Contacts of the helix formed by residues 5 - 20 (chain X) in PDB entry 3EXG
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 VAL 5 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X THR* 1.3 72.9 - - - +
6X ARG* 1.3 65.9 - - - +
8X ALA* 2.8 16.6 + - - +
9X ILE* 3.0 25.3 + - + +
147X PRO* 5.8 2.2 - - + -
148X TRP 4.0 11.4 - - - +
149X ASN 4.0 9.9 - - - +
150X SER* 3.6 12.3 - - - +
153X ALA* 3.6 26.2 - - + -
175X MET* 3.0 30.7 - - + +
176X TYR* 3.3 8.6 + - + +
178X VAL 3.3 8.3 + - - +
180X PHE* 4.0 15.0 - - + -
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Residues in contact with ARG 6 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X THR* 3.9 9.2 + - - +
5X VAL* 1.3 77.3 - - - +
7X ASP* 1.3 68.4 + - - +
9X ILE* 4.9 0.7 - - - -
10X ASN* 3.4 19.1 + - - +
37X TYR* 2.7 26.0 + - - +
38X LYS* 3.6 30.3 - - - +
39X VAL* 3.9 15.4 - - + +
41X ARG* 4.2 12.6 - - - +
173X GLU* 5.2 1.2 + - - +
176X TYR* 2.9 52.0 + - + +
177X GLY* 3.6 23.0 - - - +
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Residues in contact with ASP 7 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X VAL* 5.0 7.3 - - + -
4X THR* 2.8 27.1 + - - +
6X ARG* 1.3 83.9 - - - +
8X ALA* 1.3 62.3 + - - +
10X ASN* 3.6 9.8 - - + +
11X GLN* 2.8 38.4 + - + +
41X ARG* 3.4 24.3 + - - -
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Residues in contact with ALA 8 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X VAL* 3.9 17.4 - - + +
4X THR 2.9 11.3 + - - +
5X VAL* 2.8 9.2 + - - +
7X ASP* 1.3 74.9 - - - +
9X ILE* 1.3 64.8 + - - +
11X GLN* 3.3 8.6 - - - +
12X GLY 3.0 17.5 + - - -
150X SER* 3.6 29.6 - - - +
153X ALA* 4.9 0.7 - - + -
154X LYS* 3.4 19.5 - - + +
182X PHE* 4.0 4.9 - - + -
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Residues in contact with ILE 9 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X VAL* 3.0 27.3 + - + +
6X ARG 4.1 0.2 - - - +
8X ALA* 1.3 74.2 - - - +
10X ASN* 1.3 66.2 + - - +
12X GLY* 3.0 4.0 + - - -
13X MET* 2.9 32.1 + - + +
39X VAL* 3.8 20.6 - - + -
115X ARG* 4.2 8.1 - - - +
147X PRO* 6.0 0.4 - - + -
153X ALA* 3.8 21.8 - - + +
154X LYS* 4.6 0.2 - - - +
157X ILE* 4.3 17.0 - - + +
171X GLU* 3.5 31.2 - - + +
176X TYR* 3.7 27.6 - - + -
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Residues in contact with ASN 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X ARG 3.4 13.2 + - - +
7X ASP* 3.6 13.5 - - + +
8X ALA 3.2 0.4 - - - -
9X ILE* 1.3 79.6 - - - +
11X GLN* 1.3 58.2 + - - +
13X MET* 3.1 8.1 + - - +
14X ASP* 2.9 32.4 + - - +
38X LYS 4.8 0.8 + - - +
39X VAL 2.6 30.1 + - - +
40X SER* 3.3 4.0 - - - +
41X ARG* 3.1 37.6 + - - +
43X LEU* 4.0 13.1 - - - +
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Residues in contact with GLN 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X VAL* 4.3 23.4 - - - +
7X ASP* 2.8 26.8 + - + +
8X ALA* 3.3 7.2 - - - +
10X ASN* 1.3 75.3 + - - +
12X GLY* 1.3 52.9 + - - +
14X ASP* 3.4 6.8 - - - +
15X GLU* 2.8 46.4 + - - +
154X LYS* 2.7 35.3 + - - +
182X PHE* 3.8 11.2 - - - -
187X GLN* 4.6 6.6 - - - +
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Residues in contact with GLY 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8X ALA 3.0 6.9 + - - -
9X ILE 3.0 7.5 + - - -
11X GLN* 1.3 77.3 - - - +
13X MET* 1.3 65.0 + - - +
15X GLU* 3.3 2.4 + - - +
16X GLU* 3.1 30.4 + - - +
154X LYS* 4.0 4.0 - - - +
157X ILE* 4.3 5.8 - - - -
