Contacts of the helix formed by residues 115 - 129 (chain A) in PDB entry 3FRS
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 ALA 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ARG* 5.7 0.2 - - - +
111A GLN* 3.8 14.0 - - - +
113A GLU 3.6 6.3 + - - +
114A VAL* 1.3 72.9 - - - +
116A GLU* 1.3 69.2 + - - +
117A LEU 3.1 0.2 - - - -
118A LYS* 2.9 31.4 + - - +
119A ILE* 4.0 4.6 - - + +
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Residues in contact with GLU 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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14A ASN* 3.5 25.5 - - - +
17A LEU* 3.9 26.9 - - + +
18A VAL* 3.7 15.9 - - + -
21A ARG* 4.2 13.9 - - - +
114A VAL* 3.4 7.8 - - - +
115A ALA* 1.3 84.9 + - - +
117A LEU* 1.3 63.9 + - - +
118A LYS 3.0 2.0 - - - -
119A ILE* 3.0 27.6 + - + +
120A VAL* 3.1 14.6 + - - +
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Residues in contact with LEU 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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18A VAL* 3.5 18.9 - - + +
22A LEU* 6.0 2.0 - - + -
72A LEU* 4.2 18.2 - - + -
103A LEU* 3.7 38.1 - - + +
106A ALA 4.2 1.3 - - - +
107A ALA* 3.6 30.9 - - - +
110A LEU* 3.9 24.5 - - + -
111A GLN* 5.0 1.3 - - - -
114A VAL* 3.3 28.6 + - + +
115A ALA 3.1 0.6 + - - -
116A GLU* 1.3 78.6 - - - +
118A LYS* 1.3 60.2 + - - +
120A VAL* 3.5 9.5 + - + -
121A ALA 3.2 17.0 + - - +
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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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107A ALA* 4.7 3.1 - - - -
111A GLN* 3.6 43.3 - - + +
114A VAL 4.4 0.2 + - - -
115A ALA 2.9 15.4 + - - +
117A LEU* 1.3 77.9 - - - +
119A ILE* 1.3 60.7 + - + +
121A ALA* 3.2 4.2 + - - +
122A ASP* 2.8 57.0 + - - +
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Residues in contact with ILE 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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10A ARG* 3.5 31.2 - - - +
14A ASN* 3.3 33.7 - - + +
115A ALA 4.0 6.1 - - - +
116A GLU* 3.0 30.2 + - + +
118A LYS* 1.3 80.0 - - + +
120A VAL* 1.3 53.8 + - - +
122A ASP* 3.6 8.9 - - + +
123A GLN* 2.8 47.4 + - + +
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Residues in contact with VAL 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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11A LEU* 3.7 11.3 - - + +
14A ASN* 3.6 8.1 - - + -
15A LEU* 3.6 54.1 - - + +
18A VAL* 3.8 12.6 - - + -
76A CYS* 5.4 0.2 - - - -
103A LEU* 4.5 9.2 - - + -
116A GLU 3.1 14.1 + - - +
117A LEU* 3.7 15.7 - - + +
119A ILE* 1.3 76.5 - - - +
121A ALA* 1.3 57.6 + - - +
124A LEU* 3.0 48.5 + - + +
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Residues in contact with ALA 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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103A LEU 4.1 2.4 + - - +
104A ILE* 3.9 30.1 - - + +
107A ALA* 3.6 30.7 - - + -
117A LEU* 3.2 3.8 + - - +
118A LYS 3.7 4.7 - - - +
120A VAL* 1.3 79.1 - - - +
122A ASP* 1.3 56.3 + - - +
124A LEU* 3.3 5.1 + - - +
125A CYS* 2.8 40.4 + - - -
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Residues in contact with ASP 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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118A LYS* 2.8 52.5 + - - +
119A ILE* 3.6 9.9 - - + +
121A ALA* 1.3 79.4 - - - +
123A GLN* 1.3 60.5 + - + +
