Contacts of the helix formed by residues 107 - 123 (chain Q) 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 CYS 107 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Q LEU* 6.4 0.4 - - - -
72Q MET* 3.6 35.7 - - + -
105Q ILE 3.5 2.0 + - - -
106Q PRO* 1.3 70.2 - - - +
108Q GLU* 1.3 63.6 + - - +
110Q LEU* 3.1 22.0 + - - +
111Q VAL* 3.2 18.7 + - - +
136Q TYR* 4.4 18.8 - - - -
137Q ILE 4.1 4.7 - - - -
138Q GLY* 3.9 15.9 - - - -
140Q ASP* 3.4 13.4 - - + +
146Q GLN* 3.6 20.4 - - + +
148Q TYR* 5.4 2.0 - - - -
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Residues in contact with GLU 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Q PRO 3.2 0.6 - - - -
107Q CYS* 1.3 75.9 - - - +
109Q GLN* 1.3 60.5 + - - +
111Q VAL* 3.4 7.9 + - - +
112Q THR* 3.1 39.3 + - - +
140Q ASP* 4.5 6.5 + - - +
143Q TYR* 5.3 9.0 - - + -
146Q GLN* 3.5 16.4 - - - +
148Q TYR* 3.2 34.1 - - + +
156Q TYR* 3.5 23.0 - - - -
70Y ARG 5.7 1.4 - - - +
71Y ASN* 5.3 7.6 - - - +
73Y TYR* 4.8 9.5 + - + +
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Residues in contact with GLN 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q TYR* 3.2 27.7 - - - -
105Q ILE* 4.0 7.3 - - + +
106Q PRO* 3.4 21.4 - - - +
108Q GLU* 1.3 76.8 - - - +
110Q LEU* 1.3 63.4 + - - +
112Q THR* 3.0 26.1 + - - +
113Q ALA* 3.1 11.6 + - - +
67Y TYR* 3.6 17.4 + - - -
71Y ASN* 3.4 39.9 + - - +
73Y TYR* 3.3 29.0 + - - +
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Residues in contact with LEU 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Q LEU* 3.7 26.2 - - + -
69Q ASN* 3.7 21.5 - - - +
72Q MET* 4.6 9.6 - - + -
90Q LEU* 3.3 40.6 - - + +
93Q ILE* 4.1 18.2 - - + -
94Q ALA* 4.1 5.6 - - + +
105Q ILE* 3.8 24.9 - - + +
106Q PRO 3.4 1.9 + - - +
107Q CYS* 3.1 13.4 + - - +
109Q GLN* 1.3 76.6 - - - +
111Q VAL* 1.4 62.9 + - + +
113Q ALA* 3.4 4.8 + - - +
114Q LEU* 3.2 20.1 + - - +
136Q TYR* 5.3 2.2 - - + -
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Residues in contact with VAL 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107Q CYS* 3.2 15.7 + - - +
108Q GLU* 3.5 8.7 - - - +
110Q LEU* 1.4 74.3 - - + +
112Q THR* 1.4 65.5 + - - +
113Q ALA 3.3 0.2 + - - -
114Q LEU* 3.3 2.4 + - - +
115Q CYS* 3.1 25.4 + - - -
136Q TYR* 2.9 65.3 - - + +
148Q TYR* 4.2 11.4 - - + -
156Q TYR* 3.5 33.4 - - + -
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Residues in contact with THR 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108Q GLU* 3.1 38.0 + - - +
109Q GLN* 3.0 18.3 + - - +
111Q VAL* 1.4 74.4 - - - +
113Q ALA* 1.3 53.5 + - - +
115Q CYS 3.5 0.5 + - - -
116Q ASP* 2.8 39.4 + - - +
156Q TYR* 3.5 31.4 - - + +
81R ARG* 3.8 6.0 + - - -
70Y ARG 6.1 0.7 - - - +
71Y ASN* 5.7 0.9 + - - -
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Residues in contact with ALA 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Q ILE* 3.6 35.4 - - + -
105Q ILE* 5.8 0.2 - - + -
109Q GLN 3.1 10.7 + - - +
110Q LEU 3.6 9.0 - - - +
111Q VAL 3.2 0.2 - - - -
112Q THR* 1.3 75.0 + - - +
114Q LEU* 1.3 65.8 + - - +
116Q ASP* 3.2 20.5 + - - +
117Q ILE* 3.2 16.0 + - + +
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Residues in contact with LEU 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q LEU* 3.7 40.4 - - + +
89Q GLU* 4.1 16.8 - - + -
90Q LEU* 3.7 28.5 - - + +
93Q ILE* 4.1 2.4 - - + +
110Q LEU 3.2 4.4 + - - -
111Q VAL 3.3 2.2 + - - +
113Q ALA* 1.3 79.8 - - - +
115Q CYS* 1.3 57.8 + - - +
117Q ILE* 3.1 16.4 + - + +
118Q LYS* 2.9 33.3 + - + +
134Q LEU* 3.4 24.7 - - + -
136Q TYR* 3.3 24.0 - - - +
150Q SER* 5.4 0.7 - - - +
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Residues in contact with CYS 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111Q VAL* 3.1 26.0 + - - +
112Q THR 4.0 1.1 - - - +
114Q LEU* 1.3 73.4 - - - +
116Q ASP* 1.3 59.4 + - - +
117Q ILE 3.3 0.2 - - - -
118Q LYS* 3.7 8.7 - - - +
119Q GLN* 3.0 25.5 + - - +
136Q TYR* 4.4 3.4 - - - -
150Q SER* 3.1 33.0 - - - -
