31.1 + - - +
9C A 5.6 2.4 + - - +
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Residues in contact with VAL 126 (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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105A ILE* 3.4 3.0 - - - -
106A THR 2.6 25.0 + - - +
108A GLU* 2.8 39.7 - - + +
124A LYS* 4.0 13.5 - - + +
125A GLU* 1.3 79.6 - - - +
127A SER* 1.3 60.8 + - - +
128A LYS* 2.6 41.3 - - + +
7C T 4.1 13.0 - - - +
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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