Contacts of the helix formed by residues 75 - 86 (chain R) 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 75 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011A G 3.3 13.5 - - - -
1012A U 3.6 23.3 + - - -
69R ALA* 5.0 0.4 - - - -
70R ARG* 3.7 19.5 - - - +
74R ILE* 1.3 78.2 - - - +
76R TYR* 1.3 65.5 + - - +
77R SER* 3.7 3.6 + - - -
78R LYS* 3.3 33.3 + - - +
79R PHE* 3.0 22.9 + - - +
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Residues in contact with TYR 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A A 4.1 11.9 - - - -
1011A G 3.0 5.8 + - - +
1152A C 3.4 29.2 - - - -
1153A C 3.1 19.1 + - - -
62R ILE* 3.3 34.6 - - + +
65R ILE* 3.6 30.5 - - + -
66R ASN* 3.0 37.3 + - + +
69R ALA* 5.2 0.9 - - - -
75R SER* 1.3 71.0 - - - +
77R SER* 1.3 61.4 + - - +
79R PHE* 3.2 6.7 + - - +
80R ILE* 2.9 55.7 + - + +
92R ARG* 2.6 29.5 + - - -
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Residues in contact with SER 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010A A 4.0 3.1 - - - -
1011A G 2.8 37.6 + - - -
1151A A 3.3 20.5 + - - -
1152A C 3.2 43.8 - - - +
75R SER* 3.7 4.0 + - - -
76R TYR* 1.3 74.3 - - - +
78R LYS* 1.3 67.8 + - - +
80R ILE* 3.3 2.4 + - - +
81R ASN* 3.0 19.8 + - - +
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Residues in contact with LYS 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011A G 6.2 2.2 - - - +
1012A U 6.0 1.1 - - - -
1013A C 4.6 16.9 + - - -
1151A A 4.3 7.4 - - - +
74R ILE* 3.6 22.7 - - + +
75R SER* 3.3 20.7 + - - +
76R TYR 3.4 0.2 - - - -
77R SER* 1.3 82.9 + - - +
79R PHE* 1.3 63.9 + - - +
81R ASN* 3.3 1.6 + - - +
82R GLY* 2.9 19.2 + - - -
117R LEU* 3.4 25.1 - - + +
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Residues in contact with PHE 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R ILE* 3.6 33.2 - - + -
69R ALA* 4.4 5.6 - - + -
74R ILE* 3.5 15.5 - - + +
75R SER 3.0 18.9 + - - +
76R TYR* 3.3 5.6 - - - +
78R LYS* 1.3 75.1 - - - +
80R ILE* 1.3 65.2 + - + +
82R GLY* 3.1 3.8 + - - -
83R LEU* 2.9 51.5 + - + +
95R LEU* 4.1 10.1 - - + -
106R PHE* 4.0 20.9 - + - -
109R LEU* 4.2 11.7 - - + -
110R VAL* 3.6 42.8 - - + -
113R ALA* 3.6 12.8 - - + +
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Residues in contact with ILE 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998A C 5.4 2.7 - - - +
1152A C 3.9 21.1 - - - +
1153A C 5.7 0.2 - - - +
65R ILE* 5.0 0.9 - - + -
76R TYR* 2.9 58.7 + - + +
77R SER 3.8 3.8 - - - +
79R PHE* 1.3 86.6 - - + +
81R ASN* 1.3 67.6 + - - +
83R LEU* 3.1 10.0 + - + +
84R LYS* 2.9 24.5 + - + +
92R ARG* 3.9 25.6 - - + +
95R LEU* 4.8 11.9 - - + -
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Residues in contact with ASN 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150A C 5.6 0.3 + - - -
1151A A 3.2 38.1 + - - +
1152A C 3.1 22.9 + - - -
77R SER 3.0 17.2 + - - +
78R LYS* 3.7 5.4 - - - +
80R ILE* 1.3 76.3 - - - +
82R GLY* 1.3 57.6 + - - +
84R LYS* 3.2 13.3 + - - +
85R LYS* 2.8 58.7 + - - +
117R LEU* 3.4 16.3 - - + +
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Residues in contact with GLY 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R LYS 2.9 11.8 + - - -
79R PHE 3.1 5.1 + - - -
81R ASN* 1.3 76.9 - - - +
83R LEU* 1.3 57.2 + - - +
85R LYS 3.3 0.7 + - - -
86R ALA* 3.0 24.3 + - - +
113R ALA* 3.7 19.4 - - - -
116R ALA* 3.3 11.6 - - - +
117R LEU* 3.7 23.3 - - - +
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Residues in contact with LEU 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79R PHE* 2.9 33.5 + - + +
80R ILE* 3.1 12.8 + - + +
82R GLY* 1.3 74.1 - - - +
84R LYS* 1.3 63.3 + - - +
86R ALA* 3.3 2.0 + - + +
87R SER 3.2 3.3 + - - -
88R VAL* 3.0 57.8 + - + +
90R ILE 5.3 2.0 - - - +
95R LEU* 3.6 30.7 - - + -
109R LEU* 3.8 33.9 - - + +
112R LYS* 4.8 1.1 - - + -
113R ALA* 3.9 18.6 - - + +
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Residues in contact with LYS 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A A 4.8 11.9 + - - -
1152A C 4.0 18.3 + - - +
80R ILE* 2.9 19.1 + - + +
81R ASN* 3.7 21.0 - - - +
83R LEU* 1.3 76.6 - - - +
85R LYS* 1.3 74.3 + - - +
87R SER* 3.5 13.3 + - - +
88R VAL 5.0 2.5 - - - -
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Residues in contact with LYS 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A A 4.8 5.9 + - - -
81R ASN* 2.8 46.4 + - - +
82R GLY 3.8 4.9 - - - +
83R LEU 3.2 0.4 - - - -
84R LYS* 1.3 91.2 - - - +
86R ALA* 1.3 57.1 + - - +
87R SER* 3.2 8.3 + - - -
116R ALA* 3.8 23.4 - - + +
117R LEU* 3.8 18.6 - - + -
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Residues in contact with ALA 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R GLY 3.0 15.0 + - - +
83R LEU* 3.3 6.2 + - - +
85R LYS* 1.3 76.5 - - - +
87R SER* 1.3 70.1 + - - +
88R VAL* 3.4 4.7 + - + -
112R LYS* 4.0 30.3 - - + +
116R ALA* 3.8 12.1 - - + -
51S VAL* 3.1 21.0 - - - +
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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