Contacts of the helix formed by residues 100 - 113 (chain A) in PDB entry 3AQ8
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 THR 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLY 4.9 4.3 - - - +
99A VAL* 1.3 75.7 - - - +
101A ASP* 1.3 67.0 + - - +
102A ALA* 3.8 7.3 + - - +
103A VAL* 3.4 26.7 + - - +
104A ILE* 3.0 24.7 + - - +
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Residues in contact with ASP 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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95A LYS* 4.9 14.7 + - - +
99A VAL 5.2 0.7 - - - +
100A THR* 1.3 74.3 - - - +
102A ALA* 1.3 59.1 + - - +
104A ILE* 3.3 13.6 + - - +
105A ASN* 2.9 44.1 + - - +
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Residues in contact with ALA 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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100A THR* 3.2 8.3 + - - +
101A ASP* 1.3 77.9 - - - +
103A VAL* 1.4 64.8 + - + +
105A ASN* 3.3 11.1 + - - +
106A GLU* 3.1 28.8 + - - +
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Residues in contact with VAL 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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7A ILE* 4.7 5.6 - - + +
10A LYS* 4.0 43.3 - - + +
11A LEU* 3.6 19.7 - - + -
99A VAL* 3.6 20.9 - - + -
100A THR* 3.2 18.9 + - - +
102A ALA* 1.4 77.5 - - + +
104A ILE* 1.3 66.9 + - - +
106A GLU* 3.1 11.6 + - + +
107A ALA* 3.0 21.0 + - - +
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Residues in contact with ILE 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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91A ALA* 3.7 36.3 - - + +
94A LEU* 3.8 15.3 - - + -
95A LYS* 3.7 33.2 - - + +
99A VAL* 3.7 21.5 - - + +
100A THR 3.0 18.8 + - - +
101A ASP* 3.6 14.4 - - - +
103A VAL* 1.3 74.3 - - - +
105A ASN* 1.3 63.8 + - - +
107A ALA* 3.2 7.3 + - - +
108A ALA* 2.8 31.9 + - + +
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Residues in contact with ASN 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 ASP* 2.9 31.1 + - - +
102A ALA* 3.5 9.4 - - - +
103A VAL 3.1 0.2 - - - -
104A ILE* 1.3 83.5 - - - +
106A GLU* 1.3 57.3 + - + +
108A ALA* 3.4 7.3 + - - +
109A LYS* 2.9 37.6 + - + +
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Residues in contact with GLU 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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7A ILE* 3.6 32.7 - - + +
10A LYS* 2.7 38.4 + - - +
102A ALA* 3.1 20.2 + - - +
103A VAL* 3.1 13.4 + - - +
105A ASN* 1.3 76.8 - - + +
107A ALA* 1.4 61.1 - - - +
109A LYS* 3.3 11.2 + - + +
110A VAL* 3.3 17.8 + - - +
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Residues in contact with ALA 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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7A ILE* 4.1 15.3 - - + +
11A LEU* 4.9 2.2 - - + -
58A LEU* 3.9 25.1 - - + +
90A LEU* 5.5 1.3 - - + -
94A LEU* 4.5 15.3 - - + -
103A VAL 3.0 12.2 + - - +
104A ILE* 3.5 11.2 - - - +
106A GLU* 1.4 78.1 - - - +
108A ALA* 1.3 63.1 + - - +
110A VAL* 3.2 5.2 + - - +
111A ILE* 3.1 32.2 + - + +
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Residues in contact with ALA 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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87A ILE* 4.5 24.9 - - + +
90A LEU* 6.0 1.5 - - - +
91A ALA* 6.3 0.4 - - + -
104A ILE* 2.8 24.5 + - + +
105A ASN* 3.7 8.5 - - - +
107A ALA* 1.3 75.1 - - - +
109A LYS* 1.3 58.1 + - - +
111A ILE* 3.7 9.2 - - - +
112A GLU* 2.8 33.7 + - - +
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ASN* 2.9 23.7 + - + +
106A GLU* 3.5 9.9 - - + +
107A ALA 3.2 0.4 - - - -
108A ALA* 1.3 76.8 - - - +
110A VAL* 1.3 62.3 + - + +
112A GLU* 3.8 11.5 + - - +
113A HIS* 3.1 29.0 + - - -
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Residues in contact with VAL 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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7A ILE* 3.8 18.4 - - + -
57A LEU* 3.8 40.5 - - + +
58A LEU* 4.2 7.4 - - + -
106A GLU 3.3 12.3 + - - +
107A ALA 3.2 7.4 + - - +
109A LYS* 1.3 79.0 - - + +
111A ILE* 1.3 63.7 + - - +
113A HIS* 3.2 26.7 + - - +
114A THR* 4.5 2.6 + - - +
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.2 13.9 - - + -
57A LEU* 4.2 22.7 - - + -
58A LEU* 4.7 11.7 - - + -
83A PHE* 3.8 1.1 - - + -
87A ILE* 3.6 22.0 - - + -
90A LEU* 3.4 32.8 - - + -
107A ALA* 3.1 25.8 + - + +
108A ALA* 3.9 4.9 - - - +
110A VAL* 1.3 74.8 - - - +
112A GLU* 1.3 62.4 + - - +
114A THR* 2.7 30.2 + - - -
144A HEM 3.4 31.6 - - + -
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Residues in contact with GLU 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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83A PHE* 3.5 11.7 - - - -
87A ILE* 4.9 4.7 - - + +
108A ALA 2.8 18.9 + - - +
109A LYS* 3.8 10.3 - - - +
110A VAL 3.2 0.4 - - - -
111A ILE* 1.3 78.4 - - - +
113A HIS* 1.3 62.5 + - + +
114A THR 3.0 1.4 + - - -
115A ARG* 2.8 61.3 + - - +
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Residues in contact with HIS 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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109A LYS* 3.1 31.2 + - + -
110A VAL* 3.2 13.8 + - - +
111A ILE 3.1 1.2 + - - -
112A GLU* 1.3 79.4 - - + +
114A THR* 1.3 61.3 + - + +
115A ARG 3.5 0.7 + - - -
116A LYS* 4.1 16.8 + - - +
117A ASP* 3.8 8.9 - - - +
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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