Contacts of the helix formed by residues 10 - 32 (chain B) in PDB entry 3J41
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 TRP 10 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 1.3 101.6 - + + +
11B ARG* 1.3 63.9 + - + +
12B ALA 3.3 0.2 - - - -
13B ILE* 3.4 33.2 - - + +
14B CYS* 2.9 33.8 + - - -
88B CYS* 5.5 5.2 - - - -
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Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 2.6 50.9 + - + +
223A LEU* 2.7 45.8 + - - +
224A PHE 2.8 17.2 + - - +
225A PRO* 3.3 32.5 - - + +
226A ARG* 5.0 13.9 - - - +
9B PHE 3.3 4.4 - - - +
10B TRP* 1.3 81.1 - - + +
12B ALA* 1.3 55.8 - - - +
14B CYS* 3.3 6.7 + - - +
15B ALA* 2.9 25.8 + - - +
62B ILE* 4.1 10.5 - - + +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.6 13.9 + - - +
11B ARG* 1.3 78.7 - - - +
13B ILE* 1.3 59.0 + - - +
15B ALA* 3.1 5.1 + - - +
16B GLU* 2.9 34.3 + - - +
62B ILE* 3.5 23.0 - - - +
63B SER* 3.5 17.0 - - - -
85B ARG* 4.5 10.8 - - - +
89B TYR* 3.6 14.8 - - + +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.0 47.5 + - + +
10B TRP* 3.4 35.7 - - + +
11B ARG 3.3 0.2 - - - -
12B ALA* 1.3 78.8 - - - +
14B CYS* 1.3 60.4 + - - +
16B GLU* 3.5 4.7 + - - +
17B PHE* 3.0 26.0 + - + +
88B CYS* 3.8 22.2 - - + +
89B TYR* 4.6 11.4 - - + -
92B ALA* 3.5 19.2 - - + +
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Residues in contact with CYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 4.4 21.8 - - + -
10B TRP* 2.9 29.1 + - - -
11B ARG* 3.5 9.9 - - - +
12B ALA 3.2 0.2 - - - -
13B ILE* 1.3 76.5 - - - +
15B ALA* 1.3 60.7 + - - +
17B PHE* 3.2 6.6 + - - +
18B PHE* 2.8 46.8 + - + -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 5.1 3.5 - - + +
11B ARG 2.9 13.7 + - - +
12B ALA* 3.2 12.6 - - - +
14B CYS* 1.3 77.6 - - - +
16B GLU* 1.3 58.1 + - - +
18B PHE* 3.9 3.4 - - - +
19B ALA* 2.8 35.8 + - - +
59B VAL* 3.8 26.9 - - + +
62B ILE* 4.2 9.2 - - + -
63B SER* 3.6 16.2 - - - +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA 2.9 20.2 + - - +
13B ILE* 3.7 5.8 - - - +
15B ALA* 1.3 76.9 - - - +
17B PHE* 1.3 59.1 + - - +
19B ALA* 4.5 2.7 - - - -
20B SER* 2.5 33.8 + - - -
59B VAL* 5.1 0.3 - - - +
63B SER* 2.6 24.7 + - - +
65B ALA* 3.3 4.1 + - - -
66B HIS 2.9 20.8 + - - -
67B VAL* 2.6 28.7 + - - -
89B TYR* 3.7 30.7 - - + +
92B ALA* 4.2 13.1 - - + +
93B GLN* 3.1 15.3 - - + +
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Residues in contact with PHE 17 (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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13B ILE* 3.0 18.4 + - + +
14B CYS* 3.5 7.0 - - - +
15B ALA 3.1 0.4 - - - -
16B GLU* 1.3 78.8 - - - +
18B PHE* 1.3 93.5 + + - +
21B LEU* 3.1 30.2 + - + +
92B ALA* 3.5 28.9 - - + +
95B LEU* 3.8 17.3 - - + -
96B GLY* 3.5 27.8 - - - -
99B ALA* 4.4 15.3 - - + -
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Residues in contact with PHE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 5.9 0.7 - - + -
218A LEU* 3.5 41.7 - - + -
222A LEU* 4.6 3.8 - - + -
14B CYS* 2.8 45.2 + - + +
15B ALA* 4.1 3.4 - - - +
17B PHE* 1.3 96.4 - + - +
19B ALA* 1.3 59.0 - - - +
21B LEU* 3.2 15.2 + - + +
22B PHE* 2.9 54.5 + + + -
