Contacts of the helix formed by residues 102 - 116 (chain A) in PDB entry 4L2A
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ILE* 4.0 2.6 - - - +
97A ASN* 3.4 12.5 - - - +
100A TRP* 3.1 6.6 - - - +
101A GLY* 1.3 80.3 - - - +
103A PHE* 1.3 64.8 + - - +
104A ASP* 3.7 8.0 + - - +
105A ALA* 3.1 24.9 + - - +
106A PHE* 3.2 19.8 + - - +
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Residues in contact with PHE 103 (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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86A GLY 4.4 9.9 - - - -
87A ALA* 4.9 3.6 - - + -
88A PRO* 3.4 42.6 - - + -
96A ILE* 3.9 11.0 - - + -
97A ASN* 3.5 10.7 - - - +
102A SER* 1.3 73.4 - - - +
104A ASP* 1.3 68.1 + - - +
106A PHE* 3.1 22.2 + + - +
107A LYS* 2.9 48.3 + - + +
179A TRP* 3.9 23.1 - + - -
184A TRP* 3.7 23.3 - + - -
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Residues in contact with ASP 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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102A SER* 3.3 7.7 + - - +
103A PHE* 1.3 87.6 - - - +
105A ALA* 1.3 65.8 + - - +
107A LYS* 3.3 10.4 + - - +
108A GLU* 2.9 28.0 + - - +
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Residues in contact with ALA 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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100A TRP* 3.6 25.7 - - + +
102A SER* 3.1 19.0 + - - +
104A ASP* 1.3 76.1 - - - +
106A PHE* 1.3 57.6 + - - +
108A GLU* 2.9 19.9 + - + +
109A ALA* 2.9 29.2 + - - +
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Residues in contact with PHE 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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96A ILE* 3.6 43.1 - - + -
100A TRP* 3.3 53.5 - + + +
102A SER 3.2 4.4 + - - +
103A PHE* 3.1 19.0 + + - +
105A ALA* 1.3 78.9 - - - +
107A LYS* 1.3 58.5 + - - +
109A ALA* 3.1 2.6 + - - +
110A LEU* 2.8 49.1 + - + +
125A LEU* 3.7 22.0 - - + -
135A ILE* 3.7 18.2 - - + -
154A LEU* 6.1 1.3 - - + -
179A TRP* 3.7 23.3 - + - -
184A TRP* 4.5 4.7 - + - -
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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 PHE* 2.9 37.8 + - + +
104A ASP* 3.7 10.5 - - - +
106A PHE* 1.3 76.5 - - - +
108A GLU* 1.3 65.5 + - - +
110A LEU* 3.9 0.9 - - - +
111A ASN* 2.9 38.2 + - - +
179A TRP* 3.6 63.2 - - + +
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Residues in contact with GLU 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 ASP* 2.9 16.4 + - - +
105A ALA* 2.9 36.3 - - - +
107A LYS* 1.3 78.3 - - - +
109A ALA* 1.3 62.4 + - - +
111A ASN* 3.8 6.9 - - - +
112A ASP* 3.0 25.1 + - - +
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Residues in contact with ALA 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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100A TRP* 3.8 16.6 - - + +
105A ALA 2.9 17.8 + - - +
106A PHE 3.1 4.9 + - - +
108A GLU* 1.3 75.6 - - + +
110A LEU* 1.3 67.5 + - - +
112A ASP* 3.3 6.9 + - - +
113A LYS* 3.1 27.0 + - + +
135A ILE* 3.8 15.7 - - + -
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Residues in contact with LEU 110 (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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106A PHE* 2.8 45.2 + - + +
107A LYS 4.1 3.1 - - - +
109A ALA* 1.3 75.2 - - - +
111A ASN* 1.3 60.7 + - - +
113A LYS* 3.1 2.8 + - - +
114A ALA* 2.8 34.1 + - + -
123A THR* 3.9 24.2 - - + +
124A TRP 5.2 0.2 - - - -
125A LEU* 4.8 14.1 - - + +
135A ILE* 3.6 20.6 - - + +
154A LEU* 6.5 0.4 - - + -
156A VAL* 4.6 10.8 - - + -
175A LEU* 5.0 3.4 - - + -
178A PHE* 5.0 9.4 - - + -
179A TRP* 4.0 24.2 - - + -
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Residues in contact with ASN 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* 2.9 30.6 + - - +
108A GLU* 3.8 6.6 - - - +
110A LEU* 1.3 75.3 - - - +
112A ASP* 1.3 58.7 + - - +
114A ALA* 3.3 0.6 + - - +
115A VAL* 2.9 38.8 + - + +
175A LEU* 3.6 33.0 - - + +
179A TRP* 2.9 34.3 + - - +
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Residues in contact with ASP 112 (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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108A GLU 3.0 18.8 + - - +
109A ALA* 3.6 7.6 - - - +
110A LEU 3.2 0.2 - - - -
111A ASN* 1.3 78.3 - - - +
113A LYS* 1.3 67.8 + - - +
115A VAL* 4.2 5.9 - - - +
116A ASN* 3.0 46.0 + - - +
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Residues in contact with LYS 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 ALA* 3.1 18.2 + - + +
110A LEU 3.6 6.1 - - - +
112A ASP* 1.3 83.8 - - - +
114A ALA* 1.3 58.4 + - - +
116A ASN* 3.6 2.2 - - - -
117A ASN* 3.1 14.9 + - - +
123A THR* 4.2 0.9 - - + -
135A ILE* 3.8 39.0 + - + -
136A VAL* 5.2 0.2 - - - +
137A ASN* 2.8 59.2 + - - +
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Residues in contact with ALA 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 LEU* 2.8 19.9 + - + +
111A ASN 3.8 2.0 - - - +
113A LYS* 1.3 75.6 - - - +
115A VAL* 1.3 65.8 + - - +
117A ASN* 3.2 7.4 + - - +
123A THR* 3.4 22.4 - - + +
156A VAL* 4.4 0.9 - - + -
158A LEU* 3.8 16.6 - - + +
171A ARG* 3.0 18.2 + - - -
175A LEU* 3.8 29.2 - - + -
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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 ASN* 2.9 28.6 + - + +
112A ASP* 3.6 6.3 - - - +
114A ALA* 1.3 72.6 - - - +
116A ASN* 1.3 82.5 + - - +
171A ARG* 3.2 27.9 + - + +
172A PRO* 4.2 26.2 - - + -
175A LEU* 3.5 19.5 - - + -
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Residues in contact with ASN 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 ASP* 3.0 36.5 + - - +
113A LYS* 3.6 4.5 - - - +
114A ALA 3.2 0.6 - - - -
115A VAL* 1.3 91.2 + - - +
117A ASN* 1.3 57.8 + - - -
118A PHE* 3.0 11.0 + - - +
137A ASN* 4.7 1.9 + - - -
37B LYS* 4.5 18.4 - - - +
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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