Contacts of the helix formed by residues 120 - 133 (chain A) in PDB entry 1SVS
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 THR 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A LEU* 5.0 4.0 - - + +
113A ALA* 5.5 11.0 - - + +
118A PHE* 4.0 5.1 + - + -
119A MET* 1.3 78.7 - - - +
121A ALA* 1.3 65.7 + - - +
122A GLU* 3.6 11.8 + - - +
123A LEU* 3.1 25.7 + - - +
124A ALA* 3.0 22.0 + - - +
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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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119A MET 3.9 0.6 + - - -
120A THR* 1.3 73.7 - - - +
122A GLU* 1.3 57.5 + - - +
124A ALA* 3.4 7.3 + - - +
125A GLY* 2.9 25.8 + - - -
163A ALA* 5.8 2.7 - - - -
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Residues in contact with GLU 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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106A GLN* 3.3 20.6 + - + +
110A LEU* 3.4 34.6 - - + +
120A THR* 3.6 8.9 + - - +
121A ALA* 1.3 77.7 - - - +
123A LEU* 1.3 63.6 + - - +
125A GLY* 3.2 2.5 + - - -
126A VAL* 3.0 27.4 + - + +
129A ARG* 5.0 0.9 + - - -
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Residues in contact with LEU 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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78A ILE* 4.6 1.3 - - + -
107A LEU* 4.1 19.7 - - + +
110A LEU* 3.8 47.8 - - + +
111A ALA* 4.5 2.5 - - - +
113A ALA* 5.0 2.5 - - + -
114A ALA* 4.4 23.1 - - + +
118A PHE 4.7 4.0 - - - +
119A MET* 3.7 22.7 - - + -
120A THR* 3.1 21.7 + - - +
122A GLU* 1.3 76.9 - - - +
124A ALA* 1.3 63.2 + - - +
126A VAL* 3.2 3.9 + - + +
127A ILE* 3.0 45.8 + - + +
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Residues in contact with ALA 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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119A MET* 3.9 8.4 - - - -
120A THR 3.0 17.0 + - - +
121A ALA* 3.7 8.1 - - - +
123A LEU* 1.3 75.8 - - - +
125A GLY* 1.3 57.8 + - - +
127A ILE* 4.6 1.3 - - - -
128A LYS* 2.9 30.1 + - - +
159A LEU* 2.9 21.9 - - + +
163A ALA* 3.6 29.8 - - + -
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Residues in contact with GLY 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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121A ALA 2.9 15.4 + - - -
122A GLU 3.7 3.6 - - - -
123A LEU 3.2 0.2 - - - -
124A ALA* 1.3 77.8 - - - +
126A VAL* 1.3 61.4 + - - +
128A LYS* 3.4 9.2 + - - +
129A ARG* 3.0 45.7 + - - +
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Residues in contact with VAL 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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103A ASP* 3.2 32.9 - - + +
106A GLN* 4.1 24.0 - - + -
107A LEU* 4.0 17.9 - - + +
110A LEU* 4.6 2.7 - - + -
122A GLU* 3.0 20.6 + - + +
123A LEU* 3.5 11.0 - - + +
125A GLY* 1.3 76.6 - - - +
127A ILE* 1.3 63.5 + - - +
129A ARG* 3.4 22.3 + - - +
130A LEU* 3.1 33.9 + - + +
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Residues in contact with ILE 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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77A THR* 4.7 2.2 - - + -
78A ILE* 3.8 31.4 - - + -
81A ILE* 4.5 13.0 - - + +
107A LEU* 4.1 13.7 - - + -
119A MET* 3.9 12.8 - - + -
123A LEU* 3.0 36.7 + - + +
124A ALA 3.8 2.9 - - - +
126A VAL* 1.3 76.2 - - - +
128A LYS* 1.3 57.5 + - - +
130A LEU* 3.3 7.3 + - - +
131A TRP* 2.9 28.8 + - + +
156A LEU* 3.5 32.1 - - + -
159A LEU* 3.8 13.2 - - + -
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Residues in contact with LYS 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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124A ALA* 2.9 20.7 + - - +
125A GLY* 3.6 8.1 - - - +
127A ILE* 1.3 77.0 - - - +
129A ARG* 1.3 62.3 + - + +
131A TRP* 3.3 6.5 + - + +
132A LYS* 3.0 59.3 + - + +
156A LEU 6.0 0.2 - - - -
159A LEU* 3.2 30.8 - - + +
160A ASP* 2.9 41.8 + - - +
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Residues in contact with ARG 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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100A ARG* 3.4 29.9 + - - +
103A ASP* 2.8 46.5 + - - +
122A GLU 5.0 0.6 + - - -
125A GLY* 3.0 35.7 + - - +
126A VAL* 3.7 20.9 - - - +
128A LYS* 1.3 76.7 - - + +
130A LEU* 1.3 61.9 + - - +
132A LYS* 3.4 21.3 + - - +
133A ASP* 3.3 16.5 + - - -
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Residues in contact with LEU 130 (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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81A ILE* 4.2 13.9 - - + -
85A ILE* 3.9 21.5 - - + -
95A PHE* 3.8 29.6 - - + -
100A ARG* 3.8 27.1 - - + +
103A ASP* 4.1 5.8 - - + -
104A ALA* 4.1 10.8 - - + +
107A LEU* 4.0 11.7 - - + -
126A VAL* 3.1 37.8 + - + +
127A ILE* 3.7 5.2 - - - +
129A ARG* 1.3 77.9 - - - +
131A TRP* 1.3 62.6 + - - +
133A ASP* 3.1 11.1 + - - +
136A VAL* 3.1 24.2 - - + +
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Residues in contact with TRP 131 (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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81A ILE* 4.2 6.6 - - + +
84A ILE* 3.8 22.2 - - + -
127A ILE 2.9 18.6 + - - +
128A LYS* 3.7 7.2 - - + +
130A LEU* 1.3 76.3 - - - +
132A LYS* 1.3 66.6 + - + +
133A ASP 3.5 0.7 + - - +
136A VAL* 4.2 7.7 - - + +
137A GLN* 2.8 59.4 + - - +
140A PHE* 3.8 36.3 - + + -
153A ALA* 4.0 22.0 - - + -
156A LEU* 3.5 55.0 + - + +
157A ASN* 2.9 29.5 + - - -
159A LEU* 6.1 0.2 - - + -
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Residues in contact with LYS 132 (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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128A LYS* 3.0 54.6 + - + +
129A ARG* 3.7 19.5 - - - +
130A LEU 3.2 0.2 - - - -
131A TRP* 1.3 83.1 - - + +
133A ASP* 1.3 63.8 + - - +
134A SER* 3.5 2.1 + - - -
137A GLN* 4.6 5.0 - - - +
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Residues in contact with ASP 133 (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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95A PHE* 3.4 8.8 - - - -
96A GLY* 2.7 21.4 + - - -
97A ASP* 3.0 34.2 + - - +
100A ARG* 3.4 21.5 - - + +
129A ARG 3.3 10.3 + - - +
130A LEU 3.1 15.7 + - - +
132A LYS* 1.3 78.7 - - - +
134A SER* 1.3 58.8 + - - +
135A GLY* 2.8 13.9 + - - -
136A VAL* 3.2 13.6 + - + +
137A GLN* 2.9 27.8 + - - +
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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