Contacts of the helix formed by residues 107 - 128 (chain B) in PDB entry 4RN1
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 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B SER* 3.2 19.7 - - - -
106B GLU* 1.3 77.0 + - - +
108B ILE* 1.3 61.5 + - - -
109B PHE 3.2 3.4 - - - -
110B ASP* 3.2 18.2 + - - +
111B TYR* 2.9 26.4 + - - +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.7 3.8 - - + -
79B LEU* 3.8 20.0 - - + +
82B VAL* 4.4 9.0 - - + +
83B SER* 3.1 19.5 + - - +
98B LEU* 6.0 0.4 - - + -
103B PRO* 3.8 26.5 - - + -
104B ALA* 4.9 3.6 - - + +
106B GLU 3.4 4.8 + - - +
107B GLY* 1.3 71.8 - - - -
109B PHE* 1.3 60.3 + - - +
111B TYR* 3.5 20.5 + - + +
112B ALA* 3.0 27.0 + - - +
154B TYR* 3.6 54.1 - - + -
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Residues in contact with PHE 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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64B MET* 3.7 15.0 - - + -
67B MET* 3.6 32.1 - - + -
76B LEU* 4.1 7.0 - - + -
79B LEU* 3.6 37.0 - - + +
80B GLN* 3.6 42.8 - - + -
83B SER* 3.2 10.4 + - - +
107B GLY 3.2 0.6 - - - -
108B ILE* 1.3 81.3 - - - +
110B ASP* 1.3 72.2 + - - +
112B ALA* 3.3 5.4 + - + +
113B ALA* 2.9 35.3 + - + +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 4.2 18.0 - - + +
61B VAL* 5.4 1.2 - - - +
83B SER* 4.8 2.2 + - - -
107B GLY* 3.2 20.1 + - - +
109B PHE* 1.3 88.4 - - - +
111B TYR* 1.3 65.3 + - - +
113B ALA* 3.9 5.0 - - - +
114B ALA* 3.0 25.5 + - - +
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Residues in contact with TYR 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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27B MET* 3.6 34.0 - - + -
28B CYS* 3.9 23.0 + - + +
30B SER* 3.8 8.3 - - - +
31B LEU* 3.3 37.3 - - + +
34B ILE* 4.8 2.1 - - - +
104B ALA* 5.2 3.6 - - + -
106B GLU* 5.4 0.2 - - + -
107B GLY 2.9 13.7 + - - +
108B ILE* 3.5 32.1 - - + +
110B ASP* 1.3 78.4 - - - +
112B ALA* 1.3 67.6 + - + +
114B ALA* 3.4 3.1 + - - +
115B ILE* 3.2 55.1 + - + +
141B TRP* 3.9 15.5 + + - -
152B PHE 5.3 1.5 + - - -
154B TYR* 4.6 11.0 - + + -
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Residues in contact with ALA 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 MET* 5.6 0.9 - - - -
79B LEU* 4.5 7.4 - - + -
108B ILE 3.0 17.9 + - - +
109B PHE* 3.3 7.2 + - + +
111B TYR* 1.3 83.4 - - - +
113B ALA* 1.3 56.8 + - - +
115B ILE* 3.3 4.8 + - - +
116B GLY 2.9 24.9 + - - -
154B TYR* 4.5 13.7 - - + -
155B LEU* 3.2 40.9 - - + +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.8 19.5 - - + -
62B ALA* 3.1 24.4 + - - +
67B MET* 4.1 22.8 - - + -
109B PHE* 2.9 25.7 + - + +
110B ASP* 4.0 6.3 - - - +
112B ALA* 1.3 76.2 - - - +
114B ALA* 1.3 57.3 + - - +
117B GLY 3.0 23.2 + - - -
155B LEU* 4.6 0.2 - - - -
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Residues in contact with ALA 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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24B TYR* 3.4 17.8 - - + -
27B MET* 3.9 20.6 - - + -
59B PRO* 5.0 0.7 - - - +
60B LYS 4.2 2.8 - - - +
61B VAL* 4.3 16.8 - - + +
110B ASP 3.0 19.9 + - - +
111B TYR 3.6 4.7 - - - +
112B ALA 3.2 0.2 - - - -
113B ALA* 1.3 78.2 - - - +
115B ILE* 1.3 57.5 + - + +
117B GLY* 4.0 0.9 - - - -
118B ALA* 3.1 26.7 + - - +