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Residues in contact with ALA 19 (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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15B ALA 2.8 23.0 + - - +
16B GLU 4.3 0.2 - - - +
18B PHE* 1.3 73.1 - - - +
20B SER* 1.3 54.7 + - - +
22B PHE* 4.4 0.6 - - - -
23B TYR* 2.8 35.5 + - - +
55B LEU* 3.2 25.0 - - + +
59B VAL* 4.0 19.7 - - + +
67B VAL* 3.2 26.5 - - + -
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Residues in contact with SER 20 (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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16B GLU 2.5 24.6 + - - -
17B PHE 3.7 4.0 - - - -
18B PHE 3.2 0.2 - - - -
19B ALA* 1.3 73.9 - - - +
21B LEU* 1.3 61.5 + - - +
24B VAL* 3.0 37.2 + - - +
67B VAL* 3.4 23.1 - - - +
93B GLN* 3.3 42.1 - - - +
96B GLY* 3.9 2.2 - - - -
97B ALA* 3.8 4.0 - - - -
186B ALA* 5.8 1.3 - - - -
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Residues in contact with LEU 21 (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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136A PHE* 3.6 33.0 - - + -
17B PHE* 3.1 29.0 + - + +
18B PHE* 3.5 19.5 - - + +
20B SER* 1.3 78.1 - - - +
22B PHE* 1.3 62.6 + - + +
25B PHE* 2.7 39.3 + - + +
96B GLY* 3.0 16.1 + - - +
99B ALA* 4.0 16.6 - - + -
100B GLY* 3.5 25.4 - - - +
103B VAL* 4.9 6.5 - - + -
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Residues in contact with PHE 22 (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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136A PHE* 4.0 24.2 - + - -
139A LEU* 3.7 34.3 - - + -
140A GLN* 4.9 7.2 - - + -
143A LEU* 3.9 24.7 - - + -
218A LEU* 4.1 8.3 - - + -
18B PHE* 2.9 43.5 + + + +
19B ALA* 4.4 0.4 - - - -
21B LEU* 1.3 84.4 - - + +
23B TYR* 1.3 58.3 + - - +
25B PHE* 4.1 1.3 - - - -
26B PHE* 2.8 60.6 + + + +
55B LEU* 3.8 27.8 - - + -
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Residues in contact with TYR 23 (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 ALA 2.8 23.5 + - - +
20B SER 3.7 1.8 - - - +
22B PHE* 1.3 73.3 - - - +
24B VAL* 1.3 69.9 + - + +
26B PHE* 4.4 0.7 - - - +
27B GLY* 2.9 26.7 + - - -
48B PHE* 4.0 18.2 - + - -
51B ALA* 4.6 7.5 - - + +
52B LEU* 4.1 25.0 - - + +
55B LEU* 3.5 17.5 - - + +
67B VAL* 3.6 20.4 - - + -
68B ASN* 5.3 1.0 + - - -
141B PHE* 5.7 0.5 - - - -
168B LEU* 3.2 41.2 - - + +
172B HIS* 5.1 0.9 - - - -
182B GLY 5.1 1.6 + - - -
184B ASN* 3.6 31.7 + - - +
187B ARG* 3.9 19.3 - - + +
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Residues in contact with VAL 24 (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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20B SER* 3.0 19.3 + - - +
21B LEU 4.1 0.7 - - - +
23B TYR* 1.3 87.5 - - + +
25B PHE* 1.3 61.6 + - - +
28B LEU* 2.8 71.2 + - + +
48B PHE* 5.6 0.4 - - - -
97B ALA* 3.4 41.1 - - + +
101B ALA 4.0 4.3 - - - +
186B ALA* 5.7 0.9 - - + -
187B ARG* 4.2 14.6 - - + +
190B ALA* 4.0 8.5 - - + -
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 6.0 0.2 - - + -
133A VAL* 5.1 8.7 - - + -
136A PHE* 3.9 33.9 - + + -
174A PHE* 3.4 39.1 - + - -
21B LEU* 2.7 27.7 + - + +
22B PHE* 3.6 4.3 - - - +
24B VAL* 1.3 72.8 - - - +
26B PHE* 1.3 78.5 + + - +
29B GLY* 3.1 24.6 + - - -
100B GLY* 3.4 26.0 - - - +
103B VAL* 3.9 19.7 - - + -
