Contacts of the helix formed by residues 121 - 139 (chain A) in PDB entry 3N2E
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A PRO 3.9 12.1 + - - -
118A LEU 3.8 0.7 + - - +
119A LEU 5.1 0.4 - - - -
120A ASN* 1.3 78.3 - - - +
122A LEU* 1.3 67.9 - - - +
123A THR* 3.9 8.7 - - - +
124A GLN* 2.6 49.3 + - - +
125A ALA* 3.0 18.9 + - - +
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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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101A PHE* 3.8 28.7 - - + -
120A ASN 4.2 1.0 + - - -
121A ASN* 1.3 72.0 - - - +
123A THR* 1.3 67.6 + - - +
125A ALA* 3.0 4.5 + - - +
126A LYS* 2.9 47.2 + - - +
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Residues in contact with THR 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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121A ASN* 3.3 9.5 + - - +
122A LEU* 1.3 76.6 - - - +
124A GLN* 1.3 62.8 + - + +
126A LYS* 3.4 9.0 + - - +
127A GLU* 3.1 42.8 + - - +
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Residues in contact with GLN 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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117A PRO 5.5 0.2 - - - -
118A LEU* 3.7 36.8 - - + +
121A ASN* 2.6 41.1 + - - +
123A THR* 1.3 82.0 - - + +
125A ALA* 1.3 66.9 + - - +
127A GLU* 3.5 19.9 + - - +
128A LEU* 2.8 26.9 + - - +
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Residues in contact with ALA 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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101A PHE* 3.6 19.1 - - + -
105A ILE* 4.4 4.3 - - + -
118A LEU 3.1 17.8 + - - +
119A LEU* 4.3 15.9 - - - +
121A ASN 3.0 12.9 + - - +
122A LEU* 3.4 9.4 - - - +
124A GLN* 1.3 75.5 - - - +
126A LYS* 1.3 55.0 + - - +
128A LEU* 3.4 3.5 - - - +
129A PHE* 3.0 17.7 + - - +
2002A TLA 2.8 24.6 - - - +
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Residues in contact with LYS 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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101A PHE* 3.9 30.3 - - + -
122A LEU* 2.9 44.1 + - - +
123A THR* 3.8 7.2 - - - +
125A ALA* 1.3 73.2 - - - +
127A GLU* 1.3 59.7 + - - +
129A PHE* 3.3 4.6 + - + +
130A GLU* 2.9 46.6 + - + +
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Residues in contact with GLU 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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123A THR* 3.1 30.3 + - - +
124A GLN* 3.5 22.2 + - - +
126A LYS* 1.3 74.9 - - - +
128A LEU* 1.3 65.4 + - - +
130A GLU* 3.4 6.4 + - - +
131A LYS* 3.2 24.8 + - - +
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Residues in contact with LEU 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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118A LEU* 4.1 26.7 - - + -
119A LEU* 4.3 9.9 - - + -
124A GLN 2.8 17.7 + - - +
125A ALA* 3.4 5.8 - - - +
127A GLU* 1.3 74.0 - - - +
129A PHE* 1.3 65.9 + - - +
131A LYS* 3.2 21.2 + - - +
132A ARG* 3.0 79.5 + - - +
2001A TLA 4.5 2.9 - - - +
2002A TLA 3.3 23.8 - - - +
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Residues in contact with PHE 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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9A PHE* 3.8 29.6 - + - -
99A MET 3.9 16.6 - - - -
100A ASP* 4.7 1.1 - - - -
101A PHE* 3.7 46.2 - + + -
104A LEU* 4.2 7.9 - - + -
125A ALA 3.0 17.2 + - - +
126A LYS* 3.5 5.4 - - + +
127A GLU 3.3 0.2 - - - -
128A LEU* 1.3 75.8 - - - +
130A GLU* 1.3 75.4 + - + +
132A ARG 3.8 0.2 - - - -
133A GLN* 2.8 69.1 + - - +
2002A TLA 3.6 17.0 + - - +
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Residues in contact with GLU 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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126A LYS* 2.9 37.2 + - + +
127A GLU* 4.0 5.8 - - - +
128A LEU 3.2 0.4 - - - -
129A PHE* 1.3 94.7 - - + +
131A LYS* 1.3 60.9 + - - +
133A GLN* 3.6 8.3 + - - +
134A ALA* 3.2 23.6 + - - +
54B ASP* 5.8 0.3 - - - +
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Residues in contact with LYS 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 GLU 3.2 16.0 + - - +