125A CYS* 3.3 9.6 + - - +
126A ALA* 2.9 27.5 + - - +
130A LYS* 5.2 11.7 + - - +
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Residues in contact with GLN 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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5A GLY 4.1 4.2 + - - -
6A PHE* 3.2 25.4 - - + -
7A LYS* 3.0 32.6 + - - +
10A ARG* 3.2 41.7 - - - +
11A LEU* 3.8 33.2 - - + +
119A ILE* 2.8 32.8 + - + +
122A ASP* 1.3 72.4 - - + +
124A LEU* 1.3 65.9 + - - +
126A ALA* 3.1 4.3 + - - -
127A LYS 3.0 18.7 + - - -
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Residues in contact with LEU 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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11A LEU* 4.1 19.5 - - + +
79A LEU* 3.9 17.9 - - + -
86A ILE* 5.0 4.0 - - + -
100A VAL* 3.7 44.6 - - + +
103A LEU* 4.1 13.9 - - + -
104A ILE* 4.1 16.7 - - + +
120A VAL* 3.0 41.4 + - + +
121A ALA* 3.5 4.3 - - - +
123A GLN* 1.3 75.8 - - - +
125A CYS* 1.3 60.7 + - - +
127A LYS* 3.5 3.7 + - + -
128A TYR* 3.2 40.3 + - + +
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Residues in contact with CYS 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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104A ILE* 4.3 15.3 - - - -
121A ALA* 2.8 22.1 + - - -
122A ASP* 3.3 11.2 - - - +
124A LEU* 1.3 73.9 - - - +
126A ALA* 1.3 58.7 + - - +
128A TYR* 3.0 1.0 + - - -
129A SER* 2.6 43.0 + - - +
130A LYS* 3.7 35.7 - - + -
132A TYR* 5.9 0.2 - - - -
133A GLY* 3.8 27.1 - - - +
137A ARG* 4.4 2.7 - - - -
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Residues in contact with ALA 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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5A GLY 4.2 12.1 + - - +
6A PHE* 3.7 32.7 + - + +
122A ASP 2.9 13.4 + - - +
123A GLN* 3.1 12.5 + - - +
125A CYS* 1.3 76.8 - - - +
127A LYS* 1.3 58.9 + - - +
129A SER* 4.5 3.4 + - - +
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Residues in contact with LYS 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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6A PHE* 3.5 44.6 - - + -
11A LEU* 6.0 0.2 - - + -
86A ILE* 3.2 25.0 + - + +
87A GLN* 3.8 10.3 - - - +
88A SER* 3.5 24.7 - - - -
90A LYS 3.6 36.9 - - - +
123A GLN 3.0 8.8 + - - +
124A LEU* 3.9 5.8 - - - +
125A CYS 3.1 0.4 - - - -
126A ALA* 1.3 77.6 - - - +
128A TYR* 1.3 86.0 + - + +
129A SER 3.8 0.4 - - - -
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Residues in contact with TYR 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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85A LEU 4.6 0.9 + - - -
86A ILE* 3.3 35.3 + - + +
89A MET 4.2 1.4 + - - -
90A LYS* 4.5 11.7 - - + -
92A LEU* 3.3 62.5 - - + +
93A ASP 5.1 0.5 + - - -
96A LEU* 6.0 0.2 - - - +
100A VAL* 4.4 13.4 - - + +
124A LEU* 3.2 32.4 + - + +
125A CYS 3.0 2.2 + - - -
127A LYS* 1.3 103.4 - - + +
129A SER* 1.3 72.6 + - - +
132A TYR* 3.2 28.8 - - + +
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Residues in contact with SER 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 CYS* 2.6 23.8 + - - +
126A ALA* 4.4 3.3 + - - +
127A LYS 3.8 1.0 - - - -
128A TYR* 1.3 83.1 + - - +
130A LYS* 1.3 61.8 + - - +
131A GLU* 3.1 25.1 + - - +
132A TYR* 3.3 14.2 + - - +
133A GLY 3.3 13.5 + - - -
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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