Contacts of the helix formed by residues 100 - 112 (chain A) in PDB entry 3GJ0
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASP* 2.7 42.1 + - - +
96A VAL* 3.0 27.0 + - - +
97A THR 3.5 2.0 + - - +
98A TYR 3.1 0.4 - - - -
99A LYS* 1.3 78.5 - - - +
101A VAL* 1.3 64.1 + - - +
102A PRO 3.3 2.7 - - - -
103A ASN* 3.1 32.4 + - + +
104A TRP* 3.2 17.9 + - + +
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Residues in contact with VAL 101 (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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88A ILE* 4.2 13.9 - - + +
89A MET 4.7 1.8 - - - +
90A PHE* 4.0 13.5 - - + -
97A THR 3.6 14.6 + - - +
98A TYR* 3.1 23.5 + - + +
100A ASN* 1.3 76.7 - - - +
102A PRO* 1.3 66.6 - - + +
104A TRP* 3.1 10.0 + - + +
105A HIS* 2.9 21.0 + - - +
119A LEU* 3.8 29.8 - - + -
138A PHE* 3.5 35.0 - - + -
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Residues in contact with PRO 102 (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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98A TYR* 3.7 4.5 - - + +
99A LYS* 3.3 17.9 - - - +
100A ASN 3.5 0.2 - - - -
101A VAL* 1.3 94.8 - - + +
103A ASN* 1.3 59.1 + - - +
105A HIS* 3.7 1.9 + - - +
106A ARG* 2.9 30.6 + - - +
138A PHE* 3.7 36.2 - - + -
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Residues in contact with ASN 103 (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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99A LYS 4.7 2.3 - - - +
100A ASN* 3.1 30.1 + - + +
102A PRO* 1.3 78.1 - - - +
104A TRP* 1.3 66.7 - - + +
106A ARG* 2.9 37.9 + - - +
107A ASP* 3.0 31.6 + - - +
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Residues in contact with TRP 104 (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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16A VAL* 3.9 17.7 - - + +
17A GLY* 3.6 32.3 - - - -
18A ASP* 2.8 31.3 + - - +
70A GLU* 3.7 30.3 - - + -
73A GLY 4.6 5.6 - - - -
74A GLY* 4.9 3.6 - - - -
75A LEU* 3.9 23.8 - - + -
80A TYR* 3.5 26.4 + - - -
88A ILE* 4.2 18.2 - - + -
89A MET 5.5 0.2 - - - -
97A THR 5.5 1.3 - - - -
100A ASN* 3.2 26.0 + - + +
101A VAL* 3.1 9.5 + - + +
103A ASN* 1.3 79.1 - - + +
105A HIS* 1.3 63.9 + - - +
107A ASP* 3.3 10.9 + - - +
108A LEU* 2.9 26.0 + - - +
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Residues in contact with HIS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.9 15.4 - - + +
101A VAL 2.9 16.7 + - - +
102A PRO 3.7 2.0 + - - +
104A TRP* 1.3 77.3 - - - +
106A ARG* 1.3 63.6 + - - +
108A LEU* 3.3 2.0 + - - +
109A VAL* 2.9 53.9 + - + +
117A ILE* 3.9 14.8 - - + +
138A PHE* 3.6 28.0 - + + -
142A LYS* 3.6 33.7 + - + +
144A LEU* 3.8 30.6 - - + +
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Residues in contact with ARG 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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102A PRO 2.9 18.5 + - - +
103A ASN* 2.9 46.4 - - - +
105A HIS* 1.3 80.1 + - - +
107A ASP* 1.3 84.5 + - - +
109A VAL* 3.5 7.7 + - - +
110A ARG* 3.0 26.8 + - + +
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Residues in contact with ASP 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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74A GLY* 5.1 9.0 - - - -
75A LEU 5.5 0.5 + - - -
80A TYR* 3.8 26.1 + - + +
103A ASN* 3.0 20.7 + - - +
104A TRP* 3.7 13.5 - - - +
106A ARG* 1.3 102.0 + - - +
108A LEU* 1.3 63.1 + - - +
110A ARG* 3.6 29.0 + - - +
111A VAL* 3.8 12.3 + - - +
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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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14A VAL* 3.7 18.4 - - + -
16A VAL* 5.0 4.0 - - + -
80A TYR* 3.7 31.3 - - + -
86A ALA* 3.4 24.2 - - + -
88A ILE* 4.2 17.3 - - + -
104A TRP 2.9 16.9 + - - +
105A HIS 3.6 3.6 - - - +
107A ASP* 1.3 77.0 - - - +
109A VAL* 1.3 60.4 + - + +
111A VAL* 3.1 6.8 + - - +
112A CYS* 2.9 29.9 + - - +
115A ILE* 4.1 15.3 - - + -
117A ILE* 3.6 26.7 - - + -
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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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105A HIS* 2.9 55.6 + - + +
106A ARG* 3.8 7.9 - - + +
108A LEU* 1.3 74.4 - - + +
110A ARG* 1.3 67.7 + - - +
111A VAL 3.4 0.2 + - - -
112A CYS 3.3 25.6 - - - +
113A GLU* 3.7 13.0 + - - +
114A ASN 5.2 4.7 - - - +
115A ILE* 5.8 0.2 - - + -
117A ILE* 4.0 17.9 - - + -
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Residues in contact with ARG 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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77A ASP* 2.7 37.0 + - - -
80A TYR* 5.9 1.0 - - - -
106A ARG* 3.0 21.4 + - + +
107A ASP* 3.7 27.0 + - - +
108A LEU 3.2 0.4 - - - -
109A VAL* 1.3 79.2 - - - +
111A VAL* 1.3 69.3 + - - +
113A GLU* 5.9 0.3 - - - +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 4.0 17.5 - - + +
80A TYR* 3.7 35.4 - - + -
81A ILE* 3.9 36.6 - - + +
82A GLN 5.7 0.5 + - - -
107A ASP 3.8 9.2 + - - +
108A LEU 3.1 3.8 + - - +
110A ARG* 1.3 105.7 - - - +
112A CYS* 1.3 58.8 - - - +
113A GLU* 3.9 2.3 + - - +
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Residues in contact with CYS 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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80A TYR* 3.1 36.8 - - - -
82A GLN 4.9 1.6 - - - -
83A ALA* 3.7 21.5 - - - +
108A LEU* 2.9 18.6 + - + +
109A VAL* 3.3 17.8 - - - +
111A VAL* 1.3 82.6 - - - +
113A GLU* 1.3 64.8 + - - +
114A ASN 3.5 2.3 + - - -
115A ILE* 3.6 34.5 - - + +
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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