158X LYS* 3.7 29.6 - - - +
161X ILE* 5.2 0.2 - - - -
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Residues in contact with MET 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X ILE* 2.9 25.7 + - + +
10X ASN* 3.7 5.8 - - - +
12X GLY* 1.3 73.3 - - - +
14X ASP* 1.3 61.7 + - - +
16X GLU* 3.5 1.2 + - - +
17X LEU* 2.9 40.4 + - + +
25X LEU* 4.2 15.5 - - + -
39X VAL* 4.0 20.4 - - + +
40X SER* 4.3 3.8 - - - -
43X LEU* 3.8 26.7 - - + -
77X ILE* 4.5 17.9 - - + +
115X ARG* 4.3 28.5 - - - +
157X ILE* 4.3 11.9 - - + -
161X ILE* 4.5 12.4 - - + +
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Residues in contact with ASP 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X ASN* 2.9 19.3 + - - +
11X GLN* 3.4 10.3 - - - +
13X MET* 1.3 77.5 - - - +
15X GLU* 1.3 68.6 + - - +
17X LEU* 3.0 19.4 + - - +
18X GLU* 3.1 11.2 + - - +
43X LEU* 4.1 13.9 - - + +
46X LYS* 3.0 32.1 + - - +
47X TYR* 3.1 16.6 + - - -
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Residues in contact with GLU 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X GLN* 2.8 27.6 + - - +
12X GLY 3.3 0.6 + - - -
14X ASP* 1.3 84.7 - - - +
16X GLU* 1.3 59.1 + - - +
18X GLU* 3.6 9.1 - - - +
19X ARG* 3.1 26.7 + - - +
154X LYS* 3.2 31.2 + - - -
158X LYS* 2.7 35.2 + - - +
187X GLN 3.8 5.7 - - - +
189X LYS* 3.7 34.8 - - + +
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Residues in contact with GLU 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X GLY 3.2 16.6 - - - +
13X MET 3.9 1.6 - - - +
15X GLU* 1.3 78.2 - - - +
17X LEU* 1.3 64.7 + - - +
18X GLU 3.3 0.2 - - - -
19X ARG* 3.4 13.7 + - - +
20X ASP* 3.4 18.2 + - - +
23X VAL* 4.1 10.5 - - + +
158X LYS* 3.2 33.3 + - + +
161X ILE* 3.8 42.2 - - + +
162X ARG* 2.4 49.8 + - - -
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Residues in contact with LEU 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X MET* 2.9 30.9 + - + +
14X ASP* 3.0 3.8 + - - +
16X GLU* 1.3 78.3 - - - +
18X GLU* 1.3 59.3 + - - +
20X ASP 2.7 21.2 - - - +
21X GLU* 4.3 0.5 - - - +
23X VAL* 3.2 39.5 - - + +
24X PHE* 4.3 9.2 - - - -
25X LEU* 4.9 2.7 - - + +
43X LEU* 4.0 18.6 - - + -
47X TYR* 3.9 31.2 - - + -
51X ARG* 2.8 34.6 + - + +
52X ILE* 4.4 10.1 - - + -
77X ILE* 5.2 3.1 - - + -
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Residues in contact with GLU 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X ASP* 3.1 5.6 + - - +
15X GLU* 3.6 12.2 - - - +
17X LEU* 1.3 78.3 - - - +
19X ARG* 1.3 66.6 + - - +
20X ASP* 3.2 2.1 + - - -
21X GLU* 5.6 1.7 - - - +
46X LYS* 3.5 23.8 + - - -
47X TYR* 3.5 19.6 + - + +
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Residues in contact with ARG 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X GLU 3.1 15.4 + - - +
16X GLU* 3.4 23.2 + - - +
17X LEU 3.4 0.4 - - - -
18X GLU* 1.3 82.5 - - - +
20X ASP* 1.3 70.4 + - + +
161X ILE* 5.9 0.6 - - - +
162X ARG* 3.2 53.6 - - - +
189X LYS* 5.9 9.2 - - + +
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Residues in contact with ASP 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X GLU 3.4 7.7 + - - +
17X LEU 2.7 19.9 - - - +
18X GLU 3.2 0.8 + - - -
19X ARG* 1.3 96.8 + - + +
21X GLU* 1.3 83.7 + - - +
22X LYS* 2.5 29.7 + - - +
23X VAL* 3.7 13.6 + - + +
51X ARG* 2.9 5.2 + - - -
75X ARG* 3.1 28.4 + - - -
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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