Contacts of the helix formed by residues 105 - 113 (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 SER 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLY* 3.4 0.5 - - - -
74A GLY 3.1 19.4 + - - -
77A VAL* 3.6 16.9 - - - +
104A CYS* 1.3 79.4 - - - +
106A GLY* 1.3 63.8 + - - +
107A SER 3.1 2.5 - - - -
108A LEU* 3.0 27.0 + - - +
109A VAL 3.8 0.2 + - - -
123A THR* 3.4 9.4 - - - -
124A HIS* 4.2 3.1 - - - +
127A TYR* 5.1 0.4 - - - -
217A ARG* 3.4 21.5 - - - -
232A CIT 2.5 29.1 + - - -
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Residues in contact with GLY 106 (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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71A ILE* 3.4 18.7 - - - +
72A PRO 3.2 22.7 - - - -
73A GLY* 3.5 4.2 - - - -
77A VAL* 4.3 3.1 - - - -
102A SER* 3.5 10.8 - - - -
103A VAL 2.9 7.6 + - - -
105A SER* 1.3 77.0 - - - +
107A SER* 1.3 61.4 + - - +
109A VAL* 3.1 15.2 + - - +
110A LEU 3.3 8.5 + - - -
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Residues in contact with SER 107 (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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102A SER* 3.1 22.1 + - - -
104A CYS 3.4 4.4 + - - -
106A GLY* 1.3 77.5 - - - +
108A LEU* 1.3 57.0 + - - +
110A LEU* 3.3 5.1 + - - +
111A GLY 2.8 22.9 + - - -
116A LEU* 3.2 18.5 - - - +
122A THR 2.7 27.8 + - - -
123A THR* 3.0 22.3 + - - -
131A LEU* 4.3 1.7 - - - +
151A THR* 3.9 11.7 - - - -
152A GLY 6.1 0.4 - - - -
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Residues in contact with LEU 108 (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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77A VAL* 4.5 0.7 - - + -
81A MET* 3.7 21.7 - - + +
105A SER* 3.0 24.3 + - - +
107A SER* 1.3 77.3 + - - +
109A VAL* 1.3 57.8 + - - +
112A ALA* 2.9 27.2 + - - +
123A THR* 3.8 23.6 - - + +
127A TYR* 4.2 9.9 - - + -
130A LEU* 3.9 38.4 - - + +
131A LEU* 4.3 7.6 - - + -
134A LEU* 3.6 19.1 - - + +
217A ARG* 3.9 29.4 - - + -
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Residues in contact with VAL 109 (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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71A ILE* 4.0 8.5 - - + -
77A VAL* 3.8 35.4 - - + -
80A LEU* 4.0 31.2 - - + +
81A MET* 4.2 7.6 - - + -
87A LEU* 3.8 13.4 - - + +
90A ILE* 3.6 29.8 - - + -
106A GLY 3.1 11.4 + - - +
108A LEU* 1.3 73.7 - - - +
110A LEU* 1.3 66.4 + - - +
112A ALA* 3.1 3.7 + - - +
113A ALA* 2.9 22.5 + - - +
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Residues in contact with LEU 110 (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 ILE* 5.8 0.7 - - + -
71A ILE* 3.8 22.2 - - + -
90A ILE* 4.0 7.2 - - + -
100A VAL* 3.7 21.8 - - + -
101A THR 4.1 7.2 - - - +
102A SER* 3.6 27.1 - - - +
106A GLY 3.3 8.6 + - - +
107A SER* 3.4 7.4 - - - +
109A VAL* 1.3 77.7 - - - +
111A GLY* 1.3 62.8 + - - +
113A ALA* 3.2 10.0 + - - +
114A GLY 3.3 0.2 + - - -
115A LEU* 3.0 41.2 + - + +
116A LEU* 4.1 11.0 - - + -
149A LEU* 3.8 27.6 - - + -
151A THR* 4.3 4.7 - - + -
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Residues in contact with GLY 111 (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 2.8 12.7 + - - -
108A LEU 3.7 3.6 - - - -
109A VAL 3.1 0.4 - - - -
110A LEU* 1.3 77.4 - - - +
112A ALA* 1.3 56.2 + - - +
114A GLY* 2.9 17.8 + - - -
116A LEU* 3.6 25.1 - - - +
134A LEU* 3.8 22.6 - - - +
228A LEU* 3.4 14.0 - - - +
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Residues in contact with ALA 112 (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* 3.6 37.2 - - + +
87A LEU* 4.0 13.7 - - + +
108A LEU 2.9 17.6 + - - +
109A VAL 3.7 4.0 - - - +
111A GLY* 1.3 75.0 - - - +
113A ALA* 1.3 60.0 + - - +
114A GLY 3.2 1.1 + - - -
134A LEU* 4.0 8.8 - - - +
224A ALA* 3.9 18.1 - - + +
228A LEU* 3.7 16.3 - - - +
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Residues in contact with ALA 113 (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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87A LEU* 3.9 24.2 - - + +
90A ILE* 4.4 7.4 - - + -
91A ARG* 2.9 47.5 + - + +
109A VAL 2.9 15.1 + - - +
110A LEU 3.6 6.3 - - - +
111A GLY 3.2 0.4 - - - -
112A ALA* 1.3 74.9 - - - +
114A GLY* 1.3 58.5 + - - +
115A LEU* 3.3 14.2 + - + +
228A LEU* 4.3 3.7 - - - +
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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