Contacts of the helix formed by residues 102 - 117 (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 ASP 102 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98R ILE* 2.7 29.6 + - + +
101R PHE* 1.3 76.3 - - + +
103R LYS* 1.3 63.5 + - - +
104R VAL* 2.9 26.1 + - - +
105R ALA* 3.2 20.4 + - + +
106R PHE* 3.5 14.7 + - - +
2S TYR* 3.1 38.5 + - + +
13S ARG* 5.1 0.7 - - - +
42S ALA* 4.3 4.5 - - - +
45S GLU* 5.8 2.8 + - - -
47S VAL* 5.0 1.2 - - - +
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Residues in contact with LYS 103 (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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42K ALA* 4.7 3.0 - - - +
43K GLU* 3.7 14.9 + - - -
72R ASN* 5.6 0.2 + - - -
99R ALA* 2.6 24.8 + - - +
100R VAL* 2.4 33.5 + - - +
101R PHE 4.0 2.8 + - - +
102R ASP* 1.3 72.0 + - - +
104R VAL* 1.3 63.1 + - + +
106R PHE* 3.1 6.7 + - + +
107R THR* 2.9 33.1 + - - +
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Residues in contact with VAL 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102R ASP* 2.9 12.3 + - - +
103R LYS* 1.3 77.6 - - + +
105R ALA* 1.3 63.9 + - - +
107R THR* 3.1 10.1 + - - +
108R ALA* 3.0 21.3 + - + +
45S GLU* 3.7 44.9 - - + +
47S VAL* 4.2 5.4 - - + -
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Residues in contact with ALA 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R ILE* 4.0 9.0 - - + -
102R ASP* 3.2 25.3 + - - +
104R VAL* 1.3 79.7 - - - +
106R PHE* 1.3 58.1 + - - +
108R ALA* 3.2 5.3 - - - +
109R LEU* 2.9 30.4 + - - +
2S TYR* 3.7 4.7 - - - +
40S MET* 3.6 28.7 - - + -
47S VAL* 3.9 15.3 - - + -
49S ILE* 4.6 1.2 - - - +
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Residues in contact with PHE 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R ILE* 4.1 17.5 - - + -
68R ALA* 3.9 8.1 - - + -
69R ALA* 3.8 26.5 - - + -
72R ASN* 3.5 18.6 - - - -
79R PHE* 4.0 26.9 - + - -
95R LEU* 3.8 17.0 - - + -
98R ILE* 4.0 8.9 - - + +
99R ALA* 3.6 35.9 - - + -
102R ASP 3.5 13.8 + - - +
103R LYS* 3.1 12.2 + - + +
105R ALA* 1.3 77.3 - - - +
107R THR* 1.3 65.4 + - - +
109R LEU* 3.1 10.4 + - + +
110R VAL* 2.9 25.0 + - + +
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Residues in contact with THR 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R ASN* 3.2 24.7 + - - +
103R LYS* 2.9 14.1 + - - +
104R VAL* 3.4 10.7 - - - -
106R PHE* 1.3 74.4 - - - +
108R ALA* 1.3 64.8 + - - +
110R VAL* 3.1 8.1 + - + +
111R GLU* 2.9 45.5 + - + +
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Residues in contact with ALA 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R VAL* 3.0 13.0 + - + +
105R ALA 3.2 11.2 - - - +
106R PHE 3.2 0.2 - - - -
107R THR* 1.3 78.2 - - - +
109R LEU* 1.3 56.4 + - - +
111R GLU* 3.4 7.0 + - - +
112R LYS* 2.9 27.7 + - - +
47S VAL* 4.0 17.7 - - + -
49S ILE* 3.8 17.4 - - + +
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Residues in contact with LEU 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R PHE* 4.2 11.9 - - + -
83R LEU* 3.8 30.9 - - + +
88R VAL* 4.0 18.4 - - + -
90R ILE* 4.1 12.1 - - + -
95R LEU* 3.6 24.0 - - + -
98R ILE* 4.4 18.8 - - + -
105R ALA 2.9 18.5 + - - +
106R PHE* 3.1 15.9 + - + +
108R ALA* 1.3 73.9 - - - +
110R VAL* 1.3 65.4 + - - +
112R LYS* 3.0 6.0 + - + +
113R ALA* 2.9 23.6 + - - +
40S MET* 5.1 3.6 - - - -
49S ILE* 3.9 19.5 - - + -
