Contacts of the helix formed by residues 128 - 143 (chain A) in PDB entry 3N3B
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 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TRP* 3.2 46.4 + - + +
125A SER* 3.6 11.2 - - - +
126A GLU 3.4 1.2 - - - -
127A GLU* 1.3 75.3 - - - +
129A ALA* 1.3 63.6 + - - +
130A PRO* 3.3 7.4 - - - +
131A LEU* 3.2 29.5 + - + +
132A GLN* 3.2 26.8 + - - +
236A TYR* 3.2 24.7 - - - -
239A GLU* 3.0 20.6 - - - +
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Residues in contact with ALA 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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127A GLU 3.3 6.7 + - - +
128A ASN* 1.3 71.2 + - - +
130A PRO* 1.4 67.6 - - + +
132A GLN* 3.4 5.1 + - - +
133A ARG* 3.0 52.2 + - + +
239A GLU* 4.9 1.1 + - - +
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Residues in contact with PRO 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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128A ASN* 3.3 12.3 - - - +
129A ALA* 1.4 93.9 - - + +
131A LEU* 1.3 55.8 + - - +
133A ARG* 4.0 4.5 - - - +
134A LYS* 3.1 17.2 + - - +
232A ASN* 2.8 42.2 - - - +
235A GLN* 3.7 23.6 - - + -
236A TYR* 3.7 27.4 - - + +
239A GLU* 3.4 24.0 - - - +
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Residues in contact with LEU 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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62A GLY* 3.9 27.1 - - - +
65A LEU* 3.9 16.8 - - + -
66A LEU* 4.3 9.4 - - + +
124A TRP* 6.2 0.4 - - + -
125A SER* 3.5 40.2 - - - +
128A ASN* 3.2 20.7 - - + +
130A PRO* 1.3 77.8 - - - +
132A GLN* 1.3 58.3 + - - +
134A LYS* 3.5 23.8 + - - +
135A ALA* 3.1 26.3 + - - +
236A TYR* 3.5 28.6 - - + +
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Residues in contact with GLN 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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65A LEU* 3.7 23.5 - - - +
125A SER 3.3 16.5 - - - +
126A GLU* 3.7 30.9 + - - +
127A GLU 5.2 0.4 - - - -
128A ASN 3.2 19.9 + - - +
129A ALA* 3.9 4.7 - - - +
131A LEU* 1.3 75.0 - - - +
133A ARG* 1.3 59.7 + - - +
135A ALA* 3.4 7.9 + - - +
136A GLN* 2.9 30.4 + - - +
6B ILE 5.5 4.6 + - - -
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Residues in contact with ARG 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 ALA* 3.0 35.7 + - + +
130A PRO* 3.9 19.3 - - - +
132A GLN* 1.3 72.3 - - + +
134A LYS* 1.3 60.9 + - - +
136A GLN* 3.2 11.1 + - - +
137A ILE* 2.9 46.0 + - + +
232A ASN* 3.1 29.0 - - - +
235A GLN* 4.6 10.5 - - - +
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Residues in contact with LYS 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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66A LEU* 3.7 31.3 - - + +
130A PRO 3.1 16.2 + - - +
131A LEU* 3.6 17.7 - - - +
133A ARG* 1.3 76.0 - - - +
135A ALA* 1.3 60.1 + - - +
137A ILE* 4.0 1.6 - - - +
138A ILE* 3.2 31.8 + - + +
157A LEU* 4.5 5.6 - - + -
161A LEU* 3.8 34.0 + - + -
164A SER* 4.6 0.2 + - - -
229A LEU* 4.7 10.5 - - + -
232A ASN* 3.6 9.8 + - - +
233A GLU* 2.9 41.6 + - - +
236A TYR* 3.4 20.2 - - - -
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Residues in contact with ALA 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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65A LEU* 4.5 18.6 - - + -
66A LEU* 4.6 8.5 - - + +
69A LEU* 4.2 15.7 - - + +
131A LEU 3.1 17.6 + - - +
132A GLN* 3.6 13.0 - - - +
133A ARG 3.3 0.2 - - - -
134A LYS* 1.3 76.5 - - - +
136A GLN* 1.3 56.7 + - - +
138A ILE* 4.0 1.0 - - - +
139A GLN* 3.0 39.6 + - - +
6B ILE* 6.4 1.6 - - + -
