Contacts of the helix formed by residues 102 - 122 (chain B) in PDB entry 4ADV
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 ASN 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1073A U 2.5 47.5 + - - -
1074A G 2.6 31.8 + - - +
1102A A 4.3 6.3 + - - -
1103A C 4.4 1.0 + - - -
97B GLY 4.7 1.9 + - - +
98B GLY* 2.8 23.7 + - - +
101B THR* 1.3 73.4 - - - +
103B TRP* 1.3 65.3 + - - +
104B LYS* 2.9 11.3 + - - +
105B THR* 2.9 26.7 + - + +
106B VAL* 2.9 12.3 - - + +
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Residues in contact with TRP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY 2.8 9.3 + - - +
99B MET* 4.0 22.4 - - + -
100B LEU* 4.6 6.1 - - - +
101B THR 3.1 5.8 + - - +
102B ASN* 1.3 76.7 - - - +
104B LYS* 1.3 72.1 + - + +
106B VAL* 2.8 8.4 + - + -
107B ARG* 2.7 66.7 + - + -
110B ILE* 4.2 14.1 - - + +
150B ILE* 5.6 5.1 + - + +
153B MET* 3.1 39.3 + - - +
154B GLY* 4.3 15.0 - - - -
155B GLY* 4.1 11.1 - - - +
156B LEU* 4.5 27.6 - - + -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A U 2.5 51.1 + - - -
1074A G 2.9 22.1 + - - -
101B THR 3.9 7.4 - - - +
102B ASN* 2.9 15.4 + - - +
103B TRP* 1.3 88.1 - - + +
105B THR* 1.3 56.5 + - - +
107B ARG* 3.3 8.6 + - - +
108B GLN* 3.2 23.4 + - - -
64E GLU* 4.1 27.2 - - + +
65E LYS* 4.3 4.8 - - + +
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A G 3.5 17.5 + - - +
1073A U 5.0 3.4 - - - -
1103A C 3.5 25.9 + - - +
1104A G 4.7 10.7 + - - +
102B ASN* 2.9 39.9 + - - +
104B LYS* 1.3 78.2 - - - +
106B VAL* 1.3 68.2 + - + +
107B ARG 3.4 0.2 - - - -
108B GLN* 3.0 33.2 - - - +
109B SER* 4.1 0.7 + - - -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103A C 4.1 17.7 - - - +
96B LEU* 5.1 10.3 - - + -
97B GLY 5.0 2.9 - - - +
98B GLY* 3.3 25.8 - - - +
99B MET* 4.3 18.4 - - + +
102B ASN* 2.9 20.9 - - + +
103B TRP* 2.8 11.7 + - + +
105B THR* 1.3 79.6 - - + +
107B ARG* 1.3 52.2 - - - +
108B GLN 2.9 4.3 - - - -
109B SER* 2.7 39.1 + - - -
110B ILE* 3.7 4.1 + - + +
147B LEU* 4.5 17.9 - - + -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TRP* 2.7 57.7 + - + +
104B LYS* 3.3 9.8 + - - +
106B VAL* 1.3 72.5 - - - +
108B GLN* 1.3 96.3 + - - +
110B ILE* 2.8 44.1 + - + +
111B LYS* 3.3 14.6 + - - +
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104A G 5.9 5.8 - - - +
104B LYS 3.2 8.4 + - - +
105B THR* 3.0 29.8 - - - +
106B VAL 2.8 0.4 + - - -
107B ARG* 1.3 133.1 + - - +
109B SER* 1.3 60.4 + - - +
111B LYS* 3.3 21.7 + - - +
112B ARG* 3.8 5.2 + - - +
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103A C 3.6 10.2 + - - -
1104A G 3.2 37.2 + - - -
105B THR 4.7 0.3 + - - -
106B VAL* 2.7 20.7 + - - +
108B GLN* 1.3 71.3 - - - +
110B ILE* 1.3 63.8 + - - -
111B LYS 3.3 0.3 + - - -
112B ARG* 3.5 7.4 + - - +
113B LEU* 3.3 17.8 + - - +
143B LEU* 4.1 10.8 - - - +
147B LEU* 3.8 20.4 - - - -
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TRP* 4.2 19.1 - - + +
106B VAL* 3.9 4.7 - - + +
107B ARG* 2.8 37.8 + - + +
109B SER* 1.3 77.6 - - - +
111B LYS* 1.3 56.3 + - - +
113B LEU* 3.0 9.5 - - + +
114B LYS* 2.8 35.5 + - + +
147B LEU* 4.4 18.8 - - + -
150B ILE* 5.0 9.6 - - + +
151B LYS* 3.6 50.5 - - + +
153B MET 5.0 0.4 - - - +
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 3.3 15.7 + - - +
108B GLN* 3.5 16.6 - - - +
