Contacts of the helix formed by residues 104 - 121 (chain B) in PDB entry 2RS9
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 ASN 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.7 9.0 - - - -
52B LEU* 5.3 0.2 - - - +
102B TYR* 3.6 3.6 - - - +
103B LEU* 1.3 93.6 + - - +
105B PHE* 1.3 64.8 + - - +
106B ASP* 3.3 14.6 + - + +
107B ASP* 3.5 28.6 + - - +
108B PHE* 3.8 8.7 + - - +
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Residues in contact with PHE 105 (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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48B PHE* 3.5 20.3 - + + -
51B LEU* 5.7 2.5 - - + -
52B LEU* 3.8 26.9 - - + -
55B THR* 4.8 2.2 - - + -
104B ASN* 1.3 72.9 - - - +
106B ASP* 1.3 59.5 + - - +
108B PHE* 3.3 13.4 + + - +
109B GLU* 2.9 38.4 + - + +
144B LEU* 3.3 57.4 - - + -
147B ALA* 3.8 14.8 - - + -
148B ARG* 3.6 41.1 - - + -
151B ALA* 5.0 5.8 - - + -
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Residues in contact with ASP 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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104B ASN* 4.4 12.0 - - + +
105B PHE* 1.3 78.2 + - - +
107B ASP* 1.3 62.3 + - - +
109B GLU* 3.6 13.2 + - - +
110B GLU* 2.9 37.9 + - + +
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Residues in contact with ASP 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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101B ARG 5.6 2.0 - - - +
102B TYR* 4.3 17.3 - - + -
103B LEU 5.6 0.9 + - - -
104B ASN* 3.5 27.2 + - - +
105B PHE 3.3 0.6 - - - -
106B ASP* 1.3 75.3 - - - +
108B PHE* 1.3 58.5 + - - +
110B GLU* 3.2 6.3 + - - +
111B ASP* 3.0 42.2 + - - +
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Residues in contact with PHE 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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52B LEU* 3.9 31.9 - - + -
55B THR* 3.7 18.2 - - + -
56B LEU* 3.8 31.2 - - + -
59B LEU* 4.4 4.0 - - + -
93B MET* 3.7 31.0 - - + +
97B LEU* 3.9 22.0 - - + -
102B TYR* 4.0 31.2 - + + -
104B ASN 3.8 7.7 + - - +
105B PHE* 3.3 16.9 + + - +
107B ASP* 1.3 77.5 - - - +
109B GLU* 1.3 60.1 + - - +
111B ASP* 5.1 0.2 - - - -
112B PHE* 3.7 15.1 + - - +
144B LEU* 3.7 26.1 - - + +
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Residues in contact with GLU 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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105B PHE* 2.9 33.4 + - + +
106B ASP* 3.7 12.8 - - - +
108B PHE* 1.3 75.9 - - - +
110B GLU* 1.3 65.3 + - + +
112B PHE* 3.3 5.0 + - - +
113B ASN* 2.8 39.7 + - - +
144B LEU* 4.1 34.0 - - + +
145B ARG* 4.9 15.8 + - - -
148B ARG* 5.2 7.5 - - - -
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Residues in contact with GLU 110 (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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106B ASP* 2.9 27.7 + - + +
107B ASP* 3.2 7.6 + - - +
109B GLU* 1.3 79.7 - - + +
111B ASP* 1.3 59.8 + - - +
113B ASN* 3.4 20.3 + - - +
114B LEU* 2.9 26.7 + - - +
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Residues in contact with ASP 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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86B LYS* 5.8 1.7 + - - -
88B MET* 3.8 20.9 - - + +
93B MET* 3.6 23.6 - - - -
96B ASN* 5.4 0.6 + - - -
102B TYR* 3.5 20.2 + - + +
107B ASP* 3.0 26.0 + - - +
108B PHE 4.5 0.4 - - - +
110B GLU* 1.3 73.0 - - - +
112B PHE* 1.3 63.0 + - - +
114B LEU* 3.4 18.8 + - - +
115B ILE* 3.1 27.5 + - - +
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Residues in contact with PHE 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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59B LEU* 3.6 35.0 - - + -
90B PHE* 4.0 24.0 - + - -
93B MET* 4.2 10.4 - - + -
108B PHE 3.7 13.0 + - - +
109B GLU 3.3 9.3 + - - +
111B ASP* 1.3 74.5 - - - +
113B ASN* 1.3 68.8 + - - +
115B ILE* 3.2 14.7 + - + +
116B VAL* 3.1 34.9 + - + +
136B LEU* 3.5 50.7 - - + -
137B ARG* 4.8 2.7 - - - -
140B GLY* 4.3 4.7 - - - -
141B GLY* 4.5 1.8 - - - -
144B LEU* 3.6 27.4 - - + -
