Contacts of the helix formed by residues 102 - 117 (chain J) in PDB entry 5GAG
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 102 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100J LYS 4.0 2.0 + - - -
101J ILE* 1.3 77.5 - - - +
103J ARG* 1.3 59.4 + - - +
104J ALA* 3.1 13.3 + - - +
105J GLN* 3.0 39.2 + - - +
106J LEU* 3.2 8.5 + - - +
141J GLU 3.2 27.6 + - - -
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Residues in contact with ARG 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J SER* 1.3 74.0 - - - +
104J ALA* 1.3 56.0 + - - +
105J GLN 3.3 0.2 - - - -
106J LEU* 3.8 23.2 - - + +
107J GLN* 3.0 44.2 + - - +
126J THR* 4.9 2.2 - - + +
140J VAL* 3.5 27.5 + - + +
141J GLU* 3.3 30.7 + - - +
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Residues in contact with ALA 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J SER* 3.1 11.5 + - - +
103J ARG* 1.3 78.8 - - - +
105J GLN* 1.3 56.6 + - + +
107J GLN* 3.6 9.9 + - - +
108J GLU* 3.0 42.2 + - - +
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Residues in contact with GLN 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J ALA* 2.4 46.7 + - + +
100J LYS 4.0 3.1 - - - +
101J ILE* 3.6 15.9 - - + -
102J SER* 3.0 36.8 + - - +
104J ALA* 1.3 77.0 - - + +
106J LEU* 1.3 58.0 + - - +
107J GLN 3.4 0.4 - - - -
108J GLU* 3.8 20.2 + - - +
109J ILE* 2.9 38.1 + - - +
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J LEU* 3.9 7.4 - - + -
101J ILE* 3.7 25.6 - - + -
102J SER 3.2 9.8 + - - +
103J ARG* 3.8 23.1 - - + +
104J ALA 3.5 0.4 - - - -
105J GLN* 1.3 76.5 - - - +
107J GLN* 1.3 57.6 + - - +
109J ILE* 3.9 3.0 - - - +
110J ALA* 3.0 30.5 + - - +
126J THR* 3.2 22.1 + - + +
129J ILE* 3.7 31.1 - - + +
130J GLU* 3.8 18.2 - - + +
133J ALA* 4.1 0.4 - - + -
140J VAL* 3.5 30.1 - - + -
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Residues in contact with GLN 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J ARG* 3.0 30.9 + - - +
104J ALA* 3.9 8.9 - - - +
105J GLN 3.4 0.2 - - - -
106J LEU* 1.3 75.9 - - - +
108J GLU* 1.3 58.7 + - - +
110J ALA* 3.6 1.4 - - - +
111J GLN* 2.9 48.6 + - - +
122J ILE* 4.2 8.4 - - + +
126J THR* 3.3 25.3 - - + +
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Residues in contact with GLU 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J ALA* 5.9 0.9 - - - +
104J ALA* 3.0 36.2 + - - +
105J GLN* 3.9 19.3 - - - +
106J LEU 3.4 0.2 - - - -
107J GLN* 1.3 73.0 - - - +
109J ILE* 1.3 56.4 + - + +
110J ALA 3.2 1.3 - - - -
111J GLN* 3.2 12.7 + - - +
112J THR* 2.6 36.6 + - - -
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Residues in contact with ILE 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J ALA* 4.3 5.4 - - - -
79J LEU* 3.1 57.0 - - + +
80J LEU* 3.4 24.2 - - + -
83J ALA* 3.6 15.7 - - + -
105J GLN 2.9 22.8 + - - +
108J GLU* 1.3 76.5 - - + +
110J ALA* 1.3 56.4 + - - +
111J GLN 3.5 0.2 - - - -
112J THR* 3.4 6.8 + - - -
113J LYS* 2.9 36.8 + - + +
129J ILE* 3.6 29.4 - - + -
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Residues in contact with ALA 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J LEU 3.0 22.6 + - - +
