Contacts of the helix formed by residues 96 - 118 (chain A) in PDB entry 2L9N
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL* 1.3 77.6 - - - +
97A ASP* 1.3 67.6 + - - +
98A LYS* 3.2 21.0 + - - -
99A GLU* 3.3 26.3 + - - -
100A ARG* 3.3 20.0 + - - +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 1.3 75.0 - - - +
98A LYS* 1.3 54.4 + - + +
100A ARG* 3.1 31.5 + - - +
101A HIS* 2.7 50.7 + - - +
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 3.2 25.0 + - - -
97A ASP* 1.3 80.9 - - + +
99A GLU* 1.3 65.1 + - - +
101A HIS* 3.8 5.6 - - - +
102A THR* 2.8 36.5 + - - +
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Residues in contact with GLU 99 (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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14A ASN* 4.5 14.2 - - - +
33A LYS* 3.1 37.2 - - + +
95A VAL* 3.6 27.0 - - + +
96A SER* 3.3 29.5 + - - +
98A LYS* 1.3 87.0 + - - +
100A ARG* 1.3 58.5 + - - +
102A THR* 3.0 22.2 - - + +
103A GLN* 3.6 12.6 + - - +
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.9 14.5 + - + +
96A SER 3.3 8.9 + - - +
97A ASP* 3.1 30.5 + - - +
98A LYS 3.1 0.4 - - - -
99A GLU* 1.3 79.6 - - - +
101A HIS* 1.3 60.4 + - - +
103A GLN* 3.5 3.4 + - - +
104A LEU* 3.1 43.6 + - + +
146A THR* 5.8 2.7 - - + +
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Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 2.7 33.6 + - - +
98A LYS* 3.8 6.3 - - - +
100A ARG* 1.3 72.2 - - - +
102A THR* 1.3 60.2 + - - +
104A LEU* 3.1 13.9 + - + +
105A GLU* 2.9 55.3 + - + +
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Residues in contact with THR 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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33A LYS* 5.2 10.8 - - - +
98A LYS 2.8 19.7 + - - +
99A GLU* 3.0 24.7 - - + +
101A HIS* 1.3 73.5 - - - +
103A GLN* 1.3 74.3 + - + +
105A GLU* 3.5 5.6 + - - +
106A GLN* 3.0 25.6 + - - +
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Residues in contact with GLN 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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33A LYS* 5.8 4.5 - - - -
34A ASN* 5.2 10.4 - - - +
37A VAL* 3.6 39.3 - - + +
99A GLU 3.6 14.6 - - - +
100A ARG* 3.5 5.6 + - - +
101A HIS 3.3 0.4 - - - -
102A THR* 1.3 85.8 - - + +
104A LEU* 1.3 57.5 + - - +
106A GLN* 3.8 15.3 + - - +
107A MET* 3.0 50.7 + - - +
146A THR* 3.4 23.3 + - + +
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Residues in contact with LEU 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 ARG* 3.1 39.9 + - + +
101A HIS* 3.5 17.0 - - + +
103A GLN* 1.3 73.6 - - - +
105A GLU* 1.3 61.6 + - + +
107A MET* 3.3 2.2 + - - +
108A PHE* 2.8 58.5 + - + +
143A SER* 6.2 0.2 - - - +
144A VAL* 5.4 8.7 - - + +
146A THR* 3.7 23.1 - - + +
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Residues in contact with GLU 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 HIS* 2.9 41.5 + - + +
102A THR* 3.9 6.2 - - - +
104A LEU* 1.3 75.3 - - + +
106A GLN* 1.3 56.9 + - - +
108A PHE* 3.8 5.1 - - - +
109A ARG* 2.8 33.4 + - - +
134A GLU* 5.9 0.2 - - - -
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Residues in contact with GLN 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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34A ASN* 5.9 3.2 - - - +
102A THR 3.0 19.2 + - - +
103A GLN* 3.8 22.1 + - - +
105A GLU* 1.3 77.3 - - - +
107A MET* 1.3 77.2 + - - +
109A ARG* 3.4 7.5 + - - +
110A ASP* 3.0 44.4 + - - +
150A THR* 5.7 0.2 - - - +
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Residues in contact with MET 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 GLN* 3.0 41.5 + - - +
104A LEU* 3.8 4.3 - - - +
106A GLN* 1.3 95.0 - - - +
108A PHE* 1.3 63.6 + - - +
110A ASP* 3.2 4.9 + - - +
111A ILE* 2.9 30.9 + - + +
144A VAL* 3.5 26.5 - - + -
145A LYS 4.3 4.5 - - - +
146A THR* 3.8 21.1 - - + +
148A LYS 4.3 10.8 - - - +
149A SER* 5.6 0.4 - - - -
150A THR* 3.5 31.0 - - + +
153A GLN* 6.5 0.2 - - + -
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Residues in contact with PHE 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 LEU* 2.8 47.1 + - + +
105A GLU* 3.8 5.4 - - - +
107A MET* 1.3 71.9 - - - +
109A ARG* 1.3 62.9 + - - +