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Residues in contact with VAL 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ALA* 4.5 2.0 - - - -
72R ASN* 3.9 33.4 - - + +
74R ILE* 4.0 12.3 - - + +
79R PHE* 3.6 29.8 - - + -
106R PHE* 2.9 23.9 + - + +
107R THR* 3.1 7.8 + - - +
109R LEU* 1.3 76.6 - - - +
111R GLU* 1.3 75.0 + - - +
113R ALA* 3.5 1.4 + - - +
114R LYS* 2.8 47.1 + - + +
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Residues in contact with GLU 111 (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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72R ASN 5.4 0.2 - - - +
107R THR* 2.9 34.9 + - + +
108R ALA* 3.8 6.3 - - - +
110R VAL* 1.3 87.1 - - - +
112R LYS* 1.3 66.6 + - - +
113R ALA 3.2 0.2 - - - -
114R LYS* 3.8 19.5 + - - +
115R ALA* 2.9 25.8 + - - +
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Residues in contact with LYS 112 (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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83R LEU* 4.8 2.9 - - + -
86R ALA* 4.0 17.9 - - + +
88R VAL* 4.2 11.2 - - + -
108R ALA 2.9 14.0 + - - +
109R LEU* 3.2 13.9 - - - +
111R GLU* 1.3 78.0 - - - +
113R ALA* 1.3 57.1 + - - +
115R ALA* 3.3 6.5 + - - +
116R ALA* 3.0 25.5 + - - +
49S ILE* 3.0 43.6 + - + +
51S VAL* 3.5 29.7 - - - +
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Residues in contact with ALA 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R ILE* 5.5 3.4 - - + -
79R PHE* 3.6 35.7 - - + +
82R GLY* 3.7 24.6 - - - -
83R LEU* 3.7 8.9 - - + +
109R LEU 2.9 15.0 + - - +
110R VAL 3.8 3.8 - - - +
112R LYS* 1.3 73.3 - - - +
114R LYS* 1.3 59.3 + - - +
115R ALA 3.0 1.8 - - - -
116R ALA* 3.0 3.1 + - - +
117R LEU* 3.0 29.3 + - - +
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Residues in contact with LYS 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R ASN 2.8 28.0 + - - -
73R GLY* 3.8 18.9 + - - -
74R ILE* 4.0 24.7 - - + +
110R VAL* 2.8 38.2 + - + +
111R GLU* 4.0 21.3 + - - +
113R ALA* 1.3 73.2 - - - +
115R ALA* 1.3 56.6 + - - +
117R LEU* 4.2 4.5 - - - +
118R ALA* 3.3 23.7 + - - +
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Residues in contact with ALA 115 (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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111R GLU 2.9 18.9 + - - +
112R LYS* 3.4 7.4 - - - +
114R LYS* 1.3 78.2 - - - +
116R ALA* 1.3 63.5 + - - +
117R LEU 3.3 0.2 - - - -
118R ALA* 3.3 21.3 + - - +
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Residues in contact with ALA 116 (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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82R GLY 3.3 26.9 - - - +
85R LYS* 3.8 22.3 - - + +
86R ALA* 3.7 24.9 - - + +
112R LYS 3.0 5.2 + - - +
113R ALA 3.0 4.0 + - - +
115R ALA* 1.3 76.1 - - - +
117R LEU* 1.3 61.6 + - - +
118R ALA 4.1 4.0 - - - +
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Residues in contact with LEU 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R ILE* 5.1 4.9 - - + -
78R LYS* 3.4 41.7 - - + +
81R ASN* 3.4 26.2 - - + +
82R GLY* 3.7 23.3 - - - +
85R LYS* 3.8 17.0 - - + -
113R ALA 3.0 12.0 + - - +
114R LYS* 4.6 4.5 - - - +
116R ALA* 1.3 73.9 - - - +
118R ALA* 1.3 64.9 + - - +
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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