Contacts of the helix formed by residues 105 - 121 (chain B) in PDB entry 1RQ2
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 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 5.9 2.5 - - - -
70B ALA* 3.5 31.3 + - - +
71B ASP 4.6 0.2 - - - -
72B PRO* 4.1 4.2 - - - +
104B GLY* 1.3 71.9 - - - -
106B THR* 1.3 64.1 + - - -
107B GLY 3.1 3.4 - - - -
108B THR* 2.9 24.7 + - - +
109B GLY 4.0 0.9 + - - -
143B GLN* 4.2 7.5 - - - +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY* 4.7 0.5 - - - -
18B GLY 5.6 0.2 + - - -
42B THR* 2.7 28.0 + - - +
43B ASP* 2.6 33.6 + - - +
70B ALA* 4.1 6.0 - - - +
71B ASP 3.5 31.0 - - - +
74B VAL* 4.0 20.2 - - + -
75B GLY* 3.3 16.4 - - - -
105B GLY* 1.3 68.7 - - - -
107B GLY* 1.3 63.9 + - - +
109B GLY 3.1 3.0 + - - -
110B GLY* 3.0 18.0 + - - -
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Residues in contact with GLY 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.6 27.1 - - - +
17B GLY* 3.8 12.0 - - - -
42B THR* 3.5 3.2 + - - -
100B ALA* 3.7 8.3 - - - -
104B GLY 4.9 2.3 + - - -
105B GLY* 3.1 2.2 - - - -
106B THR* 1.3 82.8 + - - +
108B THR* 1.3 56.0 + - - +
110B GLY 4.3 0.4 - - - -
111B ALA* 2.8 33.6 + - - +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO* 3.6 18.4 - - - +
100B ALA* 4.3 14.1 - - + -
103B GLY 4.5 0.9 - - - +
104B GLY* 3.4 34.5 - - - -
105B GLY 2.9 12.7 + - - +
107B GLY* 1.3 76.7 - - - +
109B GLY* 1.3 57.0 + - - +
111B ALA* 4.4 2.1 - - - +
112B PRO* 3.2 22.3 - - - +
143B GLN* 4.6 8.2 + - - +
144B ALA* 6.5 1.6 - - - -
147B GLY* 4.6 21.8 - - - +
150B ALA* 5.6 0.3 - - - +
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Residues in contact with GLY 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO* 3.0 31.7 - - - +
76B ARG* 3.3 25.3 - - - +
106B THR 3.1 5.6 + - - -
108B THR* 1.3 83.3 + - - +
110B GLY* 1.3 59.3 + - - +
112B PRO* 3.3 11.1 - - - +
113B VAL* 3.8 5.5 - - - +
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.7 19.3 - - - -
42B THR* 4.8 0.7 - - - -
75B GLY 3.7 17.4 - - - -
79B ALA* 4.0 6.9 - - - +
106B THR 3.0 11.7 + - - -
107B GLY 3.2 2.0 + - - -
109B GLY* 1.3 77.5 - - - +
111B ALA* 1.3 65.3 + - - +
113B VAL* 3.1 13.7 + - - +
114B VAL* 3.1 15.6 + - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.7 19.4 - - + +
98B VAL* 3.6 18.3 - - + +
100B ALA* 4.6 9.9 - - + +
107B GLY 2.8 18.0 + - - +
108B THR* 4.4 2.9 - - - +
110B GLY* 1.3 75.9 - - - +
112B PRO* 1.3 64.3 - - + +
114B VAL* 3.2 2.1 + - - -
115B ALA* 2.9 27.9 + - - +
151B LEU* 3.8 19.5 - - + -
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Residues in contact with PRO 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 6.4 0.4 - - + -
108B THR 3.2 22.2 - - - +
109B GLY* 3.3 12.8 - - - +
111B ALA* 1.3 92.1 - - + +
113B VAL* 1.3 57.2 + - + +
116B SER* 2.9 26.5 + - - -
147B GLY 4.5 0.9 - - - +
150B ALA* 3.8 30.1 - - + +
151B LEU* 3.8 20.6 - - + +
