Contacts of the helix formed by residues 119 - 133 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B ASP* 3.4 16.8 + - - +
117B GLY 4.5 1.3 - - - -
118B LEU* 1.3 72.4 - - - +
120B THR* 1.3 57.3 + - - +
121B GLU* 3.5 7.1 + - - +
122B LEU* 3.0 30.2 + - - +
123B ARG* 3.0 29.7 + - - +
160B LYS* 3.6 35.2 + - + +
161B GLY 2.8 16.0 + - - +
162B VAL* 3.5 8.8 - - + +
206B TYR* 3.1 29.1 + - - -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLY 4.6 3.7 + - - -
118B LEU* 3.0 12.7 + - - -
119B ASN* 1.3 68.7 + - - +
121B GLU* 1.3 61.3 + - - +
123B ARG* 3.1 40.5 + - - +
124B ASN* 3.0 43.2 + - - +
160B LYS* 5.2 0.8 - - - +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASN* 3.3 7.2 + - - +
120B THR* 1.3 80.2 - - - +
122B LEU* 1.3 57.8 - - - +
124B ASN* 3.6 6.9 - - - +
125B LEU* 3.0 38.6 + - + +
205B GLU 5.3 0.5 - - - +
206B TYR* 3.5 31.4 - - + +
209B LEU* 3.5 29.6 - - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B MET* 3.4 31.9 - - + -
36B TYR* 5.9 0.2 - - - +
98B ASP* 5.3 0.9 - - + -
99B ALA 5.5 0.7 - - - +
100B VAL* 4.0 14.1 - - + -
119B ASN* 3.0 18.9 + - - +
121B GLU* 1.3 73.7 - - - +
123B ARG* 1.3 66.3 + - - +
125B LEU* 3.2 6.5 + - + -
126B ILE* 2.9 31.1 + - + +
162B VAL* 3.6 17.5 - - + -
202B ALA* 4.0 35.0 - - + +
203B GLU* 4.0 5.2 - - + +
206B TYR* 4.0 27.3 - - + -
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.7 36.5 - - + +
116B GLY* 3.9 21.3 - - - +
117B GLY 4.7 5.4 + - - -
119B ASN 3.0 20.5 + - - +
120B THR* 3.1 32.5 + - - +
122B LEU* 1.3 77.0 - - - +
124B ASN* 1.3 91.7 + - - +
126B ILE* 3.1 12.8 + - - +
127B VAL* 3.2 16.6 + - + +
139B VAL* 3.1 29.5 - - - +
162B VAL* 3.6 13.1 - - + +
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Residues in contact with ASN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 3.0 28.0 + - - +
121B GLU* 3.6 6.9 - - - +
123B ARG* 1.3 108.6 + - - +
125B LEU* 1.3 66.5 + - + +
127B VAL* 3.5 7.4 + - - +
128B SER* 3.1 23.2 + - - -
139B VAL* 3.9 8.0 - - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLU* 3.0 29.9 + - + +
122B LEU* 3.2 8.3 + - + +
124B ASN* 1.3 75.5 - - + +
126B ILE* 1.3 57.9 + - - +
128B SER* 3.3 6.5 + - - -
129B LYS* 2.8 36.1 + - + +
202B ALA* 3.7 17.3 - - + +
205B GLU* 3.4 37.7 - - + +
206B TYR* 3.7 46.4 - - + +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 4.1 13.0 - - + -
115B VAL* 4.4 6.5 - - + -
122B LEU* 2.9 29.5 + - + +
123B ARG 3.6 4.7 - - - +
125B LEU* 1.3 74.9 - - - +
127B VAL* 1.3 55.6 + - - +
129B LYS* 4.0 0.8 - - - +
130B LEU* 2.7 52.2 + - + +
162B VAL* 3.7 26.2 - - + -
164B LEU* 3.9 20.0 - - + -
198B ALA* 5.3 0.2 - - - +
199B ILE* 3.4 32.8 - - + -
202B ALA* 3.7 21.3 - - + -
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.5 28.3 - - + -
123B ARG* 3.2 14.9 + - + +
124B ASN* 3.8 7.2 - - - +
125B LEU 3.3 0.2 - - - -
126B ILE* 1.3 76.2 - - - +
128B SER* 1.3 58.4 + - - +
130B LEU* 3.8 0.3 - - - +
131B ASN* 2.9 43.8 + - - +
137B ALA* 3.5 31.2 - - - +
138B GLU* 3.9 15.7 - - - +
139B VAL* 4.0 15.3 - - + +
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ASN 3.1 16.4 + - - -
125B LEU* 3.5 7.6 - - - -
127B VAL* 1.3 81.0 - - - +
129B LYS* 1.3 64.1 + - - +
131B ASN* 3.3 7.8 + - - +
132B SER* 2.9 28.5 + - - -
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 2.8 25.1 + - - +
126B ILE 4.0 2.0 - - - +
128B SER* 1.3 75.8 + - - +
130B LEU* 1.3 65.9 + - - +
132B SER* 2.9 26.1 + - - +
133B LYS* 3.4 11.3 + - - +
198B ALA* 3.4 25.5 - - + +
201B GLU* 4.0 33.1 + - - +
202B ALA* 3.7 19.1 - - + +
205B GLU* 2.6 34.5 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B THR* 4.3 4.0 - - + -
115B VAL* 4.9 0.9 - - + -
126B ILE* 2.7 46.4 + - + +
129B LYS* 1.3 72.5 - - - +
131B ASN* 1.3 57.1 + - - +
133B LYS* 3.0 18.0 + - - +
135B ILE* 3.1 29.0 + - + +
137B ALA* 3.7 28.7 - - + -
164B LEU* 4.1 5.2 - - + -
195B TYR* 3.7 57.7 - - + +
198B ALA* 3.7 20.6 - - + -
199B ILE* 4.5 2.7 - - + -
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Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 2.9 38.2 + - - +
128B SER* 3.5 7.1 - - - +
130B LEU* 1.3 71.1 - - - +
132B SER* 1.3 62.2 + - - +
134B GLY* 3.2 13.3 + - - -
135B ILE 3.0 20.1 + - - -
136B ALA* 4.4 0.8 - - - +
137B ALA* 3.2 26.4 + - - +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B SER* 2.9 16.2 + - - -
129B LYS* 2.9 19.7 + - - +
130B LEU 3.2 0.4 - - - -
131B ASN* 1.3 76.1 - - - +
133B LYS* 1.3 71.6 + - - +
134B GLY 3.2 1.8 + - - -
201B GLU* 4.8 4.7 + - - -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LYS 3.5 12.8 - - - +
130B LEU 3.0 9.8 + - - +
132B SER* 1.3 88.6 + - - +
134B GLY* 1.3 61.7 + - - +
135B ILE* 3.2 20.1 + - + +
194B ASP* 3.8 37.1 - - + +
197B GLU* 4.0 18.8 - - - +
198B ALA* 4.0 4.9 - - + +
201B GLU* 2.9 36.5 + - - -
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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