Contacts of the helix formed by residues 105 - 118 (chain B) in PDB entry 2RGZ
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 ARG 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B TYR* 3.6 26.9 - - + -
82B GLU* 2.6 9.7 + - - -
102B GLU 4.5 1.6 + - - -
103B LEU 2.7 27.7 + - - +
104B HIS* 1.3 94.2 + - - +
106B LYS* 1.3 68.3 + - - +
107B GLU 3.6 1.3 - - - -
108B ALA* 3.2 12.3 + - - +
109B LEU* 2.8 24.6 + - + +
157B TYR* 4.1 0.7 - - + -
160B ASP* 4.5 1.8 - - - +
185B GLN 3.2 8.1 + - - -
186B PHE* 2.7 58.3 + - + +
188B LEU 2.8 28.9 + - - +
189B PHE* 3.1 40.1 - - - +
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Residues in contact with LYS 106 (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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75B TYR* 3.7 26.4 + - + -
78B TYR* 4.8 3.3 - - - +
79B SER* 3.2 39.7 + - - +
82B GLU* 2.9 27.4 + - + +
104B HIS* 3.8 1.0 - - - +
105B ARG* 1.3 79.1 - - - +
107B GLU* 1.3 67.7 + - - +
109B LEU* 2.8 7.1 + - - +
110B THR* 2.8 30.8 + - - +
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Residues in contact with GLU 107 (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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105B ARG 3.6 0.2 - - - -
106B LYS* 1.3 78.0 - - - +
108B ALA* 1.3 65.2 + - - +
110B THR* 3.4 18.5 - - - -
111B LYS* 3.4 30.1 + - + +
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Residues in contact with ALA 108 (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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104B HIS 5.4 0.4 - - - +
105B ARG* 3.2 21.4 + - - +
106B LYS 2.9 3.4 + - - -
107B GLU* 1.3 77.5 - - - +
109B LEU* 1.3 54.3 + - - +
111B LYS* 2.7 33.6 + - - +
112B ASP* 3.0 14.6 + - - +
185B GLN* 3.7 33.2 - - + +
186B PHE* 4.3 4.9 - - - +
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Residues in contact with LEU 109 (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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71B THR* 3.8 24.9 - - + +
74B LEU* 3.5 49.4 - - + +
75B TYR* 3.7 13.9 - - + +
78B TYR* 4.1 7.4 - - + -
105B ARG* 2.8 26.3 + - + +
106B LYS* 2.8 3.7 + - - +
108B ALA* 1.3 71.7 - - - +
110B THR* 1.3 62.4 + - - +
111B LYS 2.8 1.4 + - - -
112B ASP* 2.8 15.5 + - - +
113B MET* 3.0 19.4 + - - +
186B PHE* 3.5 43.1 - - + -
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 3.3 22.5 - - + +
106B LYS* 2.8 27.8 + - - +
107B GLU* 3.4 13.1 + - - -
109B LEU* 1.3 72.8 - - - +
111B LYS* 1.3 59.5 + - + +
114B GLU* 3.0 25.5 + - - +
121B TRP* 3.2 24.1 - - + -
122B GLU* 4.6 7.4 - - - +
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Residues in contact with LYS 111 (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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107B GLU* 3.7 28.9 - - + +
108B ALA* 2.7 15.1 + - - +
110B THR* 1.3 79.2 - - + +
112B ASP* 1.3 58.7 + - - +
113B MET 2.9 5.2 - - - -
114B GLU* 2.8 31.3 + - + +
115B TYR* 3.3 7.3 + - - +
183B GLY* 4.8 2.1 - - - -
185B GLN* 5.6 10.3 - - + -
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Residues in contact with ASP 112 (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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67B PHE* 6.3 0.2 - - + -
71B THR* 4.0 17.5 - - + +
108B ALA 3.0 11.5 + - - +
109B LEU* 2.8 8.5 + - - +
111B LYS* 1.3 76.0 - - - +
113B MET* 1.3 59.4 + - - +
115B TYR 4.4 1.6 - - - -
116B PHE* 2.9 32.4 - - + +
183B GLY* 2.8 21.1 + - - +
184B THR* 2.8 13.6 + - + -
185B GLN* 2.5 26.5 + - - +
186B PHE* 2.7 39.9 + - - +
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Residues in contact with MET 113 (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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68B LYS* 3.4 2.0 - - - +
71B THR* 3.1 41.7 - - + +
72B THR* 3.3 31.0 - - - +
75B TYR* 4.4 6.5 - - + -
109B LEU 3.0 15.9 + - - +
111B LYS 2.9 0.2 - - - -
112B ASP* 1.3 78.3 - - - +
114B GLU* 1.3 63.1 + - - +
115B TYR 3.6 0.2 - - - -
116B PHE* 4.0 4.3 - - + +
117B PHE* 3.2 50.7 + - + +
121B TRP* 3.1 61.5 - - + -
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Residues in contact with GLU 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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110B THR* 3.0 13.7 - - - +
111B LYS* 2.8 19.7 + - + +
113B MET* 1.3 76.9 - - - +
115B TYR* 1.3 62.4 + - - +
118B GLY* 2.4 50.2 + - - +
119B GLU* 4.1 18.7 - - + +
121B TRP* 2.4 33.5 + - - -
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Residues in contact with TYR 115 (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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64B LYS* 5.4 10.6 + - - -
111B LYS 3.3 3.6 + - - +
112B ASP 4.7 0.4 - - - +
114B GLU* 1.3 81.6 - - - +
116B PHE* 1.3 71.7 + + + +
118B GLY* 4.4 1.4 + - - -
176B LYS 5.2 1.7 + - - -
177B LEU* 3.3 27.6 - - + +
178B PRO* 3.7 29.5 - - + +
182B GLU* 4.3 7.2 - - + -
183B GLY* 3.6 37.5 - - - +
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Residues in contact with PHE 116 (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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64B LYS* 3.9 33.5 - - + +
67B PHE* 3.5 36.6 - + - -
68B LYS* 3.1 47.6 + - + -
71B THR* 4.8 6.3 - - + -
112B ASP* 2.9 24.1 + - + +
113B MET* 4.0 0.6 + - + -
114B GLU 3.2 1.2 - - - -
115B TYR* 1.3 82.2 - + + +
117B PHE* 1.3 68.9 + - + +
118B GLY* 3.1 5.2 + - - -
175B LEU* 4.7 1.3 - - + -
177B LEU* 3.4 36.1 - - + -
183B GLY* 3.5 21.1 - - - -
184B THR* 4.2 1.6 - - + -
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Residues in contact with PHE 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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65B GLU* 4.9 6.5 - - - -
68B LYS* 3.1 50.7 - - + +
69B LEU* 4.5 6.1 - - + -
72B THR* 3.0 27.4 - - - -
113B MET* 3.2 29.9 + - + +
116B PHE* 1.3 78.0 - - + +
118B GLY* 1.3 59.0 + - - +
119B GLU 4.0 1.0 + - - -
121B TRP* 3.1 23.7 + - + +
124B GLN* 3.2 21.9 - - - +
125B VAL* 3.5 24.2 - - + -
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Residues in contact with GLY 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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113B MET 3.6 0.2 + - - -
114B GLU* 2.4 51.6 + - - +
115B TYR 4.9 1.1 - - - -
116B PHE 3.1 4.2 + - - -
117B PHE* 1.3 73.6 - - - +
119B GLU* 1.3 60.0 + - - -
121B TRP* 3.5 2.4 - - - -
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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