154B SER* 3.2 24.9 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 3.8 28.3 - - + +
79B ALA* 3.7 20.0 - - + -
80B GLU* 3.7 38.4 - - + +
109B GLY 3.8 16.2 - - - +
110B GLY 3.1 6.0 + - - +
112B PRO* 1.3 75.0 - - + +
114B VAL* 1.3 65.8 + - - +
116B SER* 2.6 23.7 + - - +
117B ILE* 3.0 25.8 + - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.9 20.0 - - + -
16B ILE* 3.5 32.3 - - + -
40B ILE* 3.9 15.0 - - + -
79B ALA* 5.0 0.9 - - + -
86B ILE* 4.4 23.3 - - + -
90B LEU* 3.8 17.1 - - + +
98B VAL* 3.7 22.0 - - + -
110B GLY 3.1 5.3 + - - +
111B ALA 3.6 6.5 - - - +
113B VAL* 1.3 76.0 - - - +
115B ALA* 1.3 58.1 + - - +
117B ILE* 3.3 3.7 + - - +
118B ALA* 2.9 26.9 + - - +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B VAL* 4.1 8.5 - - + +
111B ALA 2.9 16.3 + - - +
112B PRO 3.8 4.3 - - - +
114B VAL* 1.3 77.7 - - - +
116B SER* 1.3 57.6 + - - +
118B ALA* 3.2 2.9 + - - +
119B ARG* 2.9 26.3 + - - +
125B THR* 3.5 12.8 - - + +
151B LEU* 3.9 4.7 - - + -
154B SER* 3.5 22.6 - - - +
155B CYS* 3.7 23.8 - - - -
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 5.3 2.3 + - - -
112B PRO 2.9 15.2 + - - -
113B VAL* 2.6 27.0 + - - +
115B ALA* 1.3 75.1 - - - +
117B ILE* 1.3 60.1 + - - +
119B ARG* 3.4 8.2 + - - +
120B LYS* 3.0 30.5 + - - +
154B SER* 3.6 16.7 - - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LYS* 3.7 40.4 - - + +
86B ILE* 3.8 14.6 - - + -
87B GLU* 3.6 36.8 - - + +
90B LEU* 4.0 11.2 - - + -
113B VAL* 3.0 26.5 + - + +
114B VAL 3.6 6.1 - - - +
116B SER* 1.3 82.2 + - - +
118B ALA* 1.3 65.6 + - - +
120B LYS* 3.3 6.5 + - - +
121B LEU* 3.1 27.0 + - + +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.9 9.1 - - + +
96B VAL* 3.8 33.4 - - + -
114B VAL 2.9 14.4 + - - +
115B ALA* 3.4 7.0 - - - +
117B ILE* 1.3 75.5 - - - +
119B ARG* 1.3 61.4 + - - +
121B LEU* 3.2 14.2 + - - +
123B ALA* 3.0 25.9 + - - +
125B THR* 3.4 18.6 - - + +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ALA 2.9 16.6 + - - +
116B SER* 3.9 8.9 + - - +
118B ALA* 1.3 76.9 - - - +
120B LYS* 1.3 57.8 + - - +
122B GLY* 3.0 18.7 + - - -
123B ALA 3.9 3.8 - - - +
125B THR* 3.2 8.5 + - - +
153B GLU 3.3 26.3 + - - -
154B SER* 3.3 19.6 + - - +
155B CYS 4.1 8.1 + - - -
156B ASP* 3.7 39.2 - - - +
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B SER 3.0 18.2 + - - +
117B ILE* 3.8 6.5 - - - +
118B ALA 3.3 0.2 - - - -
119B ARG* 1.3 76.9 - - - +
121B LEU* 1.3 60.7 + - + +
122B GLY* 3.1 1.1 + - - -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLU* 3.7 31.9 - - + +
90B LEU* 3.7 24.0 - - + +
91B ARG* 3.9 44.2 - - + +
92B GLY 5.5 1.3 - - - +
93B ALA 5.5 0.9 - - - +
117B ILE* 3.1 24.7 + - + +
118B ALA* 3.4 9.0 - - - +
119B ARG 3.2 0.4 - - - -
120B LYS* 1.3 77.2 - - - +
122B GLY* 1.3 58.7 + - - +
123B ALA* 3.4 4.1 + - + +
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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