Contacts of the helix formed by residues 96 - 114 (chain R) in PDB entry 5GJQ
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 GLY 96 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162J LYS* 5.7 1.3 - - - -
166J GLU* 5.6 7.5 + - - +
170J LYS* 4.5 6.5 - - - +
91R ALA* 5.2 0.3 - - - +
94R ASN 4.2 3.6 - - - -
95R LEU* 1.3 76.1 + - - +
97R GLU* 1.3 59.6 + - - +
98R SER 3.6 1.1 - - - -
99R GLU* 3.4 23.1 - - - +
100R ILE* 2.7 40.5 + - - +
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Residues in contact with GLU 97 (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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166J GLU* 5.9 0.4 + - - -
170J LYS* 5.2 24.0 + - - +
206J HIS 5.7 4.0 - - - +
95R LEU* 4.2 12.5 - - - +
96R GLY* 1.3 79.8 - - - +
98R SER* 1.3 64.6 + - - +
99R GLU* 2.9 1.9 + - - -
100R ILE* 3.2 13.9 + - + +
101R ARG* 3.2 12.6 + - - +
130R LYS* 5.7 9.7 - - + +
132R VAL* 6.0 6.3 - - + -
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Residues in contact with SER 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J TYR* 5.0 5.7 - - - +
162J LYS* 4.8 6.1 - - - -
206J HIS* 4.9 21.2 + - - -
97R GLU* 1.3 77.0 - - - +
99R GLU* 1.3 73.1 + - - +
101R ARG* 4.1 9.0 - - - +
102R ASP* 3.5 17.3 + - - +
131R THR 5.7 3.4 + - - -
136R HIS* 5.1 11.6 + - - -
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Residues in contact with GLU 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162J LYS* 2.8 31.5 + - - -
91R ALA* 5.6 3.4 - - + -
94R ASN 5.8 1.3 - - - +
96R GLY* 3.4 21.0 - - - +
97R GLU 2.9 0.4 + - - -
98R SER* 1.3 86.8 + - - +
100R ILE* 1.3 69.0 + - - +
102R ASP* 2.7 19.0 + - - +
103R ALA* 3.0 11.4 + - - +
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Residues in contact with ILE 100 (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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88R LEU* 5.4 2.8 - - + +
91R ALA* 3.6 30.4 - - + +
92R GLU* 4.1 18.2 - - - +
95R LEU* 4.2 10.8 - - + -
96R GLY 2.7 31.7 + - - +
97R GLU* 3.6 9.9 - - + +
99R GLU* 1.3 71.4 - - - +
101R ARG* 1.3 63.3 + - - +
103R ALA* 2.9 10.3 + - - +
104R MET* 2.9 26.8 + - + +
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Residues in contact with ARG 101 (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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97R GLU 3.2 11.2 + - - +
98R SER* 4.1 9.0 - - - +
100R ILE* 1.3 78.2 - - - +
102R ASP* 1.3 56.6 + - - +
104R MET* 3.1 13.9 - - - +
105R MET* 2.8 33.8 + - + +
127R THR* 4.4 7.2 - - - +
130R LYS* 4.0 26.9 - - + -
131R THR* 4.5 9.4 - - + +
136R HIS* 6.5 0.2 - - + -
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Residues in contact with ASP 102 (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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98R SER 3.5 12.6 + - - +
99R GLU* 2.7 20.7 + - - +
101R ARG* 1.3 70.7 - - - +
103R ALA* 1.3 60.4 + - - +
105R MET* 2.9 15.7 + - - +
106R ALA* 2.8 26.9 + - - +
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Residues in contact with ALA 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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84R LEU* 5.0 9.8 - - + +
87R GLU* 5.2 7.0 - - + -
88R LEU* 4.1 29.2 - - + +
91R ALA* 6.0 1.8 - - + -
99R GLU 3.0 7.7 + - - +
100R ILE* 2.9 12.4 + - - +
102R ASP* 1.3 74.6 - - - +
104R MET* 1.3 57.2 + - - +
106R ALA* 3.2 11.6 + - - +
107R LYS* 2.8 25.0 + - - +
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Residues in contact with MET 104 (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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88R LEU* 4.9 9.1 - - + +
100R ILE* 2.9 19.4 + - + +
101R ARG* 3.1 14.1 - - - +
103R ALA* 1.3 73.8 - - - +
105R MET* 1.3 57.7 + - - +
107R LYS* 2.5 31.0 + - + +
108R ALA* 2.8 15.4 + - - +
123R ALA* 4.9 1.7 - - + +
126R LYS* 4.0 26.7 - - - +
127R THR* 3.3 26.0 - - + +
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Residues in contact with MET 105 (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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101R ARG* 2.8 27.7 + - + +
102R ASP* 2.9 15.7 + - - +
104R MET* 1.3 73.1 - - - +
106R ALA* 1.3 47.8 - - - +
108R ALA* 5.1 2.9 - - - -
109R GLU* 2.5 40.8 + - - +
124R PHE* 5.2 4.7 - - + -
127R THR* 4.5 12.7 - - + +
131R THR* 6.5 0.4 - - + -
136R HIS* 5.7 11.4 - - + +
140R ILE* 5.9 7.9 - - + -