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Residues in contact with GLN 136 (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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132A GLN 2.9 17.7 + - - +
133A ARG* 3.6 10.7 - - - +
135A ALA* 1.3 73.7 - - - +
137A ILE* 1.3 63.8 + - + +
139A GLN* 3.3 6.7 + - - +
140A GLN* 2.9 51.5 + - - +
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Residues in contact with ILE 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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133A ARG* 2.9 37.7 + - + +
134A LYS* 4.0 3.4 - - - +
136A GLN* 1.3 78.1 - - + +
138A ILE* 1.3 63.9 + - + +
140A GLN* 3.4 11.5 + - - +
141A HIS* 3.1 27.3 + - + +
225A LEU* 3.8 28.5 - - + -
228A GLU* 3.8 35.7 - - + +
229A LEU* 4.1 18.8 - - + -
232A ASN* 5.4 5.6 - - + -
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Residues in contact with ILE 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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69A LEU* 4.1 7.2 - - + -
134A LYS 3.2 18.2 + - - +
135A ALA 4.1 2.0 - - - +
137A ILE* 1.3 77.2 - - + +
139A GLN* 1.3 62.4 + - - +
141A HIS* 3.4 6.1 + - + +
142A TYR* 3.3 51.2 + - + +
153A ALA* 3.6 32.5 - - + +
157A LEU* 4.0 28.3 - - + -
161A LEU* 4.4 6.7 - - + -
225A LEU* 5.4 1.3 - - + -
229A LEU* 3.9 34.5 - - + -
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Residues in contact with GLN 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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69A LEU* 3.8 16.8 - - + +
73A ILE* 3.4 24.9 - - + +
135A ALA* 3.0 27.3 + - - +
136A GLN* 3.8 6.0 - - - +
138A ILE* 1.3 73.6 - - - +
140A GLN* 1.3 65.4 + - - +
142A TYR* 3.3 9.7 + - - +
143A ARG* 3.2 29.7 + - + +
5B ARG* 3.3 43.1 + - - +
6B ILE* 3.9 18.8 - - - +
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Residues in contact with GLN 140 (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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136A GLN* 2.9 36.7 + - - +
137A ILE* 3.7 8.1 - - - +
138A ILE 3.3 0.2 - - - -
139A GLN* 1.3 76.2 - - - +
141A HIS* 1.3 60.7 + - + +
143A ARG* 3.5 7.1 + - + +
144A GLY* 3.2 22.5 + - - -
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Residues in contact with HIS 141 (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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137A ILE* 3.1 26.9 + - - +
138A ILE* 3.8 6.7 - - + +
139A GLN 3.3 0.4 - - - -
140A GLN* 1.3 77.6 - - + +
142A TYR* 1.3 64.9 + - - +
144A GLY* 3.4 11.6 + - - +
146A ASP 4.6 1.6 - - - +
149A LYS* 4.2 21.6 - - + +
150A LYS* 3.2 19.9 + - - +
153A ALA* 4.2 16.4 - - + -
221A PHE* 3.4 32.6 - + - -
225A LEU* 3.7 34.5 - - + +
228A GLU* 5.3 0.6 + - - -
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Residues in contact with TYR 142 (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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69A LEU* 4.4 8.5 - - + -
70A GLN* 2.6 31.6 + - - -
73A ILE* 3.7 20.8 - - + +
74A GLY* 3.6 22.6 - - - -
77A SER* 3.4 27.9 - - - +
78A LEU* 5.2 1.3 - - + -
138A ILE* 3.3 36.4 + - + +
139A GLN* 3.3 14.9 + - - +
141A HIS* 1.3 78.6 - - - +
143A ARG* 1.3 58.4 + - - +
144A GLY 3.3 0.8 - - - +
150A LYS* 3.4 50.6 - - + -
153A ALA* 4.3 3.3 + - + -
154A SER* 3.3 26.9 - - - -
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Residues in contact with ARG 143 (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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73A ILE* 3.6 41.3 - - + +
139A GLN* 3.2 24.5 + - + +
140A GLN* 3.5 7.6 + - + +
141A HIS 3.3 0.2 - - - -
142A TYR* 1.3 77.8 - - + +
144A GLY* 1.3 65.6 + - - +
5B ARG* 4.6 31.1 - - - +
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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