111A ILE* 3.4 6.5 + - + +
112A ALA* 3.0 25.8 + - - +
134A GLU* 3.2 34.0 - - + +
137A MET* 3.6 41.3 - - + -
138A LYS* 5.1 8.3 - - + -
142A TYR 3.8 19.3 - - - -
143A SER* 5.6 0.4 - - - -
144A VAL* 3.3 28.0 - - + -
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Residues in contact with ARG 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 GLU 2.8 20.1 + - - +
106A GLN* 3.6 7.6 - - - +
108A PHE* 1.3 77.4 - - - +
110A ASP* 1.3 51.9 + - - +
112A ALA* 3.4 6.9 + - + +
113A THR* 2.6 43.4 + - - +
130A VAL* 5.2 3.7 - - + +
134A GLU* 4.6 5.1 + - - -
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Residues in contact with ASP 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 GLN* 3.0 34.7 + - - +
107A MET* 3.2 10.0 + - - +
109A ARG* 1.3 75.6 - - - +
111A ILE* 1.3 62.7 - - - +
113A THR* 2.9 9.2 + - - +
114A ILE* 2.9 41.3 + - + +
150A THR* 4.6 16.1 + - + +
151A LYS* 5.7 2.6 + - - -
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Residues in contact with ILE 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 MET* 2.9 29.5 + - + +
108A PHE* 3.7 8.7 - - - +
110A ASP* 1.3 74.0 - - - +
112A ALA* 1.3 56.2 + - - +
114A ILE* 3.9 5.6 - - - +
115A VAL* 2.7 51.2 + - + +
133A ILE* 5.3 1.3 - - + -
137A MET* 3.8 28.7 - - + -
144A VAL* 3.6 32.1 - - + -
150A THR* 4.6 20.4 - - - +
153A GLN* 5.6 6.7 - - + -
154A ALA* 6.0 1.1 - - - -
157A VAL* 4.3 15.5 - - + -
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Residues in contact with ALA 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 PHE 3.0 18.2 + - - +
109A ARG* 3.7 6.7 - - + +
111A ILE* 1.3 76.6 - - - +
113A THR* 1.3 58.3 + - - +
116A ALA* 2.8 33.1 + - - +
130A VAL* 3.4 35.4 - - + +
133A ILE* 3.2 16.3 - - + +
134A GLU* 3.9 12.3 - - + -
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Residues in contact with THR 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 ARG* 2.6 28.9 + - - +
110A ASP* 2.9 12.1 + - - +
112A ALA* 1.3 75.4 - - - +
114A ILE* 1.3 62.7 + - + +
116A ALA* 4.5 0.4 - - - -
117A ASP* 2.6 50.2 + - + +
130A VAL* 4.1 12.7 - - + +
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Residues in contact with ILE 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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110A ASP* 2.9 33.1 + - + +
111A ILE* 4.0 5.6 - - - +
113A THR* 1.3 82.0 - - + +
115A VAL* 1.3 57.5 + - + +
117A ASP* 4.9 1.3 - - + -
118A LYS* 2.7 69.8 + - + +
150A THR* 5.7 2.9 - - - +
151A LYS* 5.3 14.4 - - - +
154A ALA* 6.2 4.3 - - + -
169A ARG* 5.7 2.7 - - - -
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Residues in contact with VAL 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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111A ILE* 2.7 38.5 + - + +
114A ILE* 1.3 80.0 - - + +
116A ALA* 1.3 58.6 + - - +
119A CYS* 2.9 35.8 - - + +
128A TYR* 5.2 1.7 - - - +
133A ILE* 3.7 33.0 - - + +
157A VAL* 5.0 9.6 - - + -
158A ILE* 5.4 5.4 - - + -
161A LEU* 4.6 5.4 - - + -
167A ILE* 3.3 36.0 - - + +
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Residues in contact with ALA 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 ALA 2.8 20.1 + - - +
113A THR 4.0 1.1 - - - +
115A VAL* 1.3 78.3 - - - +
117A ASP* 1.3 62.9 + - - +
119A CYS 4.3 6.3 - - - +
127A PRO* 4.5 8.0 - - - +
128A TYR 3.5 24.8 + - - +
129A THR* 4.5 0.2 - - - -
130A VAL* 3.8 19.1 - - + +
133A ILE* 3.4 14.4 - - + -
216A CYS* 4.3 5.7 - - - -
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Residues in contact with ASP 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 THR* 2.6 31.3 + - + +
114A ILE* 4.9 1.3 - - + -
116A ALA* 1.3 77.5 - - - +
118A LYS* 1.3 58.3 + - + +
214A PRO* 3.3 11.3 - - - +
216A CYS* 2.9 23.4 - - - -
217A PHE* 4.6 20.9 - - - -
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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 ILE* 2.7 48.8 + - + +
117A ASP* 1.3 76.7 - - + +
119A CYS* 1.3 73.7 + - - +
169A ARG* 3.3 35.0 - - + +
170A ALA 5.5 0.4 - - - -
214A PRO* 4.5 16.6 - - + -
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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
------------------------------------------------------------
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