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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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24B TYR* 3.9 8.3 - - - +
27B MET* 6.1 0.2 - - + -
28B CYS* 4.0 22.0 - - + -
111B TYR* 3.2 54.3 + - + +
112B ALA* 3.9 4.5 - - - +
114B ALA* 1.3 74.8 - - + +
116B GLY* 1.3 66.6 + - - +
118B ALA* 3.2 2.6 + - - +
119B THR* 3.1 22.3 + - - -
138B SER 3.6 25.8 - - - +
139B GLY* 3.9 4.0 - - - -
141B TRP* 3.6 10.1 - - + +
155B LEU* 5.7 1.6 - - + +
157B ASP* 3.9 25.1 - - + +
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Residues in contact with GLY 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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62B ALA* 4.0 6.5 - - - -
112B ALA 2.9 15.9 + - - -
113B ALA 4.0 0.9 - - - -
115B ILE* 1.3 78.0 - - - +
117B GLY* 1.3 60.2 + - - +
119B THR* 3.4 3.1 + - - -
120B ILE* 3.1 29.3 + - - +
155B LEU* 3.9 17.0 - - - +
157B ASP* 4.0 12.3 - - - +
160B LEU* 4.2 6.8 - - - +
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Residues in contact with GLY 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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60B LYS* 3.1 21.5 - - - +
61B VAL 4.1 0.4 - - - -
62B ALA* 3.5 21.8 - - - +
66B GLU* 5.6 0.2 - - - -
113B ALA 3.0 11.3 + - - -
116B GLY* 1.3 73.6 - - - +
118B ALA* 1.3 56.0 + - - +
120B ILE* 3.8 5.3 - - - +
121B THR* 2.6 38.5 + - - -
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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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19B ILE* 3.9 11.3 - - + +
24B TYR* 3.3 35.0 - - + +
59B PRO* 3.7 20.6 - - + -
60B LYS 3.6 0.6 + - - -
114B ALA 3.1 15.9 + - - +
115B ILE 3.2 3.1 + - - +
117B GLY* 1.3 76.6 - - - +
119B THR* 1.3 57.1 + - - +
121B THR* 3.4 3.0 + - - -
122B ALA* 3.1 26.7 + - - +
136B ASN* 3.7 5.8 + - - +
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Residues in contact with THR 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 ILE 3.1 10.5 + - - -
116B GLY 3.9 3.8 - - - -
117B GLY 3.3 0.2 - - - -
118B ALA* 1.3 73.8 - - - +
120B ILE* 1.3 61.8 + - - +
122B ALA* 3.3 7.4 + - - +
123B ALA* 2.9 26.0 + - - +
136B ASN* 2.8 23.8 + - - +
157B ASP* 2.8 42.9 + - - +
161B GLY* 3.8 13.2 - - - -
299B LEU* 3.8 15.6 - - + +
301B LEU* 3.9 13.8 - - + +
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Residues in contact with ILE 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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62B ALA* 4.5 8.5 - - + -
66B GLU* 3.8 40.4 - - + +
116B GLY 3.1 17.2 + - - +
117B GLY* 3.8 6.5 - - - +
119B THR* 1.3 76.8 - - - +
121B THR* 1.3 53.5 + - - +
123B ALA* 3.2 7.4 + - - +
124B GLN* 2.8 33.1 + - + +
160B LEU* 4.1 35.2 - - + +
161B GLY* 5.0 0.7 - - - -
164B ARG* 3.5 38.5 - - + +
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Residues in contact with THR 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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19B ILE* 4.0 15.7 - - + -
57B VAL* 4.0 18.4 - - + -
58B LYS 4.0 10.3 - - - +
59B PRO* 4.2 2.7 - - + -
60B LYS* 3.1 29.0 + - + +
117B GLY 2.6 25.7 + - - -
118B ALA 3.5 7.0 - - - -
120B ILE* 1.3 77.3 - - - +
122B ALA* 1.3 62.4 + - - +
124B GLN* 3.2 8.1 + - + +
