Contacts of the helix formed by residues 8 - 23 (chain E) in PDB entry 2GTL
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 SER 8 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E CYS 3.2 6.5 + - - -
7E CYS* 1.3 76.9 - - - +
9E TYR* 1.3 64.5 + - - +
10E GLU* 3.2 16.3 + - - +
11E ASP* 2.5 40.3 + - - +
12E ARG* 3.0 22.3 + - - +
5K HIS* 4.0 20.4 - - - -
8K SER* 4.0 4.9 - - - -
11K ASP* 3.8 13.2 - - - -
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Residues in contact with TYR 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E SER* 1.3 69.1 - - - +
10E GLU* 1.3 67.9 + - - +
12E ARG* 3.1 30.7 + - + +
13E ARG* 2.9 41.9 + - + +
16E ARG* 3.9 13.5 + - - -
85E ASP* 3.5 22.9 + - - -
10K GLU* 4.0 26.9 - - + -
11K ASP* 3.0 21.8 + - - +
13K ARG* 6.0 0.9 - - - -
14K ILE* 3.9 31.9 - - + +
132K ASP* 4.1 16.2 - - - -
135K ALA* 5.4 0.4 - - + -
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Residues in contact with GLU 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E SER* 3.2 11.2 + - - +
9E TYR* 1.3 75.6 + - - +
11E ASP* 1.3 59.8 + - - +
13E ARG* 3.0 17.5 + - - +
14E GLU* 2.8 32.6 + - + +
8K SER* 2.8 26.6 + - - -
9K GLU 3.9 0.9 + - - -
10K GLU* 2.8 52.1 + - + +
119N GLY 3.0 13.2 - - - +
120N CYS* 4.0 21.9 - - + -
216N HIS* 5.5 2.0 - - + -
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Residues in contact with ASP 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E CYS 3.9 1.0 - - - +
7E CYS* 4.5 0.2 - - - -
8E SER* 2.5 47.0 + - - +
10E GLU* 1.3 72.2 - - - +
12E ARG* 1.3 65.5 + - - +
14E GLU* 3.0 12.3 + - - +
15E ILE* 2.9 25.5 + - - +
131E ASN* 5.2 0.5 - - - +
134E ALA* 3.8 12.8 - - + +
137E ARG* 2.6 43.8 + - - -
138E CYS* 3.6 19.5 - - - -
5K HIS* 4.7 2.9 + - - -
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Residues in contact with ARG 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E CYS* 3.6 21.7 + - - -
8E SER 3.0 12.1 + - - -
9E TYR* 3.1 45.1 + - + +
11E ASP* 1.3 74.2 - - - +
13E ARG* 1.3 54.3 + - - +
15E ILE* 3.0 8.2 + - - +
16E ARG* 2.7 45.1 + - - +
84E LEU* 3.2 51.2 + - + +
85E ASP* 5.1 1.0 + - - -
87E THR* 4.2 1.2 - - - +
138E CYS* 4.3 2.0 - - - -
11K ASP* 4.0 2.6 + - - -
132K ASP* 2.8 41.6 + - - -
134K LEU* 3.5 35.0 - - - +
135K ALA* 3.8 5.1 - - - +
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Residues in contact with ARG 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TYR* 2.9 30.1 + - + +
10E GLU* 3.2 13.0 + - - +
12E ARG* 1.3 76.5 - - - +
14E GLU* 1.3 65.1 + - - +
16E ARG* 3.3 20.5 + - + +
17E HIS* 3.2 20.1 + - - +
10K GLU* 3.0 44.2 + - - +
13K ARG* 6.0 0.8 - - - +
214N THR* 4.7 16.7 - - + +
216N HIS* 3.1 43.0 + - + -
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Residues in contact with GLU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU* 2.8 21.0 + - + +
11E ASP* 3.0 17.0 + - - +
13E ARG* 1.3 72.9 - - - +
15E ILE* 1.3 57.8 + - + +
17E HIS* 3.2 6.9 + - - +
18E ILE* 2.8 35.3 + - + +
131E ASN* 3.4 30.2 - - - +
134E ALA* 4.3 11.0 - - + -
211N THR* 3.6 26.6 + - + +
213N ALA* 3.9 18.1 - - - +
214N THR* 3.2 24.3 + - - +
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Residues in contact with ILE 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ASP 2.9 13.5 + - - +
12E ARG* 3.5 6.3 - - - +
14E GLU* 1.3 73.5 - - + +
16E ARG* 1.3 55.6 + - - +
17E HIS 2.5 17.7 + - - -
18E ILE* 2.8 9.6 + - + -
19E TRP* 2.8 25.0 + - + +
81E ILE* 3.9 35.4 - - + -
84E LEU* 4.3 8.5 - - + -
134E ALA 3.8 10.3 - - - +
135E TRP* 4.1 34.5 - - + +
138E CYS* 3.3 38.1 - - + -
139E PHE 5.2 0.2 - - - +
