Contacts of the helix formed by residues 119 - 133 (chain A) in PDB entry 3A9L
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 ASN 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ASP* 3.6 14.5 + - - +
99A ALA 5.9 0.6 + - - +
117A GLY 3.5 0.2 - - - -
118A LEU* 1.3 74.2 - - - +
120A THR* 1.3 51.4 + - - +
121A GLU* 3.6 4.5 + - - +
122A LEU* 3.2 36.7 + - - +
123A ARG* 2.7 38.4 + - - +
160A LYS* 3.4 38.4 + - + +
161A GLY* 2.9 13.0 + - - +
162A VAL* 3.4 6.8 - - + +
206A TYR* 3.3 25.7 + - - -
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Residues in contact with THR 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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117A GLY 5.2 0.7 - - - -
118A LEU* 3.0 12.8 + - - -
119A ASN* 1.3 72.2 + - - +
121A GLU* 1.3 55.2 + - - +
123A ARG* 3.3 37.8 - - - +
124A ASN* 2.7 49.3 + - - +
160A LYS* 5.3 0.4 - - - +
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Residues in contact with GLU 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 ASN* 3.3 6.7 + - - +
120A THR* 1.3 81.4 - - - +
122A LEU* 1.3 56.6 + - - +
124A ASN* 3.5 6.7 + - - +
125A LEU* 3.0 40.2 + - + +
206A TYR* 3.8 25.7 - - + +
209A LEU* 3.1 35.4 - - + +
210A GLU* 5.0 6.2 - - - +
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Residues in contact with LEU 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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34A MET* 3.5 30.3 - - + -
98A ASP* 5.1 0.4 - - + -
99A ALA 5.2 1.3 - - - +
100A VAL* 3.8 15.0 - - + -
119A ASN* 3.2 31.9 + - - +
121A GLU* 1.3 75.5 - - - +
123A ARG* 1.3 66.5 + - - +
125A LEU* 3.3 4.0 + - + -
126A ILE* 3.0 40.8 + - + +
162A VAL* 3.7 9.2 - - + -
202A ALA* 3.7 19.7 - - + +
203A GLU* 4.2 6.7 - - + +
206A TYR* 3.7 32.2 - - + -
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Residues in contact with ARG 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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115A VAL* 3.7 36.7 - - + +
116A GLY* 4.0 17.2 - - - +
117A GLY 4.4 7.1 + - - -
119A ASN 2.7 24.7 + - - +
120A THR* 3.3 28.3 + - - +
122A LEU* 1.3 72.4 - - - +
124A ASN* 1.3 88.7 + - - +
126A ILE 3.5 0.2 + - - -
127A VAL* 3.3 22.7 + - - +
139A VAL* 3.1 34.9 - - + +
162A VAL* 3.3 17.5 - - + +
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Residues in contact with ASN 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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120A THR* 2.7 35.5 + - - +
121A GLU* 3.9 6.6 - - - +
123A ARG* 1.3 102.7 + - - +
125A LEU* 1.3 59.4 + - + +
127A VAL* 3.2 11.4 + - + +
128A SER* 2.9 30.8 + - - -
139A VAL* 4.0 6.4 - - - +
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Residues in contact with LEU 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 GLU* 3.0 44.2 + - + +
122A LEU* 3.7 6.7 - - - +
123A ARG 3.3 0.4 - - - -
124A ASN* 1.3 78.4 - - + +
126A ILE* 1.3 57.2 + - - +
128A SER* 3.2 8.1 + - - -
129A LYS* 2.8 35.9 + - + +
202A ALA* 3.7 18.2 - - + +
205A GLU* 3.2 31.0 - - + +
206A TYR* 4.2 24.0 - - + +
209A LEU* 4.2 11.2 - - + -
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Residues in contact with ILE 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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100A VAL* 4.2 15.0 - - + -
115A VAL* 4.6 7.0 - - + -