128A LEU* 4.0 21.4 - - - +
130A GLU* 1.3 76.5 - - - +
132A ARG* 1.3 69.7 + - - +
134A ALA* 3.5 8.1 + - - +
135A LEU* 3.1 26.4 + - + +
1001A OSA 6.2 1.6 - - - -
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Residues in contact with ARG 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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9A PHE* 3.9 15.3 - - + -
116A ARG* 3.3 4.6 - - - +
128A LEU* 3.0 52.4 + - - +
131A LYS* 1.3 86.2 - - - +
133A GLN* 1.3 64.9 + - - +
135A LEU* 3.1 4.0 + - + +
136A TYR* 2.9 29.7 + - + -
1001A OSA 3.2 67.8 + - + +
2001A TLA 2.6 52.7 + - - -
2002A TLA 3.3 14.5 + - - -
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Residues in contact with GLN 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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9A PHE* 4.2 2.6 - - + -
96A TYR* 2.5 32.8 + - - +
98A LYS* 3.1 35.5 + - - +
99A MET 4.2 2.2 + - - -
129A PHE* 2.8 57.8 + - + +
130A GLU* 3.9 10.3 - - - +
132A ARG* 1.3 72.2 - - - +
134A ALA* 1.3 52.8 - - - +
136A TYR* 2.8 9.2 + - - +
137A GLU* 2.7 49.7 + - - +
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Residues in contact with ALA 134 (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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130A GLU 3.2 15.9 + - - +
131A LYS* 3.5 7.6 - - - +
132A ARG 3.3 0.2 - - - -
133A GLN* 1.3 76.8 - - - +
135A LEU* 1.3 57.6 + - - +
137A GLU* 3.9 11.4 - - - +
138A LYS* 2.9 31.7 + - - +
49B GLU 4.5 3.7 - - - +
50B GLU 6.2 0.2 - - - +
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Residues in contact with LEU 135 (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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83A VAL* 3.6 26.8 - - + +
84A MET* 4.8 5.4 - - + -
131A LYS* 3.1 14.6 + - + +
132A ARG* 3.1 9.0 + - + +
133A GLN 3.1 1.0 - - - -
134A ALA* 1.3 75.2 - - - +
136A TYR* 1.3 61.8 + - - +
138A LYS* 4.3 11.0 - - + -
139A ASN* 2.8 58.1 + - - +
1001A OSA 2.9 34.3 - - + +
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Residues in contact with TYR 136 (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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7A ILE* 3.7 24.9 - - + +
8A GLY 3.1 32.0 + - - -
9A PHE* 3.5 36.8 + + - -
80A GLY* 2.5 33.1 + - - -
82A ILE* 5.9 0.4 - - + -
83A VAL* 3.8 19.7 - - + -
96A TYR* 3.5 35.4 - + + +
132A ARG 2.9 20.3 + - - -
133A GLN 2.8 9.6 + - - +
135A LEU* 1.3 73.3 - - - +
137A GLU* 1.3 61.1 + - - +
139A ASN 3.5 2.8 + - - -
140A ALA* 3.0 29.0 + - - +
1001A OSA 3.5 15.2 + + - -
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Residues in contact with GLU 137 (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 TYR* 3.7 17.0 - - + -
98A LYS* 3.1 33.8 + - - -
133A GLN* 2.7 28.7 + - - +
134A ALA* 3.9 10.2 - - - +
136A TYR* 1.3 75.5 - - - +
138A LYS* 1.3 65.8 + - - +
139A ASN 3.4 0.2 + - - -
140A ALA* 3.5 8.4 + - - +
143A ILE* 3.9 16.2 - - + +
48B PHE 5.7 3.7 - - - +
49B GLU* 4.7 4.7 - - - +
115B LYS* 2.9 27.6 + - - +
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Residues in contact with LYS 138 (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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89A LYS* 6.5 1.1 - - - +
134A ALA 2.9 21.9 + - - +
135A LEU* 3.7 14.6 - - + +
137A GLU* 1.3 75.4 - - - +
139A ASN* 1.3 68.1 + - - +
140A ALA 3.3 5.7 + - - +
49B GLU* 3.5 40.8 + - + +
50B GLU* 3.4 33.2 + - - +
115B LYS* 4.7 0.7 + - - -
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Residues in contact with ASN 139 (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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7A ILE* 4.2 3.4 - - + +
83A VAL* 3.3 28.5 - - + +
85A HIS 5.6 1.0 - - - +
88A LEU* 4.2 11.0 - - + +
89A LYS* 4.8 16.2 + - - -
94A THR* 2.7 30.1 + - - +
135A LEU* 2.8 44.8 + - - +
136A TYR 3.5 3.3 + - - +
137A GLU 3.3 1.2 - - - -
138A LYS* 1.3 89.1 - - - +
140A ALA* 1.3 50.2 + - - +
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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