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Residues in contact with ASN 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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109B GLU* 2.8 41.4 + - - +
110B GLU* 3.5 22.6 + - - +
112B PHE* 1.3 81.9 - - - +
114B LEU* 1.3 56.0 + - - +
116B VAL* 3.4 8.5 + - - +
117B SER* 3.0 33.9 + - - +
137B ARG* 5.6 5.7 - - - +
144B LEU* 5.0 1.8 - - - +
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Residues in contact with LEU 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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86B LYS* 3.3 60.6 - - + +
88B MET* 3.6 22.9 - - + -
110B GLU 2.9 14.9 + - - +
111B ASP* 3.4 21.5 - - - +
112B PHE 3.3 0.4 - - - -
113B ASN* 1.3 74.7 - - - +
115B ILE* 1.3 55.9 + - - +
117B SER* 3.3 6.3 + - - -
118B ASN* 2.9 42.1 + - - +
121B LYS* 5.3 5.6 - - - +
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Residues in contact with ILE 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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68B PHE* 4.3 32.3 - - + -
88B MET* 3.4 29.8 - - + +
89B ASP* 3.7 22.7 - - - +
90B PHE* 4.3 11.7 - - + +
93B MET* 3.6 32.1 - - + -
111B ASP 3.1 17.3 + - - +
112B PHE* 3.2 13.4 + - + +
114B LEU* 1.3 71.8 - - - +
116B VAL* 1.3 67.3 + - - +
118B ASN* 3.5 12.6 + - - +
119B CYS* 3.6 10.6 + - - +
136B LEU* 5.1 4.5 - - + -
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Residues in contact with VAL 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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68B PHE* 5.7 1.6 - - - -
112B PHE* 3.1 28.8 + - + +
113B ASN* 3.5 10.8 - - - +
115B ILE* 1.3 74.3 - - - +
117B SER* 1.3 65.1 + - - +
119B CYS* 3.2 20.1 + - - +
120B LEU* 3.4 24.4 + - + +
133B ALA* 3.6 23.7 - - - +
136B LEU* 4.0 28.9 - - + -
137B ARG* 4.0 23.8 - - + +
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B ASN* 3.0 19.8 + - - +
114B LEU* 3.3 8.3 + - - -
116B VAL* 1.3 76.5 - - - +
118B ASN* 1.3 56.8 + - - +
120B LEU* 3.2 13.5 + - - +
121B LYS* 3.0 46.8 + - - +
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Residues in contact with ASN 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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80B TYR* 3.9 23.3 + - - +
84B ILE* 3.4 32.9 - - + +
86B LYS 2.9 26.5 + - - +
87B PRO* 3.7 1.6 - - - +
88B MET 3.7 17.1 + - - +
114B LEU* 2.9 31.1 + - - +
115B ILE* 3.9 8.0 - - - +
116B VAL 3.3 0.4 - - - -
117B SER* 1.3 73.1 - - - +
119B CYS* 1.3 60.8 + - - +
121B LYS* 3.0 29.9 + - - +
122B TYR* 3.8 7.4 + - - +
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Residues in contact with CYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ALY 3.7 24.7 - - + -
68B PHE* 3.9 17.3 - - + -
80B TYR* 5.6 0.9 - - - -
115B ILE 3.6 3.9 + - - +
116B VAL 3.2 11.7 + - - +
118B ASN* 1.3 77.1 - - - +
120B LEU* 1.3 55.4 + - - +
122B TYR 2.9 25.3 + - - +
123B ASN* 2.9 22.6 - - - +
129B PHE* 3.2 32.3 - - - -
133B ALA* 3.6 13.5 - - + -
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Residues in contact with LEU 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 VAL* 3.6 28.7 - - + +
117B SER* 3.2 14.5 + - - +
119B CYS* 1.3 73.2 - - - +
121B LYS* 1.3 59.8 + - + +
122B TYR 3.4 0.2 - - - -
123B ASN* 3.2 19.7 + - - +
130B TYR* 3.6 46.6 - - + +
133B ALA* 4.0 7.9 - - + -
134B VAL* 4.4 9.0 - - + -
137B ARG* 5.0 11.7 - - - +
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Residues in contact with LYS 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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83B HIS* 5.3 9.1 + - - +
84B ILE* 3.6 21.7 - - + +
85B LYS* 5.2 8.5 - - - +
86B LYS* 5.6 2.2 - - - +
114B LEU* 5.3 6.7 - - - +
117B SER* 3.0 29.7 + - - +
118B ASN* 3.0 29.1 + - - +
119B CYS 3.1 0.4 + - - -
120B LEU* 1.3 79.3 - - + +
122B TYR* 1.3 61.8 + - - +
123B ASN 4.0 1.1 - - - -
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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
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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