104B LEU* 3.5 35.0 - - + +
107B VAL* 5.2 5.2 - - + -
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Residues in contact with PHE 26 (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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136A PHE* 3.4 17.3 - - + -
137A LEU* 3.6 25.6 - - + -
140A GLN* 3.3 40.4 - - + -
170A LEU* 4.0 35.4 - - + +
171A GLY* 4.9 1.3 - - - -
174A PHE* 3.8 26.7 - + + +
22B PHE* 2.8 48.3 + + + +
23B TYR 4.4 0.7 - - - +
25B PHE* 1.3 89.2 - + - +
27B GLY* 1.3 64.5 + - - +
30B ALA* 3.0 26.9 + - - +
47B ALA* 4.8 1.4 - - - +
51B ALA* 4.6 4.9 - - + -
55B LEU* 6.2 0.2 - - + -
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Residues in contact with GLY 27 (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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23B TYR 2.9 19.0 + - - -
26B PHE* 1.3 78.8 - - - +
28B LEU* 1.3 60.5 + - - +
30B ALA* 3.4 4.1 + - - +
31B SER* 2.8 26.5 + - - -
47B ALA* 5.2 1.1 - - - -
48B PHE* 3.4 39.6 - - - -
51B ALA* 5.1 1.0 - - - +
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Residues in contact with LEU 28 (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 VAL* 2.8 46.1 + - + +
27B GLY* 1.3 72.5 - - - -
29B GLY* 1.3 59.1 + - - +
31B SER* 2.8 18.4 + - - -
32B LEU* 3.0 19.4 + - - +
48B PHE* 4.4 1.1 - - + -
101B ALA* 3.9 18.4 - - + -
104B LEU* 4.0 13.7 - - + -
116B LEU* 3.3 22.0 - - + +
117B ALA* 4.0 4.9 - - + -
187B ARG* 3.5 45.3 - - + +
191B PRO* 3.8 16.6 - - + -
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Residues in contact with GLY 29 (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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174A PHE* 3.5 24.0 - - - +
177A TYR* 5.4 5.0 - - - -
178A TYR* 4.3 6.1 + - - -
25B PHE 3.1 20.8 + - - -
28B LEU* 1.3 78.6 - - - +
30B ALA* 1.3 59.6 + - - +
31B SER 3.4 0.9 + - - -
32B LEU* 3.5 21.1 + - - +
104B LEU* 3.8 12.3 - - - +
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Residues in contact with ALA 30 (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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173A LEU* 4.0 21.8 - - + +
174A PHE* 3.8 9.1 - - + +
177A TYR* 5.2 4.9 - - - -
26B PHE 3.0 19.2 + - - +
27B GLY 4.0 1.8 - - - +
29B GLY* 1.3 75.7 - - - +
31B SER* 1.3 58.1 + - - +
32B LEU 3.5 0.7 - - - -
33B ARG* 3.0 20.8 + - - -
43B GLN* 4.9 6.3 - - + +
44B VAL* 3.6 8.3 + - + +
47B ALA* 3.6 28.3 - - + -
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY 2.8 16.4 + - - -
28B LEU 2.8 10.8 + - - -
30B ALA* 1.3 79.5 - - - +
32B LEU* 1.3 65.9 + - - +
33B ARG* 3.3 5.9 + - - +
40B HIS* 3.8 15.3 - - - -
44B VAL* 3.2 32.9 - - - +
48B PHE* 3.4 6.9 - - - -
117B ALA* 3.5 22.2 - - - +
176B MET* 5.8 1.3 - - - -
187B ARG* 5.0 1.4 + - - -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR* 5.2 5.7 - - - -
178A TYR* 3.6 24.2 - - - +
28B LEU 3.0 22.9 - - - +
29B GLY* 3.7 16.9 - - - +
30B ALA 3.5 1.5 - - - +
31B SER* 1.3 76.9 - - - +
33B ARG* 1.3 80.2 + - - +
104B LEU* 4.1 13.0 - - + -
108B THR* 3.6 17.9 - - + +
112B VAL* 3.4 30.3 - - + +
113B ARG* 4.3 5.4 - - - +
116B LEU* 4.3 11.2 - - + -
117B ALA* 4.2 20.2 - - - +
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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