Contacts of the helix formed by residues 117 - 131 (chain A) in PDB entry 1LWZ
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU* 4.0 6.3 - - - -
110A THR* 2.8 36.5 + - - +
115A ASP* 2.6 24.2 + - - -
116A GLY* 1.3 70.7 - - - +
118A HIS* 1.3 64.4 + - - +
119A ILE 3.8 1.1 - - - +
120A LYS* 3.2 35.3 + - - +
121A GLY* 3.5 8.5 + - - -
142A GLU* 5.4 0.5 + - - -
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Residues in contact with HIS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.6 10.6 + - - +
59A LYS* 6.4 2.0 - - + -
60A ILE* 5.5 9.2 - - + +
62A ASN 5.5 0.6 + - - -
63A VAL* 4.3 28.0 - - + +
64A ARG 5.5 4.7 - - - -
116A GLY* 2.7 32.9 + - - -
117A SER* 1.3 73.9 - - - +
119A ILE* 1.3 58.4 + - - +
122A LEU* 2.7 42.0 + - + +
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Residues in contact with ILE 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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29A LEU* 4.5 4.9 - - + -
30A THR 4.6 2.0 - - - +
31A GLU* 3.2 30.1 + - + +
56A LEU* 3.2 36.1 - - + -
76A GLU* 3.9 7.2 - - - +
108A ILE* 3.6 20.6 - - + -
110A THR* 3.3 28.5 - - + -
117A SER* 2.8 1.5 - - - -
118A HIS* 1.3 78.3 - - - +
120A LYS* 1.3 65.1 + - - +
122A LEU* 2.9 4.3 + - - -
123A LEU* 2.7 65.9 + - + +
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Residues in contact with LYS 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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108A ILE* 3.8 20.4 - - + -
110A THR* 4.8 1.3 - - + -
115A ASP* 5.1 5.4 - - - +
117A SER* 3.2 24.2 - - - +
119A ILE* 1.3 80.0 - - - +
121A GLY* 1.3 65.7 + - - +
123A LEU* 4.0 0.8 - - + +
124A ILE* 2.9 41.6 + - + +
140A LEU* 4.3 19.0 - - - +
141A GLU* 4.2 7.9 - - - +
142A GLU* 3.3 42.9 + - - +
144A ILE* 5.9 0.4 - - - +
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Residues in contact with GLY 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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117A SER 3.5 9.9 + - - -
118A HIS 4.5 0.4 - - - -
119A ILE 3.2 0.6 - - - -
120A LYS* 1.3 78.6 - - - +
122A LEU* 1.3 63.5 + - - +
124A ILE* 3.0 8.7 - - - +
125A ASN* 2.5 38.5 + - - +
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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
----------------------------------------------------------
73A GLU* 2.9 50.9 - - + +
76A GLU* 5.2 0.2 - - - +
118A HIS* 2.7 33.2 - - + +
119A ILE* 2.9 5.2 + - - +
121A GLY* 1.3 79.4 - - - +
123A LEU* 1.3 61.0 + - + +
125A ASN* 3.3 7.8 + - - +
126A PHE* 2.8 31.4 + - - +
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Residues in contact with LEU 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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29A LEU* 3.1 35.4 - - + -
73A GLU* 5.2 0.7 - - - +
76A GLU* 3.3 17.9 - - - +
80A ILE* 4.0 15.5 - - + -
106A ILE* 5.1 5.6 - - + -
108A ILE* 3.2 26.7 - - + -
119A ILE* 2.7 53.5 + - + +
120A LYS* 4.0 2.9 - - + +
122A LEU* 1.3 73.9 - - + +
124A ILE* 1.3 61.8 + - - +
126A PHE* 3.2 6.9 + - + +
127A ILE* 2.9 37.8 + - + +
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Residues in contact with ILE 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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120A LYS* 2.9 36.2 + - + +
121A GLY* 3.0 20.6 - - - +
123A LEU* 1.3 76.9 - - - +
125A ASN* 1.4 70.8 + - - +
127A ILE* 3.3 11.2 + - + +
128A HIS* 2.9 28.6 + - + +
135A LEU* 4.0 17.8 - - + +
140A LEU* 4.9 14.4 - - + -
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Residues in contact with ASN 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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121A GLY* 2.5 28.2 + - - +
122A LEU* 3.6 8.1 + - - +
124A ILE* 1.4 88.9 - - - +
126A PHE* 1.3 52.3 + - - +
128A HIS* 3.1 8.1 + - - +
129A HIS* 2.8 36.5 + - - +
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Residues in contact with PHE 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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73A GLU* 5.6 0.7 - - - +
77A ILE* 3.2 53.2 - - + -
80A ILE* 4.5 23.3 - - + -
81A ILE* 3.5 22.7 - - + -
86A LEU* 5.6 8.5 - - + -
122A LEU 2.8 18.8 + - - +
123A LEU* 3.6 4.5 - - + +
125A ASN* 1.3 73.1 - - - +
127A ILE* 1.3 76.6 + - + +
129A HIS* 4.7 2.5 - - - -
130A ASN* 2.8 84.0 + - + +
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Residues in contact with ILE 127 (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 ILE* 6.4 0.7 - - + -
106A ILE* 5.8 3.1 - - + -
123A LEU* 2.9 29.0 + - + +
124A ILE* 3.6 9.4 - - + +
126A PHE* 1.3 89.5 - - + +
128A HIS* 1.3 58.3 + - - +
130A ASN* 4.9 0.7 - - - -
131A TRP 2.8 43.7 + - - +
134A LEU* 4.0 20.0 - - + -
135A LEU* 2.9 29.8 - - + +
139A PHE* 4.1 27.1 - - + -
140A LEU* 4.9 11.2 - - + -
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Residues in contact with HIS 128 (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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124A ILE* 2.9 15.0 + - + +
125A ASN* 3.5 11.4 - - - +
127A ILE* 1.3 78.2 - - - +
129A HIS* 1.3 66.0 + - + +
132A PRO* 3.0 35.4 - - + +
135A LEU* 3.7 23.6 - - + +
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Residues in contact with HIS 129 (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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125A ASN 2.8 20.0 + - - +
126A PHE* 4.0 3.4 - - - +
128A HIS* 1.3 81.4 - - + +
130A ASN* 1.3 77.1 + - - +
132A PRO* 4.2 2.6 - - - +
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Residues in contact with ASN 130 (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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81A ILE* 5.6 1.2 - - - +
86A LEU* 6.1 1.1 - - + -
126A PHE* 2.8 72.3 + - + +
127A ILE* 4.3 0.9 - - - +
129A HIS* 1.3 86.1 + - - +
131A TRP* 1.4 97.0 + - + +
132A PRO* 3.7 1.3 - - - +
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Residues in contact with TRP 131 (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* 4.5 11.2 - - + -
87A GLN 4.6 2.8 + - - -
88A TYR* 3.0 18.8 - + + +
89A LYS* 2.8 61.8 - - + +
91A ASN* 5.1 15.0 - - + -
127A ILE* 2.8 22.2 + - - +
130A ASN* 1.4 101.7 + - + +
132A PRO* 1.3 74.0 - - + +
133A SER* 3.4 2.5 - - - +
134A LEU* 2.9 43.3 - - + +
135A LEU* 3.3 6.1 - - - +
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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