107J GLN 3.6 1.8 - - - +
108J GLU 3.2 0.2 - - - -
109J ILE* 1.3 75.3 - - - +
111J GLN* 1.3 59.1 + - - +
113J LYS* 4.0 7.6 - - - -
114J ALA* 2.9 23.3 + - - +
122J ILE* 4.2 5.0 - - + +
125J MET* 3.3 46.5 - - + +
126J THR* 3.4 9.4 - - - +
129J ILE* 3.8 2.9 - - + -
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Residues in contact with GLN 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J GLN* 2.9 36.1 + - - +
108J GLU* 3.2 10.9 + - - +
110J ALA* 1.3 75.3 - - - +
112J THR* 1.3 59.0 + - - +
114J ALA* 3.1 11.7 + - + +
115J ALA* 3.0 23.9 + - - +
122J ILE* 3.6 36.7 - - + +
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Residues in contact with THR 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J THR* 3.2 37.9 - - + +
74J PRO* 4.9 4.5 - - + -
79J LEU* 3.7 23.0 - - + +
108J GLU 2.6 25.7 + - - -
109J ILE* 3.4 7.4 - - - -
111J GLN* 1.3 72.5 - - - +
113J LYS* 1.3 58.5 + - - +
115J ALA* 3.0 27.7 + - - +
116J ASP 3.2 3.3 + - - -
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Residues in contact with LYS 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059A G 3.0 26.7 + - - +
1060A U 2.3 32.1 + - - -
73J THR* 3.0 30.8 + - - +
74J PRO 3.9 4.0 + - - +
76J ALA 3.9 13.2 - - - +
79J LEU* 4.7 0.7 - - + -
109J ILE* 2.9 32.4 + - + +
110J ALA* 3.8 3.8 - - - -
112J THR* 1.3 71.7 - - - +
114J ALA* 1.3 55.4 + - - +
115J ALA 3.3 0.2 - - - -
116J ASP* 2.9 33.5 + - - +
117J MET* 2.6 51.8 + - + +
125J MET* 4.9 0.2 - - - -
129J ILE* 3.4 19.5 - - + -
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Residues in contact with ALA 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J ALA 2.9 22.7 + - - +
111J GLN* 3.1 20.5 + - + +
113J LYS* 1.3 72.7 - - - +
115J ALA* 1.3 63.7 + - - +
116J ASP 3.5 0.2 + - - -
117J MET 4.0 6.4 + - - +
122J ILE* 5.6 2.5 - - + -
125J MET* 3.5 29.7 - - + +
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Residues in contact with ALA 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J THR* 4.2 11.2 - - + -
111J GLN 3.0 10.8 + - - +
112J THR* 3.1 14.6 - - - +
114J ALA* 1.3 76.8 - - - +
116J ASP* 1.3 61.0 + - - +
117J MET 3.9 0.2 - - - -
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Residues in contact with ASP 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058A U 4.3 2.1 + - - +
1059A G 3.7 15.6 + - - +
70J VAL* 6.0 0.3 - - - +
72J LYS* 3.0 46.3 + - - +
73J THR* 2.9 24.0 + - - +
112J THR 3.2 4.0 + - - +
113J LYS* 2.9 48.5 + - - +
115J ALA* 1.3 81.3 - - - +
117J MET* 1.3 58.5 + - - -
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Residues in contact with MET 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058A U 3.9 6.7 - - - +
1059A G 3.3 49.6 - - - +
1081A U 5.7 2.7 - - - -
43I LYS* 3.3 16.0 + - - -
113J LYS* 2.6 29.9 + - + +
114J ALA 4.0 5.7 + - - +
115J ALA 3.9 2.0 - - - -
116J ASP* 1.3 75.5 - - - +
118J THR* 1.3 65.6 + - - +
119J GLY 3.5 9.4 - - - +
125J MET* 3.4 46.2 - - + +
128J SER* 3.5 21.3 - - - -
129J ILE* 3.5 16.6 - - + -
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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