Contacts of the helix formed by residues 104 - 119 (chain R) in PDB entry 5A0Q
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 VAL 104 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R VAL* 3.9 15.2 - - + +
103R THR* 1.3 73.9 + - - +
105R GLU* 1.3 66.0 + - - +
107R ILE* 3.3 4.0 + - - +
108R THR* 2.7 37.5 + - - +
133R ILE* 4.1 12.1 - - + -
134R VAL* 3.5 32.1 - - - +
135R GLY* 3.4 18.8 - - - +
136R PHE 3.1 28.3 - - - +
137R ASP* 3.8 4.3 - - - +
143R ARG* 4.5 5.8 - - + +
145R TYR* 4.6 7.2 - - + -
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Residues in contact with GLU 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R THR* 2.9 22.9 + - + +
104R VAL* 1.3 84.5 - - - +
106R TYR* 1.4 58.5 + - - +
108R THR* 3.3 8.6 + - - -
109R ARG* 2.9 44.3 + - + +
137R ASP* 2.8 24.9 - - - +
143R ARG* 3.6 20.2 + - - +
145R TYR* 3.2 28.0 - - + +
153R TYR* 4.9 3.6 - - + +
72Z GLU* 5.0 6.8 - - - +
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Residues in contact with TYR 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R GLU* 3.2 33.0 - - + -
94R HIS* 4.0 27.6 - + + +
102R VAL* 3.5 13.9 - - + -
103R THR* 3.2 19.5 + - + +
105R GLU* 1.4 74.3 - - - +
107R ILE* 1.3 64.9 + - - +
109R ARG* 3.4 37.9 + - + +
110R TYR* 3.0 21.6 + - + +
66Z TYR* 6.0 3.1 - + - -
69Z ARG* 5.6 5.1 + - + -
70Z ASN* 3.8 16.2 - - + -
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Residues in contact with ILE 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R LEU* 3.9 13.7 - - + -
69R VAL* 4.0 15.7 - - + -
87R ALA* 4.4 0.4 - - + +
90R GLU* 3.2 22.0 - - - +
91R CYS* 3.4 26.9 - - - -
102R VAL* 3.5 26.5 - - + -
103R THR 3.3 12.7 + - - +
104R VAL 3.4 7.4 - - - +
106R TYR* 1.3 75.3 - - - +
108R THR* 1.3 59.4 - - - +
110R TYR* 3.2 2.6 + - - +
111R ILE* 3.0 51.2 + - + +
133R ILE* 4.0 14.6 - - + -
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Residues in contact with THR 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R VAL 2.7 21.0 + - - -
105R GLU* 3.3 8.5 + - - -
107R ILE* 1.3 75.8 - - - +
109R ARG* 1.4 56.5 + - - +
111R ILE* 4.0 1.0 - - - +
112R ALA* 3.0 31.2 + - - +
133R ILE* 3.8 16.8 - - + +
145R TYR* 3.6 32.5 - - + +
147R THR* 3.5 21.4 + - - +
153R TYR* 3.5 29.2 - - + -
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Residues in contact with ARG 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R THR* 4.6 4.2 - - - +
105R GLU* 2.9 21.0 + - + +
106R TYR* 3.4 52.3 - - + +
108R THR* 1.4 75.0 - - - +
110R TYR* 1.3 60.7 + - - +
112R ALA* 3.5 2.3 + - - +
113R SER* 2.9 28.6 + - - -
153R TYR* 3.4 36.0 + - + +
86S LYS* 6.4 0.9 - - + -
69Z ARG* 3.2 28.1 + - - +
70Z ASN* 3.6 28.4 + - - +
71Z LYS* 5.0 5.7 - - - +
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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
----------------------------------------------------------
86R ARG* 3.2 42.4 + - + +
87R ALA* 4.6 6.5 - - - -
90R GLU* 3.1 56.3 - - + +
106R TYR* 3.0 13.5 + + + +
107R ILE 3.2 1.1 + - - +
109R ARG* 1.3 76.1 - - - +
111R ILE* 1.3 61.3 + - + +
113R SER* 2.9 24.1 + - - -
114R LEU* 2.9 45.9 + - + +
117R ARG* 3.4 28.8 + - - -
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Residues in contact with ILE 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R LEU* 4.4 0.7 - - + -
71R MET* 4.2 15.7 - - - -
83R VAL* 4.0 16.4 - - + -
87R ALA* 3.6 32.8 - - + -
90R GLU* 5.3 0.2 - - - +
107R ILE* 3.0 24.7 + - + +
110R TYR* 1.3 79.7 - - + +
112R ALA* 1.3 57.2 + - - +
114R LEU* 3.3 8.0 + - + +
115R LYS* 2.9 55.1 + - + +
131R ALA* 5.2 2.9 - - + -
133R ILE* 3.5 32.8 - - + -
147R THR* 4.4 2.0 - - + -