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Residues in contact with ALA 106 (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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84R LEU* 3.4 23.7 - - + +
102R ASP* 2.8 11.4 + - - +
103R ALA* 3.4 12.6 - - - +
104R MET 3.0 0.2 - - - -
105R MET* 1.3 74.5 - - - +
107R LYS* 1.3 60.1 + - - +
109R GLU* 3.5 11.1 - - - +
110R TYR* 2.9 27.9 + - - +
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Residues in contact with LYS 107 (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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81R LEU* 6.4 2.7 - - + -
84R LEU* 4.1 15.0 - - + -
85R ASP* 6.3 3.1 - - - -
88R LEU* 5.8 4.3 - - + -
103R ALA 2.8 11.0 + - - +
104R MET* 2.5 21.9 + - + +
106R ALA* 1.3 67.4 - - - +
108R ALA* 1.3 58.8 + - - +
110R TYR* 2.7 26.7 + - + +
111R LEU* 2.9 17.9 + - + +
123R ALA* 4.6 10.8 - - + -
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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
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104R MET 2.8 12.5 + - - +
105R MET* 4.6 1.8 - - - +
107R LYS* 1.3 75.1 - - - +
109R GLU* 1.3 62.3 + - - +
111R LEU* 3.0 4.8 + - - -
112R CYS 2.9 16.8 + - - -
120R ALA* 3.1 16.4 - - - +
123R ALA* 3.1 26.9 - - + -
124R PHE* 2.9 42.3 - - + +
127R THR* 5.7 0.4 - - + -
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Residues in contact with GLU 109 (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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14R ASN* 4.6 11.9 + - - +
105R MET 2.5 26.3 + - - +
106R ALA* 3.5 10.9 - - - +
108R ALA* 1.3 78.7 - - - +
110R TYR* 1.3 70.5 + - - +
112R CYS* 2.7 30.2 + - + +
113R ARG* 2.9 22.2 + - - +
124R PHE* 3.8 6.5 - - + -
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Residues in contact with TYR 110 (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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49R ASN* 4.6 4.1 - - - -
76R ALA 4.1 0.5 + - - -
77R ASN* 3.0 50.1 + - + -
80R GLU* 3.9 21.3 - - + +
81R LEU* 4.0 19.7 - - + -
84R LEU* 3.9 14.1 - - + -
106R ALA 2.9 21.5 + - - +
107R LYS* 2.7 13.9 + - - +
109R GLU* 1.3 79.5 + - - +
111R LEU* 1.3 51.8 + - + -
113R ARG* 3.2 12.3 + - + +
114R ILE* 2.6 63.9 + - + +
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Residues in contact with LEU 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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107R LYS* 2.9 20.7 + - + +
108R ALA* 3.1 12.8 - - - +
110R TYR* 1.3 79.9 - - + +
112R CYS* 1.3 48.6 + - - +
114R ILE* 2.9 8.0 - - - -
115R GLY 2.4 28.1 + - - -
116R ASP* 2.7 25.7 + - + +
119R GLY* 3.9 9.9 - - - -
120R ALA* 3.4 30.7 - - + +
123R ALA* 5.5 0.2 - - + -
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Residues in contact with CYS 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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14R ASN 4.1 18.2 - - - +
15R PRO* 3.8 30.7 - - + +
108R ALA 2.9 8.1 + - - +
109R GLU* 2.7 26.2 + - + +
111R LEU* 1.3 68.1 - - - +
113R ARG* 1.3 56.8 + - - +
115R GLY* 2.6 24.5 + - - +
120R ALA* 5.0 2.5 - - + -
124R PHE* 5.1 6.7 - - + -
147R ILE* 5.8 4.9 - - + -
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Residues in contact with ARG 113 (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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14R ASN 4.9 4.1 - - - +
47R ASP 5.7 0.2 - - - +
48R ASN* 4.0 28.0 - - + +
49R ASN* 5.4 1.6 - - - -
50R MET* 3.5 22.0 - - - +
109R GLU* 2.9 20.8 + - - +
110R TYR* 3.6 18.4 - - + +
112R CYS* 1.3 75.7 - - - +
114R ILE* 1.3 67.3 + - + +
115R GLY 3.3 0.2 + - - -
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Residues in contact with ILE 114 (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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48R ASN 4.1 3.8 - - - +
49R ASN* 4.1 12.1 - - - +
50R MET* 4.8 8.2 - - - +
51R ALA* 5.0 2.0 - - + +
52R PRO* 3.5 32.9 - - + +
53R TYR* 5.8 0.9 - - - -
77R ASN* 3.1 39.3 - - + +
110R TYR* 2.6 59.0 + - + +
111R LEU* 2.9 10.1 - - - +
113R ARG* 1.3 76.3 - - + +
115R GLY* 1.3 62.7 + - - +
116R ASP* 2.9 6.7 + - + +
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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
------------------------------------------------------------
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