Contacts of the helix formed by residues 110 - 130 (chain A) in PDB entry 1IL6
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 GLU 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A GLN 4.2 13.4 - - - +
104A ASN* 3.3 21.5 - - - +
106A PHE* 2.7 28.0 + - - +
107A GLU* 4.3 13.0 - - - +
108A SER 3.3 3.2 + - - -
109A SER* 1.3 77.5 - - - +
111A GLU* 1.3 62.4 + - - +
113A ALA* 3.2 3.1 + - - +
114A ARG* 3.0 28.7 + - - +
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Residues in contact with GLU 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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109A SER* 2.9 1.9 + - - -
110A GLU* 1.3 79.2 - - - +
112A GLN* 1.3 65.4 + - + +
114A ARG* 3.0 12.2 + - + +
115A ALA* 3.0 19.3 + - - +
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Residues in contact with GLN 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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35A ASP 4.9 1.0 - - - +
36A GLY* 4.5 10.0 - - - +
39A ALA* 3.0 28.6 - - + +
40A LEU* 3.4 21.7 - - + +
109A SER* 2.8 34.9 + - - +
111A GLU* 1.3 75.9 - - + +
113A ALA* 1.3 61.6 + - - +
115A ALA* 2.9 21.3 + - - +
116A VAL 3.3 9.0 + - - -
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Residues in contact with ALA 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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40A LEU* 3.2 12.7 - - - +
102A LEU 2.7 30.8 - - - +
103A GLN* 4.5 8.0 - - - +
106A PHE* 3.5 24.5 - - + -
109A SER 3.2 3.6 + - - -
110A GLU* 3.2 9.8 + - - +
112A GLN* 1.3 78.2 - - - +
114A ARG* 1.3 60.4 + - - +
116A VAL* 3.1 20.8 - - - +
117A GLN* 3.2 10.0 + - - +
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Residues in contact with ARG 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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103A GLN* 5.5 14.6 + - + +
110A GLU* 3.0 18.6 + - + +
111A GLU* 3.0 14.0 + - + +
113A ALA* 1.3 75.2 - - - +
115A ALA* 1.3 59.3 + - - +
117A GLN* 3.9 14.1 - - - +
118A MET* 2.8 65.3 + - + +
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Residues in contact with ALA 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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32A TYR* 4.8 14.8 - - + +
36A GLY* 5.1 6.5 - - - -
111A GLU 3.0 10.1 + - - +
112A GLN* 2.9 22.5 + - - +
114A ARG* 1.3 80.8 - - - +
116A VAL* 1.3 58.2 + - - +
118A MET* 4.5 1.7 - - - +
119A SER* 3.6 20.4 + - - -
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Residues in contact with VAL 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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33A ILE* 3.1 39.4 - - + +
36A GLY* 4.3 3.4 - - - -
37A ILE* 3.4 22.2 - - + -
40A LEU* 2.9 30.7 - - + -
99A LEU* 4.0 15.3 - - + -
102A LEU* 5.4 6.3 - - + -
112A GLN 3.3 2.8 + - - +
113A ALA* 3.1 12.6 - - + +
115A ALA* 1.3 79.5 - - - +
117A GLN* 1.3 60.4 + - + +
119A SER* 3.9 0.7 + - - -
120A THR* 2.7 41.8 + - + +
171A PHE* 4.5 0.2 - - + -
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Residues in contact with GLN 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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96A GLU* 3.4 20.4 + - - +
99A LEU* 3.8 33.2 - - + +
103A GLN* 3.2 38.9 + - + +
113A ALA 3.2 12.7 + - - +
114A ARG* 4.3 12.5 - - - +
116A VAL* 1.3 78.6 - - - +
118A MET* 1.3 72.8 + - - +
120A THR* 2.4 22.1 + - - +
121A LYS* 2.9 24.2 + - + +
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Residues in contact with MET 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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114A ARG* 2.8 54.0 + - + +
115A ALA* 4.9 2.2 - - - +
117A GLN* 1.3 83.0 - - - +
119A SER* 1.3 62.2 + - - +
121A LYS* 3.2 8.4 + - - +
122A VAL* 3.0 25.9 + - + +
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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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29A GLN* 3.4 19.8 + - - -
32A TYR* 3.7 15.7 - - - +
33A ILE* 3.9 19.7 - - - -
115A ALA 3.6 19.6 + - - -
116A VAL 4.1 0.7 - - - -
117A GLN 3.1 0.8 - - - -
118A MET* 1.3 76.3 - - - +
120A THR* 1.3 53.1 + - - +
121A LYS 2.9 4.5 - - - -
122A VAL* 2.7 22.5 + - - +
123A LEU* 2.7 28.5 - - - +
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Residues in contact with THR 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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33A ILE* 3.1 41.7 - - + +
92A LEU* 4.2 8.9 - - + +
99A LEU* 2.9 27.1 - - + +
116A VAL 2.7 21.1 + - - +
117A GLN* 2.4 21.3 + - - +
119A SER* 1.3 75.1 - - - +
