Contacts of the helix formed by residues 99 - 120 (chain A) in PDB entry 1AV1
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 PRO 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ALA 3.4 15.5 - - - +
96A LYS 4.9 2.5 - - - +
97A VAL* 3.4 3.6 - - - +
98A GLN* 1.3 97.3 - - + +
100A TYR* 1.3 70.2 + - + +
102A ASP* 2.9 28.6 - - + +
103A ASP* 3.2 4.9 + - - +
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Residues in contact with TYR 100 (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 LYS 5.0 2.9 - - - +
97A VAL* 2.6 23.9 + - + +
99A PRO* 1.3 77.2 - - + +
101A LEU* 1.3 68.0 + - - +
103A ASP* 2.7 48.5 + - + +
104A PHE* 5.6 1.8 + - - +
158B ALA* 5.8 0.7 - - - +
159B LEU* 3.5 29.3 + - + +
162B HIS* 2.9 60.1 + + + +
163B LEU* 4.0 13.5 - - + -
166B TYR* 6.1 1.6 - + + -
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Residues in contact with LEU 101 (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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97A VAL* 2.7 21.3 + - + +
98A GLN* 3.3 35.0 - - - +
100A TYR* 1.3 81.0 - - - +
102A ASP* 1.3 57.5 + - - +
104A PHE* 2.5 46.1 + - + +
105A GLN* 4.9 12.8 - - + -
159B LEU* 4.0 13.5 - - + -
163B LEU* 5.4 4.3 - - + -
43D MET 5.0 11.4 - - - +
44D LEU* 6.0 4.0 - - + -
45D LYS* 3.8 25.6 - - - +
46D LEU* 4.8 19.7 - - + -
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Residues in contact with ASP 102 (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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98A GLN* 2.6 36.1 + - - +
99A PRO* 2.9 27.0 - - + +
101A LEU* 1.3 74.1 - - - +
103A ASP* 1.3 63.8 + - - +
105A GLN* 2.7 43.6 + - - +
106A LYS* 3.6 2.6 + - - +
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Residues in contact with ASP 103 (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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99A PRO 3.2 3.6 + - - +
100A TYR* 2.7 44.2 + - + +
101A LEU 2.7 2.8 + - - -
102A ASP* 1.3 75.3 - - - +
104A PHE* 1.3 64.1 + - - +
106A LYS* 3.1 17.6 + - - +
107A LYS* 3.2 36.2 + - - +
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Residues in contact with PHE 104 (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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100A TYR* 5.6 1.5 + - - +
101A LEU* 2.5 23.3 + - + +
103A ASP* 1.3 76.2 - - - +
105A GLN* 1.3 56.9 + - + +
107A LYS* 2.6 38.2 + - + +
108A TRP* 2.9 25.5 + + + -
152B ALA* 5.0 4.0 - - + -
155B HIS* 3.1 53.6 - + + -
156B VAL* 3.7 16.8 - - + -
159B LEU* 4.0 27.1 - - + -
45D LYS* 4.5 17.9 - - - -
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Residues in contact with GLN 105 (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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101A LEU* 3.6 10.7 + - + -
102A ASP* 2.7 39.1 + - - +
104A PHE* 1.3 77.3 - - + +
106A LYS* 1.3 61.6 + - - +
108A TRP* 3.0 11.2 + - + +
109A GLN* 3.0 27.4 + - + +
43D MET* 4.3 36.5 + - - +
45D LYS* 6.3 0.2 - - - +
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Residues in contact with LYS 106 (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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102A ASP 3.6 2.4 + - - +
103A ASP* 3.1 12.5 + - - +
105A GLN* 1.3 79.9 - - - +
107A LYS* 1.3 58.1 + - + +
109A GLN* 3.3 14.5 - - + +
110A GLU* 2.9 27.8 + - + +
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Residues in contact with LYS 107 (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 ASP* 3.2 37.8 + - - +
104A PHE* 2.6 26.5 + - + +
106A LYS* 1.3 79.4 - - + +
108A TRP* 1.3 60.3 + - - +
110A GLU* 3.1 33.6 + - - +
111A GLU* 3.4 12.0 + - - +
155B HIS* 3.7 28.3 + - + +
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Residues in contact with TRP 108 (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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104A PHE* 2.9 25.0 + + + +
105A GLN* 3.0 12.3 + - + +
107A LYS* 1.3 74.8 - - - +
109A GLN* 1.3 71.9 + - - +
110A GLU 3.0 0.7 + - - -
111A GLU* 3.1 10.8 + - + -
112A MET* 2.9 56.8 + - + +
148B MET* 5.8 3.1 - - + +
152B ALA* 5.9 6.3 - - + -
155B HIS* 5.6 0.9 - - - -
223C GLU* 3.2 37.9 - - - -
225C PHE* 6.3 1.8 - + - -
43D MET* 4.8 25.4 - - + -
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Residues in contact with GLN 109 (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 GLN* 3.0 20.0 + - + +
106A LYS* 3.3 20.2 - - + +
108A TRP* 1.3 83.0 - - - +
110A GLU* 1.3 61.8 + - - +
112A MET* 3.6 12.0 - - - +
113A GLU* 3.5 25.8 + - - +
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Residues in contact with GLU 110 (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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106A LYS* 2.9 12.1 + - + +