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Residues in contact with ARG 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TYR* 3.9 18.6 + - - -
12E ARG* 2.7 24.8 + - - +
13E ARG* 3.3 22.6 + - + +
15E ILE* 1.3 71.1 - - - +
17E HIS* 1.3 56.2 + - - +
19E TRP* 4.4 1.5 - - - +
20E ASP* 3.2 26.3 - - - +
81E ILE* 4.5 21.1 - - + +
82E ASN* 5.3 7.4 - - - +
84E LEU* 5.3 6.2 + - + +
85E ASP* 2.8 50.3 + - - +
27H HIS* 6.6 0.2 - - + -
28H ALA* 4.4 21.5 - - + +
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Residues in contact with HIS 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ARG 3.2 8.8 + - - +
14E GLU 3.2 8.3 + - - +
15E ILE 2.5 4.9 + - - -
16E ARG* 1.3 75.7 - - - +
18E ILE* 1.3 72.2 + - + +
19E TRP 3.0 1.3 - - - -
20E ASP* 2.8 28.7 + - + +
21E ASP* 3.5 7.6 + - + +
129E CYS 6.0 0.2 - - - -
124F CYS* 6.2 0.8 - - - -
213N ALA* 4.0 35.2 + - + +
214N THR* 3.7 24.1 - - + +
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Residues in contact with ILE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E GLU* 2.8 31.9 + - + +
15E ILE* 3.7 15.0 - - + +
17E HIS* 1.3 78.0 - - + +
19E TRP* 1.3 65.6 + - + +
21E ASP* 3.2 19.8 + - - +
22E VAL* 3.7 7.6 + - + +
123E LEU* 5.6 0.7 - - + -
127E LEU* 3.7 15.8 - - + +
129E CYS 4.5 11.0 - - - +
130E PHE* 3.5 35.4 - - + -
131E ASN* 3.7 37.0 - - + +
135E TRP* 4.9 10.5 - - + +
213N ALA* 5.4 4.3 - - + -
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Residues in contact with TRP 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ILE* 2.8 14.6 + - + +
16E ARG 4.7 1.3 - - - +
18E ILE* 1.3 74.7 - - + +
20E ASP* 1.3 59.3 + - - +
21E ASP 2.5 17.7 + - - -
22E VAL* 2.7 41.8 + - + +
23E TRP* 2.8 52.4 + + + +
34E ILE* 6.5 0.9 - - + -
35E VAL* 6.3 2.7 - - + -
74E ALA* 5.8 0.9 - - + -
77E LEU* 3.8 22.7 - - + -
78E LYS* 3.2 52.2 - - + +
81E ILE* 3.3 40.2 - - + -
82E ASN* 4.9 3.4 - - - -
119E PHE* 5.2 3.6 - + - -
123E LEU* 5.0 9.2 - - + -
135E TRP* 4.0 22.2 - + - -
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Residues in contact with ASP 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ARG* 3.2 21.5 - - - +
17E HIS* 2.8 23.3 + - + +
19E TRP* 1.3 74.5 - - - +
21E ASP* 1.3 56.6 + - - +
23E TRP* 4.4 9.1 - - - +
24E SER* 4.1 16.5 - - - -
82E ASN* 5.1 3.3 - - - +
27H HIS* 3.8 28.2 - - - +
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Residues in contact with ASP 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E HIS* 3.5 7.1 + - + +
18E ILE* 3.2 14.1 + - - +
19E TRP 2.5 6.7 + - - -
20E ASP* 1.3 76.2 - - - +
22E VAL* 1.3 59.5 + - - +
23E TRP 3.6 0.2 - - - -
24E SER* 3.9 9.3 + - - -
30E ARG* 3.4 18.9 + - - -
127E LEU* 3.2 32.4 - - + +
128E SER 5.0 3.3 + - - +
14F SER* 4.3 17.0 + - - -
18F ARG* 4.7 17.6 + - - -
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ILE* 3.7 14.6 - - + +
19E TRP* 2.7 53.0 + - + +
21E ASP* 1.3 70.8 - - - +
23E TRP* 1.3 65.9 + - + +
24E SER 3.2 7.3 + - - -
30E ARG* 3.0 33.5 + - - +
31E ARG* 5.0 3.6 + - - +
34E ILE* 4.1 18.7 - - + +
123E LEU* 4.3 14.1 - - + -
126E VAL* 5.1 0.2 - - + -
127E LEU* 3.8 29.4 - - + -
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Residues in contact with TRP 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TRP* 2.8 56.1 + + + +
20E ASP* 4.4 5.7 - - - +
22E VAL* 1.3 79.8 - - + +
24E SER* 1.3 63.7 + - - +
25E SER 3.8 3.5 - - - +
31E ARG* 3.4 51.8 - - + +
35E VAL* 5.2 1.6 - - + -
74E ALA* 3.2 37.5 - - + -
75E ASN* 3.2 34.5 - - - +
78E LYS* 3.0 40.5 - - + +
27H HIS* 5.2 8.6 + - - -
78H ASP* 5.0 4.2 + - - -
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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