121A LYS* 1.3 58.1 + - - +
123A LEU* 3.7 4.5 + - - +
124A ILE* 3.1 27.4 + - - +
171A PHE* 3.6 19.3 - - + -
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Residues in contact with LYS 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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96A GLU* 3.9 36.6 + - + +
117A GLN* 2.9 25.3 + - - +
118A MET* 3.4 11.0 - - - +
119A SER 2.9 0.8 - - - -
120A THR* 1.3 76.2 - - - +
122A VAL* 1.3 67.1 + - - +
123A LEU 3.0 1.8 - - - -
124A ILE* 3.0 23.6 + - + +
125A GLN* 3.1 21.0 + - - +
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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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29A GLN* 4.1 24.0 - - + +
118A MET* 3.0 17.9 + - + +
119A SER* 2.7 17.2 + - - +
121A LYS* 1.3 79.2 - - - +
123A LEU* 1.3 56.9 + - + +
125A GLN* 5.1 1.3 - - - -
126A PHE* 2.7 69.7 + - + +
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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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26A ILE* 3.2 34.8 - - + +
29A GLN* 3.1 39.5 - - + -
30A ILE* 3.5 16.4 - - + -
33A ILE* 3.7 13.7 - - + -
92A LEU* 3.9 19.7 - - + -
119A SER* 2.7 33.9 - - - +
120A THR 3.9 3.4 - - - +
121A LYS 3.0 0.6 - - - -
122A VAL* 1.3 81.6 - - + +
124A ILE* 1.3 65.1 + - - +
126A PHE* 4.2 1.6 - - + -
127A LEU* 2.9 34.5 + - + +
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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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89A ILE* 5.2 6.1 - - + +
92A LEU* 3.7 39.5 - - + +
93A LEU* 3.7 27.8 - - + +
96A GLU* 3.9 22.0 - - + -
120A THR* 3.1 20.9 - - - +
121A LYS* 3.0 20.8 + - + +
123A LEU* 1.3 77.5 - - - +
125A GLN* 1.3 63.4 + - + +
127A LEU* 4.0 3.3 - - - +
128A GLN* 3.3 33.5 + - - +
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Residues in contact with GLN 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 LYS* 3.1 18.3 + - - +
122A VAL* 5.1 0.9 - - - -
124A ILE* 1.3 78.2 - - + +
126A PHE* 1.3 77.9 + - + +
127A LEU 3.0 3.1 + - - -
128A GLN* 4.5 6.1 - - + +
129A LYS* 3.0 50.0 + - + +
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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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22A SER* 5.7 2.2 - - - -
25A ARG* 4.8 26.7 - - + -
26A ILE* 3.5 20.4 - - + -
29A GLN* 5.1 10.3 - - + -
122A VAL* 2.7 54.1 + - + +
123A LEU* 4.1 0.9 - - + +
125A GLN* 1.3 84.7 - - + +
127A LEU* 1.3 51.7 + - - +
129A LYS* 4.3 7.6 - - + +
130A LYS* 2.6 40.5 + - + +
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Residues in contact with LEU 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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26A ILE* 3.3 35.2 - - + -
85A LEU* 4.2 17.7 - - + -
88A ILE* 4.2 11.0 - - + -
89A ILE* 3.7 33.2 - - + -
92A LEU* 4.1 22.7 - - + -
123A LEU* 2.9 23.5 + - + +
124A ILE* 4.0 3.6 - - - +
126A PHE* 1.3 76.8 - - - +
128A GLN* 1.3 53.4 + - - +
129A LYS 2.9 4.5 - - - -
130A LYS* 3.6 19.3 - - - -
131A ALA* 2.6 43.5 + - + +
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Residues in contact with GLN 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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89A ILE* 4.4 8.0 - - + +
93A LEU* 4.6 15.8 - - - +
124A ILE* 3.3 22.1 + - - +
125A GLN* 4.1 6.9 - - - +
127A LEU* 1.3 79.8 - - - +
129A LYS* 1.3 63.9 + - + +
131A ALA* 4.1 10.6 + - - +
136A ALA* 4.1 35.9 + - + +
138A THR 4.4 8.7 + - - -
139A THR* 5.1 3.0 - - - -
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Residues in contact with LYS 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 GLN* 3.0 42.3 + - + +
126A PHE* 4.3 7.8 - - + +
127A LEU 2.8 1.2 + - - -
128A GLN* 1.3 81.6 - - + +
130A LYS* 1.3 57.9 + - + +
131A ALA 3.1 7.8 + - - -
132A LYS 4.7 1.6 + - - -
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Residues in contact with LYS 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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22A SER* 3.5 38.1 - - - +
23A SER* 3.8 26.3 + - - +
26A ILE* 4.0 10.3 - - + -
85A LEU* 4.2 16.2 - - - +
126A PHE* 2.6 27.5 + - + +
127A LEU* 3.6 24.9 - - - -
129A LYS* 1.3 77.0 - - + +
131A ALA* 1.3 56.9 + - - +
132A LYS* 2.9 27.1 + - + +
182A LEU* 5.3 1.1 - - - +
185A MET* 6.3 0.2 - - - -
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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
------------------------------------------------------------
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