107A LYS* 3.2 28.8 - - - +
108A TRP 3.0 0.2 - - - -
109A GLN* 1.3 78.4 - - - +
111A GLU* 1.3 78.6 + - - +
113A GLU* 3.8 6.9 + - - +
114A LEU* 3.9 10.6 + - - +
155B HIS* 4.9 1.7 + - - -
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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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107A LYS 3.7 11.4 - - - +
108A TRP* 3.1 11.6 + - + +
110A GLU* 1.3 86.0 - - - +
112A MET* 1.3 66.5 + - - +
114A LEU* 3.2 23.0 + - - +
115A TYR 3.3 4.2 + - - -
148B MET* 4.0 18.6 - - + +
151B ARG* 3.1 50.9 + - + +
152B ALA* 5.4 3.8 - - + +
155B HIS* 3.1 32.8 + - + +
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Residues in contact with MET 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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108A TRP* 2.9 58.4 + - + +
109A GLN* 3.6 17.3 - - - +
110A GLU 3.2 0.2 - - - -
111A GLU* 1.3 76.5 - - - +
113A GLU* 1.3 66.4 + - + +
115A TYR* 3.1 14.3 + - - +
116A ARG* 2.9 49.5 + - - +
148B MET* 4.3 15.2 - - + +
225C PHE* 5.1 17.3 - - + -
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Residues in contact with GLU 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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109A GLN 3.5 14.8 + - - +
110A GLU 4.4 3.1 - - - +
111A GLU 3.5 0.8 - - - -
112A MET* 1.3 78.7 - - + +
114A LEU* 1.3 51.4 + - - +
116A ARG* 2.9 26.0 + - - +
117A GLN* 2.8 61.3 + - + +
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Residues in contact with LEU 114 (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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110A GLU 3.9 9.0 + - - +
111A GLU* 3.2 13.5 + - - +
113A GLU* 1.3 78.5 - - - +
115A TYR* 1.3 57.4 + - - +
117A GLN* 3.0 23.8 + - + +
118A LYS* 3.0 16.6 + - + +
147B GLU* 5.8 1.6 - - - +
151B ARG* 3.3 33.0 - - - +
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Residues in contact with TYR 115 (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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111A GLU 3.3 1.0 + - - -
112A MET* 3.1 10.6 + - - +
114A LEU* 1.3 73.9 - - - +
116A ARG* 1.3 63.0 + - - +
117A GLN 2.6 15.1 + - - -
118A LYS* 3.1 4.8 + - + +
119A VAL* 3.1 53.6 + - + +
141B LEU* 4.0 13.5 - - + +
144B LEU* 5.0 16.2 - - + -
145B GLY* 5.2 1.8 - - - -
148B MET* 3.1 46.7 - - + -
225C PHE* 3.1 33.2 - + - -
227C VAL* 2.8 39.1 - - + +
229C PHE* 4.4 2.3 - + - -
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Residues in contact with ARG 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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112A MET* 2.9 39.9 + - - +
113A GLU* 3.1 34.0 + - - +
115A TYR* 1.3 82.5 - - + +
117A GLN* 1.3 63.1 + - - +
119A VAL* 4.7 2.0 - - - +
120A GLU* 3.0 35.7 + - + +
243D GLN* 4.0 34.7 + - - +
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Residues in contact with GLN 117 (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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113A GLU* 2.8 35.7 + - + +
114A LEU* 3.0 16.4 - - + +
115A TYR 2.6 2.2 + - - -
116A ARG* 1.3 101.3 + - - +
118A LYS* 1.3 66.7 + - - +
119A VAL 3.0 1.3 - - - -
120A GLU* 3.0 17.7 + - - +
121A PRO* 3.0 20.1 - - - +
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Residues in contact with LYS 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 LEU* 3.0 13.6 + - + +
115A TYR* 3.1 5.6 + - + +
117A GLN* 1.3 74.4 - - - +
119A VAL* 1.3 60.2 + - + +
121A PRO* 2.9 19.5 - - + +
122A LEU* 3.7 21.9 - - + +
140B LYS* 4.9 12.5 - - - +
144B LEU* 3.9 30.9 - - + +
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Residues in contact with VAL 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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115A TYR* 3.2 50.0 - - + +
116A ARG* 4.7 1.8 - - - +
117A GLN 3.0 0.8 - - - -
118A LYS* 1.3 80.2 - - + +
120A GLU* 1.3 66.3 + - - +
121A PRO* 2.9 5.4 - - - -
122A LEU* 2.9 37.1 + - + +
123A ARG* 3.4 5.6 + - + +
141B LEU* 5.1 8.1 - - + -
144B LEU* 5.7 4.0 - - + -
229C PHE* 3.6 35.2 - - + -
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Residues in contact with GLU 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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116A ARG* 3.0 24.8 + - + +
117A GLN* 3.0 28.4 + - - +
119A VAL* 1.3 76.9 - - - +
121A PRO* 1.3 58.0 - - + +
123A ARG* 2.9 54.4 + - - +
124A ALA* 3.8 3.6 + - - +
243D GLN 4.7 6.8 - - - +
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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