125B CYS* 3.0 29.2 + - - -
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Residues in contact with ALA 122 (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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19B ILE* 3.7 22.7 - - + -
118B ALA 3.1 13.8 + - - +
119B THR* 3.3 7.4 + - - +
121B THR* 1.3 75.7 - - - +
123B ALA* 1.3 62.5 + - - +
125B CYS* 3.3 8.0 + - - +
126B LEU* 3.2 17.9 + - - +
134B ALA* 3.5 21.6 - - + +
136B ASN* 4.8 3.8 - - + -
299B LEU* 3.5 25.1 - - + -
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Residues in contact with ALA 123 (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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119B THR 2.9 14.7 + - - +
120B ILE* 3.5 9.2 - - - +
122B ALA* 1.3 77.2 - - - +
124B GLN* 1.3 56.2 + - - +
126B LEU* 3.1 11.4 + - - +
127B ILE* 3.0 31.1 + - - +
161B GLY* 3.7 23.8 - - - +
164B ARG* 3.8 13.9 - - + -
165B LEU* 3.7 15.0 - - + +
299B LEU* 4.3 6.9 - - + +
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Residues in contact with GLN 124 (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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120B ILE* 2.8 20.6 + - + +
121B THR* 3.2 8.3 + - - +
123B ALA* 1.3 73.2 - - - +
125B CYS* 1.3 58.1 + - - +
127B ILE* 3.1 18.1 + - - +
128B ASP* 2.8 68.2 + - - +
164B ARG* 2.8 42.7 + - - +
167B ARG* 4.6 4.5 + - - +
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Residues in contact with CYS 125 (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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17B VAL* 4.2 14.8 - - + -
57B VAL* 4.3 19.7 - - - -
121B THR* 3.0 27.1 + - - -
122B ALA* 3.5 9.0 - - - +
124B GLN* 1.3 76.9 - - - +
126B LEU* 1.3 61.1 + - - +
128B ASP* 3.5 2.3 + - - +
129B GLY 3.3 2.8 + - - -
130B MET* 3.1 61.3 + - + +
131B CYS* 3.9 18.5 + - - -
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Residues in contact with LEU 126 (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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122B ALA 3.2 15.2 + - - +
123B ALA* 3.1 14.5 + - - +
125B CYS* 1.3 77.3 - - - +
127B ILE* 1.3 64.9 + - - +
129B GLY* 3.3 12.1 + - - -
131B CYS* 3.5 36.7 - - - +
132B LYS 3.9 15.9 - - - +
134B ALA* 3.9 10.1 - - + +
165B LEU* 3.9 15.3 - - + -
168B LYS* 4.4 5.9 + - - -
169B PHE* 4.4 7.2 - - - -
297B ALA* 4.0 22.0 - - + +
298B THR 3.7 18.2 - - - +
299B LEU* 3.8 21.3 - - + -
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Residues in contact with ILE 127 (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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123B ALA 3.0 14.1 + - - +
124B GLN* 3.1 29.4 + - - +
126B LEU* 1.3 75.9 - - - +
128B ASP* 1.3 59.9 + - - +
129B GLY 3.0 4.3 + - - -
164B ARG* 4.1 11.4 - - + +
165B LEU* 3.7 22.2 - - + +
167B ARG* 5.2 5.8 - - + -
168B LYS* 3.4 47.5 + - + +
169B PHE* 3.6 25.4 - - + -
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLN* 2.8 50.1 + - - +
125B CYS* 3.5 6.8 + - - +
127B ILE* 1.3 77.3 - - - +
129B GLY* 1.3 62.0 + - - +
130B MET* 3.3 14.9 + - + +
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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
------------------------------------------------------------
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