122A LEU* 3.0 31.2 + - + +
123A ARG 3.9 4.3 - - - +
124A ASN 3.4 0.2 - - - -
125A LEU* 1.3 72.1 - - - +
127A VAL* 1.3 66.0 + - - +
129A LYS* 4.1 2.1 - - - +
130A LEU* 3.0 42.5 + - + +
162A VAL* 3.7 22.4 - - + -
164A LEU* 4.0 18.6 - - + -
199A ILE* 3.6 34.8 - - + +
202A ALA* 3.7 20.4 - - + -
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Residues in contact with VAL 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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115A VAL* 3.5 31.4 - - + -
123A ARG 3.3 11.1 + - - +
124A ASN* 3.3 14.1 - - - +
126A ILE* 1.3 80.2 - - - +
128A SER* 1.3 67.5 + - - +
130A LEU* 3.3 2.0 + - - +
131A ASN* 3.2 35.6 + - - +
137A ALA* 4.4 12.8 - - - +
138A GLU* 3.9 22.0 - - - +
139A VAL* 4.0 14.6 - - + +
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Residues in contact with SER 128 (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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124A ASN 2.9 17.3 + - - -
125A LEU* 3.2 10.5 + - - -
127A VAL* 1.3 82.1 - - - +
129A LYS* 1.3 64.0 + - - +
131A ASN* 3.7 8.4 + - - +
132A SER* 3.3 21.7 + - - -
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Residues in contact with LYS 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 LEU* 2.8 23.0 + - + +
126A ILE 4.1 2.7 - - - +
128A SER* 1.3 77.8 - - - +
130A LEU* 1.3 67.3 + - - +
132A SER* 2.9 24.4 + - - +
133A LYS* 3.2 10.0 + - - +
198A ALA* 3.3 34.1 - - + +
201A GLU* 3.6 40.6 + - + +
202A ALA* 3.6 10.8 - - + +
205A GLU* 3.2 26.6 + - - -
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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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113A THR* 4.2 8.7 - - + -
115A VAL* 4.8 0.7 - - + -
126A ILE* 3.0 41.3 + - + +
127A VAL* 3.3 1.1 + - - +
129A LYS* 1.3 74.8 - - - +
131A ASN* 1.3 64.9 + - - +
133A LYS* 2.9 13.3 + - - -
134A GLY 3.3 0.2 + - - -
135A ILE* 2.9 30.3 + - + +
137A ALA* 3.6 27.8 - - + -
164A LEU* 4.6 0.4 - - + -
195A TYR* 3.9 45.1 - - + +
198A ALA* 3.4 23.8 - - + -
199A ILE* 3.8 13.7 - - + -
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Residues in contact with ASN 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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127A VAL* 3.2 20.8 + - - +
128A SER* 3.8 10.2 - - - +
130A LEU* 1.3 76.6 - - - +
132A SER* 1.3 53.7 + - - +
133A LYS 3.0 0.2 - - - -
134A GLY* 2.7 24.3 + - - -
135A ILE 3.1 18.0 + - - +
136A ALA* 4.5 0.8 - - - +
137A ALA* 3.3 30.5 + - - +
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Residues in contact with SER 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 SER 3.3 11.8 + - - -
129A LYS* 2.9 24.5 + - - +
131A ASN* 1.3 78.8 - - - +
133A LYS* 1.3 67.7 + - - +
134A GLY 3.2 1.3 - - - -
201A GLU* 4.9 3.5 + - - -
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Residues in contact with LYS 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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129A LYS 3.5 12.1 - - - +
130A LEU 2.9 8.4 + - - +
132A SER* 1.3 85.2 - - - +
134A GLY* 1.3 61.1 + - - +
135A ILE* 3.2 22.5 + - + +
194A ASP* 3.8 41.7 - - + +
197A GLU* 3.3 23.0 + - - +
198A ALA* 4.1 7.2 - - + +
201A GLU* 2.7 30.9 + - - +
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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