Contacts of the helix formed by residues 124 - 135 (chain A) in PDB entry 3NOR
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 HIS 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A CYS* 3.5 39.6 + - - -
105A SER 4.2 1.6 - - - +
123A THR* 1.3 80.9 + - - +
125A TRP* 1.3 97.7 + + - +
126A ALA* 3.1 21.2 + - + +
127A TYR* 2.9 32.3 + + + -
128A HIS 3.4 6.4 + - - -
153A GLY 3.6 13.3 + - - -
154A GLY* 5.5 4.3 - - - -
155A ILE 6.0 0.7 - - - -
232A CIT 3.9 26.1 + - + +
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Residues in contact with TRP 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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123A THR 3.3 5.9 + - - -
124A HIS* 1.3 103.7 + + - +
126A ALA* 1.3 80.2 + - + +
127A TYR 3.1 1.1 + - - -
128A HIS* 3.4 23.6 + - + +
140A HIS* 5.7 3.9 - - + +
153A GLY* 5.5 0.8 - - - -
193A GLY 5.3 5.1 + - - -
195A PRO* 3.7 46.5 - - + +
203A VAL* 4.2 11.4 - - + -
206A ALA* 3.9 27.8 - - + -
207A ARG* 3.5 49.7 + - + -
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Residues in contact with ALA 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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124A HIS* 2.9 23.0 + - + +
125A TRP* 1.3 100.7 - - + +
127A TYR* 1.3 70.9 + - + +
128A HIS 3.6 0.4 - - - -
129A GLU* 4.9 2.8 - - - +
207A ARG* 5.8 1.3 - - + +
210A ALA* 4.3 20.9 - - + -
214A LEU* 3.9 23.0 - - - +
232A CIT 4.7 0.9 - - - +
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Residues in contact with TYR 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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105A SER* 5.1 0.4 - - - -
108A LEU* 4.2 16.2 - - + -
123A THR* 3.7 9.7 - - + +
124A HIS* 2.9 21.4 + - + +
126A ALA* 1.3 90.6 - - + +
128A HIS* 1.3 63.3 + - - +
129A GLU* 3.1 4.0 - - - -
130A LEU* 2.9 25.0 + - + +
210A ALA* 4.3 5.1 - - + +
213A SER* 2.6 31.4 + - - -
214A LEU* 3.8 37.0 - - + -
217A ARG* 3.5 34.5 - - - -
232A CIT 3.1 51.8 + - + -
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 2.9 28.3 + - - -
123A THR* 3.7 24.2 - - - -
124A HIS 3.4 2.2 + - - -
125A TRP* 3.4 18.2 + - - +
126A ALA 3.6 0.6 + - - -
127A TYR* 1.3 76.5 - - - +
129A GLU* 1.3 58.2 + - - +
130A LEU 3.0 5.1 + - - -
131A LEU* 3.2 30.4 + - + +
132A ALA 4.7 0.3 + - - -
138A PRO* 3.8 11.9 - - + +
139A VAL 3.1 32.9 + - - -
140A HIS* 3.2 41.7 + + + -
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Residues in contact with GLU 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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126A ALA 4.9 2.6 - - - +
127A TYR 3.1 2.3 + - - -
128A HIS* 1.3 76.9 - - - +
130A LEU* 1.3 71.0 + - + +
131A LEU 3.2 2.0 - - - -
132A ALA* 4.2 3.5 + - - +
133A PRO* 3.3 20.4 - - - +
214A LEU* 3.7 24.6 - - + +
218A ARG* 3.0 35.6 + - - -
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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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108A LEU* 3.9 25.8 - - + -
127A TYR* 2.9 25.9 + - + +
129A GLU* 1.3 90.2 - - + +
131A LEU* 1.3 63.6 + - - +
132A ALA 3.6 0.2 - - - -
133A PRO* 3.6 11.1 - - + +
134A LEU* 3.6 22.3 - - - +
214A LEU* 4.3 8.5 - - + -
217A ARG* 3.7 27.6 - - + -
218A ARG* 3.7 35.9 - - + +
221A THR* 3.6 26.8 - - + +
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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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107A SER* 4.3 2.5 - - - +
108A LEU* 4.3 7.0 - - + -
116A LEU* 4.0 25.6 - - + -
121A ALA* 3.7 10.1 - - + +
122A THR* 3.7 42.2 - - - +
123A THR* 3.8 17.7 - - + +
128A HIS* 3.2 34.0 + - + +
130A LEU* 1.3 77.0 - - - +
132A ALA* 1.3 67.2 + - - +
134A LEU* 3.0 15.6 + - + +
135A GLY 3.3 0.2 + - - -
136A ALA* 3.2 27.8 + - + +
138A PRO* 4.0 12.8 - - + -
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Residues in contact with ALA 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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129A GLU 4.2 4.1 + - - +
131A LEU* 1.3 77.7 - - - +
133A PRO* 1.3 65.7 - - + +
135A GLY* 2.9 20.6 + - - -
136A ALA 3.7 12.2 - - - +
138A PRO* 4.1 17.2 - - + +
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Residues in contact with PRO 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 GLU 3.3 21.8 - - - +
130A LEU* 3.6 9.6 - - + +
131A LEU 3.5 2.5 - - - -
132A ALA* 1.3 94.8 - - + +
134A LEU* 1.3 58.8 + - - +
135A GLY* 3.2 1.3 + - - -
221A THR* 3.9 18.2 - - + -
222A LEU* 4.2 20.9 - - + -
225A ALA* 3.3 23.6 - - + +
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Residues in contact with LEU 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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81A MET* 4.2 4.9 - - + -
108A LEU* 3.6 39.5 - - + +
111A GLY* 3.8 34.7 - - - +
112A ALA* 4.1 7.2 - - - +
114A GLY* 5.8 0.5 - - - -
116A LEU* 4.1 18.2 + - + +
117A GLN* 4.1 7.6 + - - +
130A LEU 3.6 17.3 - - - +
131A LEU* 3.0 9.8 + - - +
133A PRO* 1.3 78.0 - - - +
135A GLY* 1.3 59.3 - - - +
136A ALA 3.3 2.5 + - - +
221A THR* 3.8 30.7 - - + +
224A ALA* 4.4 3.8 - - + -
225A ALA* 4.3 12.1 - - + +
228A LEU* 4.7 8.6 - - + +
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Residues in contact with GLY 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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116A LEU 3.5 4.3 - - - -
117A GLN* 3.5 23.9 + - - -
118A GLY* 2.8 25.0 + - - -
132A ALA 2.9 13.3 + - - -
133A PRO 3.2 2.5 + - - -
134A LEU* 1.3 78.6 - - - +
136A ALA* 1.3 63.8 + - - +
137A ILE* 5.1 0.9 - - - +
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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