Contacts of the helix formed by residues 111 - 126 (chain A) in PDB entry 3CRX
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ASP 4.1 1.2 + - - -
110A SER* 1.3 72.2 - - - +
112A ALA* 1.3 57.9 + - - +
114A SER* 4.3 7.0 - - - -
115A LEU* 2.9 63.3 + - - +
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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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68A PRO* 4.4 17.3 - - + -
69A GLU* 3.9 22.4 - - - +
72A ARG* 3.9 20.5 + - - +
110A SER* 3.2 1.5 - - - -
111A ASN* 1.3 79.5 - - - +
113A VAL* 1.3 57.9 + - - +
115A LEU* 3.7 6.6 - - - +
116A VAL* 3.0 27.9 + - - +
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Residues in contact with VAL 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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68A PRO* 3.5 25.8 - - + +
71A VAL* 4.0 13.2 - - + -
72A ARG* 4.3 3.4 - - - +
75A LEU* 3.8 12.1 - - + -
92A LEU* 3.7 32.8 - - + -
107A PRO 3.2 33.2 - - - +
108A SER* 4.2 2.5 - - - -
110A SER* 3.4 9.0 + - - +
112A ALA* 1.3 72.4 - - - +
114A SER* 1.3 66.6 + - - +
116A VAL* 3.1 9.1 - - - +
117A MET* 3.0 23.4 + - - +
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Residues in contact with SER 114 (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 SER* 3.0 20.8 + - - +
109A ASP 4.7 0.2 - - - -
110A SER 2.8 21.5 + - - -
111A ASN* 3.8 10.0 - - - -
113A VAL* 1.3 77.7 - - - +
115A LEU* 1.3 62.7 + - - +
117A MET* 3.6 5.9 + - - +
118A ARG* 3.3 22.0 + - - +
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Residues in contact with LEU 115 (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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72A ARG* 6.2 0.7 - - - +
111A ASN* 2.9 48.5 + - - +
112A ALA* 3.7 5.6 - - - +
114A SER* 1.3 76.2 - - - +
116A VAL* 1.3 59.6 + - - +
118A ARG* 3.3 13.6 + - + +
119A ARG* 3.0 27.6 + - - +
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Residues in contact with VAL 116 (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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72A ARG* 3.8 29.8 - - + +
75A LEU* 3.4 29.2 - - + -
76A LEU* 3.6 35.0 - - + -
112A ALA 3.0 13.3 + - - +
113A VAL* 3.1 20.0 - - - +
115A LEU* 1.3 73.4 - - - +
117A MET* 1.3 66.5 + - - +
119A ARG* 3.2 9.5 + - + +
120A ILE* 2.9 38.6 + - + +
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Residues in contact with MET 117 (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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75A LEU* 4.1 19.5 - - - -
85A VAL* 4.0 17.3 - - + -
88A ILE* 3.9 28.3 - - + +
89A GLN* 3.5 35.0 - - + +
92A LEU* 4.2 19.3 - - + -
113A VAL 3.0 12.4 + - - +
114A SER* 3.9 6.3 - - - +
116A VAL* 1.3 81.5 - - + +
118A ARG* 1.3 57.7 + - - +
120A ILE* 3.4 10.3 + - + +
121A ARG* 3.0 34.0 + - + +
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Residues in contact with ARG 118 (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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114A SER 3.3 12.6 + - - +
115A LEU* 3.6 17.6 - - + +
116A VAL 3.2 0.4 - - - -
117A MET* 1.3 79.9 - - - +
119A ARG* 1.3 62.1 + - - +
121A ARG* 3.4 35.0 + - - +
122A LYS* 3.1 28.2 + - + +
21F C 4.8 0.2 + - - -
22F G 2.9 60.1 + - - -
23F T 3.3 14.4 + - - -
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Residues in contact with ARG 119 (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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72A ARG* 3.3 25.1 - - - +
76A LEU* 3.4 31.7 - - - +
79A GLN* 5.2 1.2 + - - -
115A LEU 3.0 13.5 + - - +
116A VAL* 3.5 12.8 - - - +
118A ARG* 1.3 78.6 - - - +
120A ILE* 1.3 60.1 + - + +
122A LYS* 3.8 7.4 - - - +
123A GLU* 2.9 66.1 + - + +
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Residues in contact with ILE 120 (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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75A LEU* 3.8 41.1 - - + +
76A LEU* 4.3 5.6 - - + +
79A GLN* 3.9 24.2 - - + +
85A VAL* 4.8 3.6 - - + -
88A ILE* 3.7 31.4 - - + -
116A VAL* 2.9 30.2 + - + +
117A MET* 3.8 14.8 - - + +
119A ARG* 1.3 75.5 - - + +
121A ARG* 1.3 68.3 + - - +
124A ASN* 2.9 38.5 + - - +
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Residues in contact with ARG 121 (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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85A VAL* 3.9 30.0 - - + +
89A GLN* 4.4 10.0 + - - +
117A MET* 3.0 20.2 + - + +
118A ARG* 3.4 42.2 + - - +
120A ILE* 1.3 76.6 - - - +
122A LYS* 1.3 65.3 + - - +
124A ASN* 4.2 0.5 - - - +
125A VAL* 2.9 41.9 + - + +
23F T 5.7 1.6 + - - -
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Residues in contact with LYS 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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118A ARG* 3.1 20.9 + - + +
119A ARG* 3.8 8.3 - - - +
121A ARG* 1.3 81.8 - - - +
123A GLU* 1.3 72.9 + - - +
125A VAL* 3.3 5.8 + - - +
126A ASP* 3.0 37.1 + - - +
23F T 5.5 6.7 - - - +
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Residues in contact with GLU 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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79A GLN* 2.9 27.8 + - - +
119A ARG* 2.9 59.8 + - + +
120A ILE 3.8 2.2 - - - +
122A LYS* 1.3 85.0 - - + +
124A ASN* 1.3 51.8 + - - +
126A ASP* 2.8 11.5 + - - +
127A ALA* 2.7 35.8 + - - +
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Residues in contact with ASN 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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79A GLN* 3.0 38.6 + - - +
82A GLY 5.9 0.8 - - - -
83A LEU 3.8 18.6 + - - -
85A VAL* 3.7 17.7 - - + +
120A ILE* 2.9 25.4 + - - +
123A GLU* 1.3 74.3 - - - +
125A VAL* 1.3 61.6 + - - +
127A ALA* 3.3 17.2 + - - +
128A GLY 3.5 0.9 + - - -
129A GLU* 3.1 44.8 + - - +
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Residues in contact with VAL 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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85A VAL* 5.0 6.7 - - + -
121A ARG* 2.9 34.6 + - + +
122A LYS* 3.6 7.0 - - - +
123A GLU 3.1 1.0 - - - -
124A ASN* 1.3 76.5 - - - +
126A ASP* 1.3 65.8 + - - +
128A GLY* 3.4 11.6 + - - -
129A GLU* 3.9 12.4 + - + +
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Residues in contact with ASP 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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122A LYS* 3.0 30.5 + - - +
123A GLU* 2.8 10.6 + - - +
125A VAL* 1.3 76.2 - - - +
127A ALA* 1.3 57.8 + - - +
128A GLY* 3.0 10.2 + - - -
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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