Contacts of the helix formed by residues 96 - 106 (chain A) in PDB entry 1TAG
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 ARG 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A TYR* 3.4 21.8 - - + -
93A ASP* 2.8 43.4 + - - +
95A ALA* 1.3 94.4 + - - +
97A GLN* 1.3 57.7 + - - +
99A ASP* 2.9 33.8 + - - +
100A ALA* 2.8 28.6 + - - +
125A ARG* 3.6 46.8 + - - +
126A LEU* 3.8 8.3 - - + +
129A ASP* 3.3 23.7 + - - +
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Residues in contact with GLN 97 (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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90A GLN* 2.7 29.1 + - - +
91A TYR* 3.5 30.3 - - + -
94A SER* 3.1 23.0 + - - +
96A ARG* 1.3 76.9 - - - +
98A ASP* 1.3 61.7 + - - +
100A ALA* 3.4 3.8 + - - +
101A ARG* 3.1 53.5 + - - +
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Residues in contact with ASP 98 (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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94A SER 4.4 6.2 - - - +
95A ALA* 3.5 12.2 + - - +
96A ARG 3.2 0.6 - - - -
97A GLN* 1.3 73.8 + - - +
99A ASP* 1.3 69.2 + - - +
101A ARG* 3.3 27.6 + - - +
102A LYS* 2.9 24.3 + - - +
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Residues in contact with ASP 99 (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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95A ALA 4.0 6.3 - - - +
96A ARG* 2.9 39.2 + - - +
98A ASP* 1.3 80.4 - - - +
100A ALA* 1.3 56.9 + - - +
102A LYS* 3.3 5.0 + - - +
103A LEU* 2.8 30.8 + - - +
122A ILE* 3.4 23.1 - - + +
125A ARG* 2.9 42.8 + - - +
126A LEU* 4.1 8.3 - - + -
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Residues in contact with ALA 100 (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 VAL* 3.8 15.8 - - + +
91A TYR* 3.2 28.7 - - + +
96A ARG 2.8 10.4 + - - +
97A GLN* 3.6 9.4 - - - +
99A ASP* 1.3 77.2 - - - +
101A ARG* 1.3 57.3 + - + +
103A LEU* 3.2 7.5 + - - +
104A MET* 2.9 34.9 + - + +
126A LEU* 4.1 9.4 - - + +
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Residues in contact with ARG 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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97A GLN* 3.1 46.7 + - - +
98A ASP* 3.5 34.0 + - - +
100A ALA* 1.3 77.7 - - + +
102A LYS* 1.3 64.4 + - - +
104A MET* 3.4 8.4 + - - +
105A HIS* 3.1 22.4 + - - +
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Residues in contact with LYS 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 ASP 2.9 16.3 + - - +
99A ASP* 3.7 5.8 - - - +
101A ARG* 1.3 75.8 - - - +
103A LEU* 1.3 53.1 + - - +
105A HIS* 3.1 22.5 + - + +
106A MET* 2.8 51.9 + - - +
118A GLU* 3.4 26.3 + - - +
122A ILE* 3.5 22.9 - - + -
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Residues in contact with LEU 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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74A LEU* 4.0 16.6 - - + -
77A ILE* 4.1 20.9 - - + -
78A LEU* 4.0 18.6 - - + -
81A VAL* 4.3 9.0 - - + -
99A ASP 2.8 17.6 + - - +
100A ALA* 3.3 5.8 - - - +
102A LYS* 1.3 76.6 - - - +
104A MET* 1.3 57.5 + - + +
106A MET* 3.2 5.0 + - + -
107A ALA* 2.9 28.9 + - - +
119A MET* 4.0 15.7 - - + +
122A ILE* 4.0 14.1 - - + +
123A ILE* 3.9 20.9 - - + -
126A LEU* 3.5 24.7 - - + -
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Residues in contact with MET 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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78A LEU* 3.6 36.3 - - + +
81A VAL* 3.3 35.2 - - + -
82A ARG* 3.9 25.8 - - + -
100A ALA 2.9 21.1 + - - +
101A ARG* 3.8 7.4 - - - +
103A LEU* 1.3 75.1 - - + +
105A HIS* 1.3 63.3 + - - +
107A ALA* 3.4 14.8 + - - +
108A ASP* 3.4 18.3 + - - +
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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
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101A ARG 3.1 14.2 + - - +
102A LYS* 3.3 28.9 - - + +
104A MET* 1.3 77.4 - - - +
106A MET* 1.3 63.2 + - + +
108A ASP* 3.1 17.5 + - - +
109A THR* 3.0 24.4 + - + -
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Residues in contact with MET 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 LYS* 2.8 34.4 + - - +
103A LEU* 3.7 4.5 - - - +
105A HIS* 1.3 74.3 - - + +
107A ALA* 1.3 58.0 + - - +
109A THR* 2.7 27.6 + - - -
110A ILE* 2.9 22.3 + - + +
116A PRO* 4.1 19.3 - - + -
118A GLU* 3.8 46.9 - - + +
119A MET* 3.8 32.5 - - + +
122A ILE* 4.2 12.8 - - - -
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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