Contacts of the helix formed by residues 110 - 122 (chain A) in PDB entry 1L9X
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 CYS 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLY* 3.9 2.9 - - - -
74A GLY 5.1 7.4 - - - -
109A THR* 1.3 68.0 - - - +
111A LEU* 1.3 69.0 + - - +
113A PHE* 2.9 13.9 + - - +
114A GLU* 3.0 19.9 + - - +
170A PHE 3.9 17.3 - - - -
171A HIS* 4.0 6.5 - - - -
217A VAL 2.8 14.0 + - - -
218A GLN* 3.6 34.9 + - - +
220A HIS* 3.3 35.4 - - + +
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Residues in contact with LEU 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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17A GLN* 3.7 22.4 - - - +
72A PRO 3.5 5.8 - - - +
74A GLY* 3.4 30.5 - - - +
75A SER* 4.8 0.2 - - - -
76A VAL* 3.7 30.7 - - + +
78A LEU* 3.5 28.9 - - + -
83A TYR* 3.6 31.2 - - + +
109A THR 2.9 1.4 + - - -
110A CYS* 1.3 81.3 - - - +
112A GLY* 1.3 58.8 + - - +
114A GLU* 3.2 13.8 + - - +
115A GLU* 2.9 27.2 + - - +
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Residues in contact with GLY 112 (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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71A PHE* 3.4 29.5 - - - -
83A TYR* 3.6 11.2 + - - -
108A GLY* 3.6 6.9 - - - -
109A THR 2.9 8.4 + - - -
111A LEU* 1.3 77.0 - - - +
113A PHE* 1.3 59.2 + - - +
115A GLU* 3.4 4.9 + - - +
116A LEU* 3.0 32.6 + - - +
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Residues in contact with PHE 113 (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 GLY* 3.6 9.8 - - - +
110A CYS* 2.9 10.2 + - - +
112A GLY* 1.3 73.4 - - - +
114A GLU* 1.3 71.8 + - + +
116A LEU* 3.1 10.1 + - - +
117A SER* 3.0 20.3 + - - -
126A LEU* 6.5 0.2 - - + -
175A LEU* 4.0 22.2 - - + -
204A ILE* 3.5 36.8 - - + -
205A SER 4.4 2.7 - - - -
207A MET* 3.6 37.3 - - + +
216A GLY* 3.5 26.7 - - - -
217A VAL 3.4 24.0 - - - +
218A GLN* 3.4 27.4 - - + -
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Residues in contact with GLU 114 (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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78A LEU* 3.8 18.4 - - + +
110A CYS* 3.0 15.0 + - - +
111A LEU* 3.6 14.1 - - - +
113A PHE* 1.3 80.9 - - + +
115A GLU* 1.3 60.9 + - - +
117A SER* 2.8 25.3 + - - -
118A LEU* 3.2 9.0 + - - +
126A LEU* 4.0 32.9 - - + +
171A HIS* 4.2 5.4 - - - +
173A TRP* 3.4 22.4 - - - +
218A GLN* 3.1 31.4 + - - +
1001A BME 5.7 0.9 - - - -
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Residues in contact with GLU 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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71A PHE* 4.4 5.6 - - + -
78A LEU* 3.3 34.5 - - + +
83A TYR* 4.4 6.3 - - + -
84A ALA* 3.7 26.4 - - - +
87A ALA* 3.7 23.0 - - + +
111A LEU 2.9 16.9 + - - +
112A GLY* 3.6 9.6 - - - +
113A PHE 3.2 0.2 - - - -
114A GLU* 1.3 77.0 - - - +
116A LEU* 1.3 57.1 + - - +
118A LEU* 3.2 13.2 + - - +
119A LEU* 2.9 61.7 + - + +
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Residues in contact with LEU 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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71A PHE* 4.0 24.7 - - + -
91A TYR* 4.5 7.4 - - + -
106A VAL* 4.2 5.8 - - + -
107A TRP 4.8 0.7 - - - -
108A GLY* 4.0 10.3 - - - +
112A GLY 3.0 20.3 + - - +
113A PHE* 3.1 7.1 + - - +
115A GLU* 1.3 74.6 - - - +
117A SER* 1.3 63.7 + - - +
119A LEU* 3.1 11.3 + - + -
120A ILE* 2.9 31.4 + - + +
190A PHE* 4.5 14.4 - - + -
207A MET* 5.0 3.1 - - + -
214A VAL* 3.7 28.0 - - + -
215A TYR 3.3 29.4 - - - +
216A GLY* 4.3 5.4 - - - -
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Residues in contact with SER 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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113A PHE* 3.0 13.5 + - - -
114A GLU* 2.8 22.5 + - - -
116A LEU* 1.3 75.4 - - - +
118A LEU* 1.3 52.6 + - - +
121A SER* 2.7 41.3 + - - -
123A GLU 4.5 2.7 + - - -
124A CYS* 6.1 0.2 - - - -
125A LEU* 5.4 3.2 + - - +
126A LEU* 4.5 12.3 - - - +
175A LEU* 4.0 31.8 - - - +
186A LEU* 3.8 14.5 - - - +
207A MET* 4.8 6.2 - - - +
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Residues in contact with LEU 118 (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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78A LEU* 3.2 41.3 - - + +
79A ARG* 5.2 6.1 - - + -
114A GLU 3.2 8.2 + - - +
115A GLU* 3.4 17.5 - - - +
116A LEU 3.1 0.2 - - - -
117A SER* 1.3 80.4 + - - +
119A LEU* 1.3 59.8 + - + +
122A GLY* 2.7 39.4 + - - +
123A GLU* 3.4 35.4 - - - +
124A CYS* 4.2 4.3 - - + +
1001A BME 4.7 11.2 - - - -
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Residues in contact with LEU 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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71A PHE* 4.5 1.6 - - + -
87A ALA 4.2 7.4 - - - +
88A LYS* 3.8 35.2 - - + -
91A TYR* 3.7 46.3 + - + -
115A GLU* 2.9 51.9 + - + +
116A LEU* 3.1 14.1 + - + +
118A LEU* 1.3 80.9 - - + +
120A ILE* 1.3 66.6 + - + +
122A GLY* 4.1 3.6 + - - -
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Residues in contact with ILE 120 (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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91A TYR* 3.4 39.9 - - + +
116A LEU* 2.9 25.9 + - + +
119A LEU* 1.3 81.9 - - + +
121A SER* 1.3 62.9 + - - +
185A LYS* 3.5 41.6 + - + +
186A LEU* 3.8 15.0 - - + -
189A PHE* 3.7 27.4 - - + -
190A PHE* 3.6 25.6 - - + -
214A VAL* 4.8 1.6 - - + -
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Residues in contact with SER 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 2.7 23.7 + - - -
120A ILE* 1.3 78.8 - - - +
122A GLY* 1.3 59.5 + - - +
123A GLU* 3.0 34.4 + - - +
125A LEU* 4.2 5.0 - - - +
183A ASN* 3.6 26.9 + - - -
185A LYS* 3.7 27.0 + - - +
186A LEU* 3.7 13.0 - - - +
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Residues in contact with GLY 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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118A LEU* 2.7 30.5 + - - +
119A LEU 4.7 3.1 - - - -
120A ILE 3.4 2.0 - - - -
121A SER* 1.3 73.7 - - - +
123A GLU* 1.3 61.9 + - - +
185A LYS* 5.6 2.7 - - - -
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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