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Residues in contact with ALA 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108R THR 3.0 19.6 + - - +
109R ARG 3.7 3.8 - - - +
111R ILE* 1.3 78.1 - - - +
113R SER* 1.4 59.1 + - - +
115R LYS* 3.7 0.6 + - - +
116R GLN* 3.2 19.4 + - - +
147R THR* 3.8 19.9 - - + +
151R GLY* 3.3 32.0 - - - +
153R TYR* 3.7 18.6 - - + -
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Residues in contact with SER 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109R ARG 2.9 13.9 + - - -
110R TYR* 2.9 29.1 + - - -
112R ALA* 1.4 72.0 - - - +
114R LEU* 1.3 61.0 + - - +
116R GLN* 3.5 9.7 + - - +
117R ARG* 3.2 40.3 + - - +
87S THR* 5.9 6.3 - - - -
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Residues in contact with LEU 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R VAL* 4.2 25.6 - - + +
86R ARG* 4.0 22.7 - - + +
87R ALA 4.9 1.1 - - - +
110R TYR* 2.9 53.0 + - + +
111R ILE* 3.4 7.9 - - + +
113R SER* 1.3 75.3 + - - +
115R LYS* 1.3 63.1 + - + +
117R ARG* 3.3 34.3 + - - +
118R TYR* 3.6 29.4 - - + +
127R PHE* 4.2 12.1 - - + -
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Residues in contact with LYS 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R VAL* 4.7 4.3 - - + -
111R ILE* 2.9 35.2 + - + +
112R ALA 4.0 3.8 - - - +
114R LEU* 1.3 74.9 - - + +
116R GLN* 1.4 63.0 + - - +
117R ARG 3.4 0.2 + - - -
118R TYR* 3.7 11.3 + - - +
119R THR* 4.1 7.6 - - - +
126R PRO* 4.7 4.3 - - - +
127R PHE* 4.1 25.8 - - + +
129R ILE* 3.2 41.7 + - - +
131R ALA* 3.5 24.0 - - - +
147R THR* 3.6 23.7 + - + -
148R ASP 3.7 16.4 + - - +
149R PRO* 3.6 25.0 - - + +
151R GLY* 4.6 0.7 - - - -
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Residues in contact with GLN 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112R ALA 3.2 16.2 + - - +
113R SER* 3.6 9.7 - - - +
114R LEU 3.3 0.4 - - - -
115R LYS* 1.4 75.7 - - - +
117R ARG* 1.3 72.7 + - - +
118R TYR 3.2 0.2 + - - -
119R THR* 2.8 26.0 + - - +
120R GLN* 3.7 24.1 + - - +
150R SER 3.9 19.1 - - - +
151R GLY* 4.4 2.0 - - - -
83S ALA* 4.2 14.8 - - + +
84S ASP* 3.3 36.9 + - - +
87S THR* 3.8 25.3 + - + +
135S ARG* 4.1 5.3 - - - +
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Residues in contact with ARG 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ARG* 5.7 2.2 - - - +
110R TYR* 3.4 32.1 + - - -
113R SER* 3.2 39.3 + - - +
114R LEU* 3.4 25.7 - - - +
115R LYS 3.2 1.0 - - - -
116R GLN* 1.3 88.6 - - - +
118R TYR* 1.3 61.3 + - + +
120R GLN* 2.6 32.1 - - - +
121R SER* 2.7 14.1 + - - +
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Residues in contact with TYR 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123Q GLN* 4.1 11.0 - - + -
124Q PHE* 4.7 10.6 - + - -
114R LEU* 3.6 27.2 - - + +
115R LYS 3.7 8.2 + - - +
116R GLN 3.2 0.4 - - - -
117R ARG* 1.3 82.1 - - + +
119R THR* 1.3 63.0 + - - +
121R SER* 3.6 12.4 - - - +
124R ARG* 3.3 72.7 + - + +
125R ARG 3.6 27.4 + - - +
126R PRO* 4.4 2.0 - - + -
127R PHE* 3.4 37.7 - + + -
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Residues in contact with THR 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R ILE* 5.7 0.2 - - - +
8R THR* 3.3 32.6 + - - -
19R VAL* 3.8 26.2 - - + -
115R LYS 4.1 7.6 - - - +
116R GLN* 2.8 23.6 + - - +
118R TYR* 1.3 78.6 - - - +
120R GLN* 1.3 60.8 + - - +
121R SER 3.3 8.3 + - - +
126R PRO* 3.9 23.8 - - + -
149R PRO 4.6 5.4 - - - +
150R SER 5.1 4.1 + - - +
134S SER* 5.6 0.7 - - - -
135S ARG* 3.2 31.6 + - - +
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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
------------------------------------------------------------
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