154Q GLY* 4.2 6.0 - - - -
155Q ASN 3.4 20.4 - - - +
156Q TYR* 4.3 2.5 - - + -
81R ARG* 2.8 30.2 + - - +
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Residues in contact with ASP 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112Q THR* 2.8 28.0 + - - +
113Q ALA* 3.2 12.2 + - - +
115Q CYS* 1.3 74.8 - - - +
117Q ILE* 1.4 65.1 + - + +
119Q GLN* 3.4 2.4 + - - +
120Q ALA* 3.3 22.5 + - - +
81R ARG* 2.9 19.4 + - - -
82R ILE* 3.0 21.1 - - + +
85R ASN* 4.1 11.7 - - - +
70Y ARG* 5.5 3.1 + - - -
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Residues in contact with ILE 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q LEU* 6.2 1.1 - - + -
89Q GLU* 3.9 33.0 - - + +
93Q ILE* 3.8 30.1 - - + -
96Q ARG* 6.2 0.4 - - - +
113Q ALA 3.4 9.0 - - - +
114Q LEU* 3.1 15.3 + - + +
116Q ASP* 1.4 78.0 - - + +
118Q LYS* 1.3 61.6 + - - +
120Q ALA* 3.6 10.8 + - + +
121Q TYR* 3.4 22.4 - - + -
130Q PHE* 4.7 15.0 - - + -
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Residues in contact with LYS 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q LEU* 4.2 23.3 - - + -
114Q LEU* 2.9 22.6 + - - +
115Q CYS* 3.7 9.4 - - - +
117Q ILE* 1.3 75.3 - - - +
119Q GLN* 1.3 63.3 + - - +
121Q TYR* 3.1 21.1 + - - +
122Q THR* 3.7 7.3 + - - +
129Q PRO* 5.1 1.6 - - - +
130Q PHE* 4.0 35.3 + - + +
132Q VAL 2.7 28.9 + - - -
134Q LEU* 4.5 4.8 - - - +
150Q SER* 3.1 28.4 + - - +
151Q ASP 3.5 17.2 + - - +
152Q PRO* 4.1 9.3 - - + +
153Q SER* 4.5 6.3 - - - +
154Q GLY 4.9 5.6 - - - +
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Residues in contact with GLN 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Q CYS 3.0 18.1 + - - +
116Q ASP 3.4 4.7 + - - +
118Q LYS* 1.3 77.0 - - - +
120Q ALA* 1.3 61.0 + - - +
122Q THR* 2.8 40.3 + - - -
123Q GLN* 3.0 23.6 + - + +
153Q SER* 4.3 4.9 - - - +
154Q GLY* 3.2 26.7 - - - +
78R ALA* 3.5 31.9 + - - +
79R ASP* 3.4 7.2 - - - +
82R ILE* 3.8 21.8 - - + -
125R ARG* 3.1 20.1 + - - -
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Residues in contact with ALA 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Q ASP 3.3 11.3 + - - +
117Q ILE* 3.7 13.0 - - - +
118Q LYS 3.2 0.6 - - - -
119Q GLN* 1.3 77.9 - - - +
121Q TYR* 1.4 61.6 + - + +
123Q GLN* 4.4 3.1 - - - -
124Q PHE* 3.1 59.0 + - + +
82R ILE* 6.3 0.4 - - - +
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Residues in contact with TYR 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P GLN* 3.8 19.9 + - + +
9Q THR 4.7 2.3 - - - +
10Q THR* 5.4 0.5 - - - -
117Q ILE* 3.4 24.2 - - + -
118Q LYS 3.1 11.0 + - - +
120Q ALA* 1.4 79.1 - - + +
122Q THR* 1.3 62.7 + - - +
124Q PHE 3.7 11.0 - - - +
126Q GLY 5.3 0.2 + - - -
127Q LYS* 3.3 50.2 + - + +
128Q ARG 3.4 17.5 - - - -
129Q PRO* 3.9 17.2 - - + +
130Q PHE* 3.5 31.6 - + + -
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Residues in contact with THR 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q THR 5.1 3.6 - - - -
10Q THR* 3.1 27.5 + - - -
18Q LEU* 4.3 11.6 - - + +
20Q GLN* 5.8 0.7 - - + -
21Q VAL* 3.9 25.1 - - + -
118Q LYS 3.7 5.8 + - - +
119Q GLN* 2.8 43.2 + - - +
121Q TYR* 1.3 78.4 - - - +
123Q GLN* 1.4 57.9 + - - +
124Q PHE 3.5 0.2 + - - -
129Q PRO* 3.9 25.8 - - + -
153Q SER* 5.1 8.5 - - - -
125R ARG* 3.7 13.3 + - - -
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Residues in contact with GLN 123 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Q THR* 3.3 8.7 + - - -
119Q GLN* 3.0 34.7 + - + +
120Q ALA* 4.1 1.8 - - - +
121Q TYR 3.5 0.2 - - - -
122Q THR* 1.4 77.1 + - - +
124Q PHE* 1.3 76.8 + - + +
79R ASP* 3.1 38.2 + - - +
82R ILE* 5.5 3.3 - - + +
118R TYR* 4.1 7.0 - - + -
124R ARG* 3.6 1.6 - - - +
125R ARG* 3.3 50.8 + - - +
127R PHE* 3.3 34.7 - - + -
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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
------------------------------------------------------------
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