Contacts of the helix formed by residues 75 - 84 (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 PRO 75 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1060A U 3.2 23.3 - - + +
1061A U 5.8 0.2 - - - +
1063A G 5.3 0.7 - - - +
12J GLN* 3.3 39.7 - - - +
54J PRO 3.0 19.3 - - - +
56J PRO* 3.5 8.3 - - + -
73J THR 3.5 0.2 - - - -
74J PRO* 1.4 86.8 - - + +
76J ALA* 1.3 58.4 + - - +
77J ALA* 3.2 8.1 - - + +
78J VAL* 3.5 23.1 - - + +
79J LEU* 2.7 32.9 + - - +
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Residues in contact with ALA 76 (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 3.4 11.9 - - - +
1060A U 3.0 9.6 + - - +
75J PRO* 1.3 71.0 - - - +
77J ALA* 1.3 56.6 + - - +
80J LEU* 3.0 37.2 + - - +
109J ILE* 4.3 6.5 - - - -
113J LYS* 3.9 4.4 - - - +
129J ILE* 3.3 35.0 - - + -
132J THR* 3.4 27.1 - - + +
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Residues in contact with ALA 77 (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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1060A U 4.5 1.9 + - + -
1062A G 3.1 35.4 - - - +
1063A G 3.4 22.2 - - - +
75J PRO* 3.9 7.2 - - + +
76J ALA* 1.3 78.9 - - - +
78J VAL* 1.3 56.1 + - - +
81J LYS* 3.0 33.2 + - - +
132J THR* 3.4 6.0 - - + +
136J MET* 3.3 16.8 - - - +
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Residues in contact with VAL 78 (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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1063A G 4.8 1.1 - - - +
12J GLN* 4.1 8.7 - - - +
52J GLY 4.7 1.3 - - - +
53J LEU* 3.6 29.2 - - + +
54J PRO* 3.5 41.3 - - + +
74J PRO* 4.4 1.8 - - + -
75J PRO* 3.3 28.4 + - + -
77J ALA* 1.3 73.1 - - - +
79J LEU* 1.3 59.7 + - - +
81J LYS* 3.2 34.2 - - + +
82J LYS 3.0 22.9 + - - -
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Residues in contact with LEU 79 (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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53J LEU* 3.9 2.9 - - + -
73J THR* 4.5 0.9 - - - +
74J PRO* 3.2 46.4 - - + +
75J PRO 2.7 16.2 + - - +
78J VAL* 1.3 71.9 - - - +
80J LEU* 1.3 56.8 + - - +
82J LYS* 3.3 28.1 - - + +
83J ALA* 3.0 30.3 + - - +
109J ILE* 3.1 39.2 - - + +
112J THR* 3.7 35.9 - - + +
113J LYS* 4.7 1.1 - - + -
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Residues in contact with LEU 80 (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 3.0 26.7 + - - +
77J ALA 3.8 1.8 - - - +
79J LEU* 1.3 72.4 - - - +
81J LYS* 1.3 60.4 + - - +
82J LYS 3.5 0.2 - - - -
83J ALA* 4.0 2.9 - - - +
84J ALA* 3.2 18.6 - - - +
101J ILE* 3.5 32.5 - - + -
105J GLN 4.8 0.2 - - - +
106J LEU* 3.9 11.2 - - + -
109J ILE* 3.4 22.7 - - + -
129J ILE* 3.3 31.9 - - + +
132J THR 3.8 5.8 - - - +
133J ALA* 3.5 23.6 - - + +
136J MET* 4.3 0.7 - - - -
138J LEU* 3.0 31.4 - - + +
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Residues in contact with LYS 81 (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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1063A G 3.7 32.8 + - - -
1064A C 3.6 21.4 + - - +
53J LEU* 5.9 0.4 - - + -
54J PRO* 5.7 1.2 - - - +
77J ALA 3.0 22.3 + - - +
78J VAL* 3.2 38.4 + - + +
80J LEU* 1.3 77.9 - - - +
82J LYS* 1.3 56.7 + - - +
86J ILE* 2.7 48.7 + - + +
87J LYS 3.5 25.1 - - - +
89J GLY 4.6 0.4 - - - +
136J MET* 3.5 12.6 - - + -
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Residues in contact with LYS 82 (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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50J GLU* 3.2 36.6 + - - +
53J LEU* 3.5 43.1 - - + +
78J VAL 3.0 8.1 + - - +
79J LEU* 3.3 23.5 - - + +
81J LYS* 1.3 78.4 - - - +
83J ALA* 1.3 66.6 + - + +
85J GLY* 3.5 12.3 + - - -
86J ILE 4.7 1.8 - - - -
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Residues in contact with ALA 83 (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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79J LEU 3.0 21.0 + - - +
82J LYS* 1.3 77.5 - - + +
84J ALA* 1.3 57.6 + - - +
85J GLY 3.2 4.7 - - - -
100J LYS 4.3 0.9 - - - +
101J ILE* 3.7 7.4 - - + -
105J GLN* 2.4 49.6 + - + +
108J GLU* 5.9 1.3 - - - +
109J ILE* 3.6 19.7 - - + -
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Residues in contact with ALA 84 (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 3.2 21.8 + - - +
83J ALA* 1.3 75.3 - - - +
85J GLY* 1.3 55.2 + - - +
86J ILE* 3.1 15.9 + - + +
99J GLY* 4.3 6.4 - - - -
100J LYS 3.9 27.3 + - - +
101J ILE* 3.9 5.8 - - + +
138J LEU* 3.6 28.5 - - + -
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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