109B SER 3.2 0.6 - - - -
110B ILE* 1.3 73.5 - - - +
112B ARG* 1.3 56.1 + - - +
113B LEU 2.9 9.8 + - - -
114B LYS* 2.9 11.9 + - + +
115B ASP* 2.6 44.1 + - + +
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLN 3.8 5.1 + - - +
109B SER* 3.5 9.8 + - - +
111B LYS* 1.3 78.3 - - + +
113B LEU* 1.3 57.5 + - - +
115B ASP* 2.8 32.0 + - - +
116B LEU* 2.8 20.7 - - + +
136B ARG* 3.8 26.3 - - - +
139B GLU* 3.3 30.7 + - - +
143B LEU* 4.1 2.5 - - + -
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B SER 3.3 11.2 + - - +
110B ILE* 3.0 12.8 + - - +
111B LYS 2.9 0.2 - - - -
112B ARG* 1.3 77.3 - - - +
114B LYS* 1.3 64.7 + - - +
116B LEU* 3.0 5.6 + - - +
117B GLU* 2.9 40.4 + - + +
140B LEU* 4.0 0.6 - - + +
143B LEU* 3.3 54.3 - - + +
144B GLU* 3.6 13.0 - - + +
147B LEU* 3.7 18.4 - - + -
148B GLY 3.9 0.7 - - - +
151B LYS* 3.3 36.8 - - + -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE* 2.8 29.9 + - + +
111B LYS* 2.9 10.3 + - + +
113B LEU* 1.3 78.2 - - + +
115B ASP* 1.3 58.0 + - - +
117B GLU* 2.8 44.5 + - - +
118B THR* 3.2 11.0 + - - +
151B LYS* 4.9 18.2 + - + +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS* 2.6 45.4 + - + +
112B ARG* 2.8 33.7 + - - +
114B LYS* 1.3 74.0 - - - +
116B LEU* 1.3 75.3 + - - +
118B THR* 2.6 27.4 + - - +
119B GLN* 3.4 13.6 - - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 2.8 14.8 - - + +
113B LEU 3.0 8.7 + - - +
114B LYS 3.0 0.4 - - - -
115B ASP* 1.3 82.0 + - - +
117B GLU* 1.3 63.8 + - - +
119B GLN* 3.1 33.7 - - + +
120B SER 4.2 0.7 + - - -
136B ARG* 3.7 21.3 - - + +
137B THR* 5.0 1.8 - - + -
139B GLU* 3.1 46.7 - - + +
140B LEU* 3.5 36.2 - - + +
143B LEU* 3.7 8.1 - - + -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 2.9 26.5 + - + +
114B LYS* 2.8 35.1 + - - +
116B LEU* 1.3 76.5 - - - +
118B THR* 1.3 64.4 + - + +
119B GLN 2.9 1.7 + - - -
120B SER* 3.0 23.7 + - - -
121B GLN* 3.3 4.8 + - - +
140B LEU* 4.3 13.7 - - + -
144B GLU* 3.9 12.2 - - - +
151B LYS* 2.7 31.5 + - - -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LYS 3.7 11.2 - - - +
115B ASP* 2.6 29.1 + - - +
117B GLU* 1.3 75.9 - - + +
119B GLN* 1.3 62.7 + - - +
121B GLN* 2.7 48.0 + - + +
124B THR* 3.1 6.5 - - - +
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASP* 3.4 13.0 - - - +
116B LEU* 3.1 29.5 - - + +
117B GLU 2.9 1.8 + - - -
118B THR* 1.3 77.0 + - - +
120B SER* 1.3 59.9 + - - +
122B ASP 3.1 0.9 - - - +
124B THR* 2.9 43.0 + - - +
125B PHE* 2.8 29.9 + - + +
127B LYS* 3.3 19.1 - - - +
136B ARG* 3.9 27.4 + - + +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU 4.2 1.0 + - - -
117B GLU* 3.0 14.1 + - - -
119B GLN* 1.3 77.5 - - - +
121B GLN* 1.3 69.9 + - - +
122B ASP 3.2 6.8 - - - +
125B PHE* 3.4 25.4 - - - -
137B THR* 6.4 1.8 - - - -
140B LEU* 5.2 9.6 - - - +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU 3.3 3.2 + - - +
118B THR* 2.7 43.0 + - + +
120B SER* 1.3 83.0 + - - +
122B ASP* 1.3 93.0 + - - +
124B THR* 4.1 3.6 - - - +
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B THR 3.5 1.6 + - - -
119B GLN 3.1 5.9 - - - +
120B SER 3.2 4.2 - - - +
121B GLN* 1.3 112.9 - - - +
123B GLY* 1.3 59.9 + - - +
124B THR* 2.9 16.0 + - + +
125B PHE* 3.0 18.7 - - - -
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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