Contacts of the helix formed by residues 11 - 28 (chain A) in PDB entry 3GNI
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A HIS* 4.4 9.0 + - - -
10A LYS* 1.3 72.4 - - - +
12A PRO* 1.3 75.9 - - - +
13A ALA* 3.7 7.4 + - - +
14A ASP* 3.1 31.9 + - - +
15A ILE* 3.0 25.1 + - - +
69A GLN* 5.4 1.1 - - - -
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Residues in contact with PRO 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A HIS* 6.0 1.3 - - + -
10A LYS 3.8 2.0 - - - +
11A SER* 1.3 83.9 - - - +
13A ALA* 1.3 56.5 + - - +
15A ILE* 3.3 11.3 + - + +
16A VAL* 2.9 35.5 + - - +
53A ILE* 4.5 14.1 - - + -
66A ALA* 3.7 24.2 - - + +
69A GLN* 3.4 29.6 - - + +
70A LEU* 3.9 30.2 - - + +
73A GLU* 4.6 0.7 - - - -
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A SER* 3.2 9.1 - - - +
12A PRO* 1.3 80.0 - - - +
14A ASP* 1.3 61.0 + - - +
16A VAL* 3.5 3.5 + - - +
17A LYS* 3.0 38.9 + - - +
69A GLN* 5.8 0.2 - - - +
73A GLU* 3.9 32.0 - - + +
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 4.8 11.6 - - + +
11A SER* 3.1 24.7 + - - +
13A ALA* 1.3 77.6 - - - +
15A ILE* 1.3 61.0 + - - +
17A LYS* 3.6 17.9 + - - +
18A ASN* 2.9 41.5 + - - +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 3.4 40.4 - - + +
11A SER 3.0 13.9 + - - +
12A PRO* 3.6 7.2 - - + +
14A ASP* 1.3 74.1 - - - +
16A VAL* 1.3 64.0 + - - +
18A ASN* 3.4 8.0 + - - +
19A LEU* 3.0 23.7 + - - +
46A ASN* 3.8 23.4 - - + +
49A ALA* 4.2 15.9 - - + -
50A MET* 3.7 29.8 - - + -
53A ILE* 3.7 26.5 - - + -
70A LEU* 5.6 0.7 - - + -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO 2.9 19.6 + - - +
13A ALA 3.8 3.8 - - - +
15A ILE* 1.3 75.2 - - - +
17A LYS* 1.3 58.5 + - - +
19A LEU* 3.3 2.4 + - - +
20A LYS* 2.9 30.6 + - + +
50A MET* 3.7 24.5 - - + -
70A LEU* 3.8 11.2 - - + -
73A GLU* 3.7 32.8 - - + +
74A LEU* 4.2 10.3 - - + +
77A SER* 3.6 31.2 - - - +
79A LEU* 3.7 6.2 - - + +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.0 26.2 + - - +
14A ASP* 3.6 19.7 + - - +
16A VAL* 1.3 74.6 - - - +
18A ASN* 1.3 68.4 + - - +
20A LYS* 3.3 10.7 + - + +
21A GLU* 3.1 39.2 + - + +
73A GLU* 5.8 2.7 - - - -
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Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 4.2 25.5 + - - +
14A ASP* 2.9 29.8 + - - +
15A ILE* 3.6 4.2 - - - +
16A VAL 3.4 0.2 - - - -
17A LYS* 1.3 75.2 - - - +
19A LEU* 1.3 56.9 + - - +
21A GLU* 3.4 12.4 + - - +
22A SER* 2.9 31.9 + - - -
46A ASN* 3.5 25.4 + - - +
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE 3.0 13.6 + - - +
16A VAL 3.7 3.8 - - - +
18A ASN* 1.3 77.1 - - - +
20A LYS* 1.3 56.7 + - - +
22A SER* 3.2 1.1 + - - +
23A MET* 2.8 49.6 + - + +
43A VAL* 3.7 47.6 - - + +
46A ASN* 3.7 14.1 - - + +
47A LEU* 3.6 24.7 - - + -
50A MET* 3.5 27.8 - - + -
79A LEU* 4.2 12.1 - - + -
83A LEU* 4.4 8.3 - - + -
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Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 2.9 17.5 + - + +
17A LYS* 3.4 11.0 - - + +
19A LEU* 1.3 75.6 - - - +
21A GLU* 1.3 62.0 + - + +
23A MET* 3.6 2.6 + - - +
24A ALA* 3.2 22.7 + - - +
77A SER* 3.7 39.5 + - - +
79A LEU* 4.1 20.1 - - + +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.1 29.4 + - + +
18A ASN* 3.7 13.7 + - - +
20A LYS* 1.3 75.1 - - + +
22A SER* 1.3 64.8 + - - +
24A ALA* 3.6 7.8 + - - +
25A VAL* 3.4 25.6 + - - +
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN 2.9 17.9 + - - -
19A LEU* 3.9 3.6 - - - -
21A GLU* 1.3 75.5 - - - +
23A MET* 1.3 64.0 + - - +
25A VAL* 3.3 10.2 + - - +
26A LEU* 3.2 24.4 + - - +
39A ALA* 3.9 8.8 + - - +
42A GLU* 3.0 36.6 + - - +
43A VAL* 3.6 22.4 - - - -
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Residues in contact with MET 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 2.8 30.1 + - + +
20A LYS* 3.9 5.4 - - - +
22A SER* 1.3 71.1 - - - +
24A ALA* 1.3 62.5 + - - +
26A LEU* 3.2 10.3 + - + +
27A GLU* 3.1 28.1 + - - +
43A VAL* 3.8 26.5 - - - -
79A LEU* 4.5 6.1 - - + -
82A THR* 4.3 18.2 - - + +
83A LEU* 3.9 27.1 - - + -
86A ASP* 3.1 42.0 - - + +
89A LEU* 4.7 5.4 - - + -
90A ILE* 4.2 14.6 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS 3.2 16.5 + - - +
21A GLU* 3.7 9.4 - - - +
22A SER 3.3 0.2 - - - -
23A MET* 1.3 79.4 - - - +
25A VAL* 1.3 62.3 + - + +
27A GLU* 3.6 22.3 + - - +
28A LYS* 3.7 18.5 + - - +
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU 3.4 15.0 - - - +
22A SER* 3.3 9.6 + - - +
23A MET 3.2 0.6 - - - -
24A ALA* 1.3 75.0 - - + +
26A LEU* 1.3 62.9 + - - +
28A LYS* 3.1 41.4 + - - +
31A ILE* 3.5 27.6 - - + +
35A LYS* 4.0 19.1 - - + +
39A ALA* 3.6 21.1 - - + -
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER 3.2 9.6 + - - +
23A MET* 3.2 16.9 + - + +
25A VAL* 1.3 77.8 - - - +
27A GLU* 1.3 56.9 + - - +
28A LYS 3.2 0.8 - - - +
31A ILE* 5.1 1.1 - - - -
36A ALA* 3.6 31.9 - - + +
39A ALA* 3.8 11.0 - - + -
40A THR* 3.7 14.8 - - - +
43A VAL* 3.9 26.9 - - + -
89A LEU* 3.5 43.5 - - + +
90A ILE* 5.0 0.9 - - + -
-12B HIS* 2.9 26.9 + - - -
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A MET 3.1 16.6 + - - +
24A ALA* 3.8 17.7 - - - +
25A VAL 3.2 0.8 - - - -
26A LEU* 1.3 76.9 - - - +
28A LYS* 1.3 59.3 + - + +
82A THR* 3.7 12.1 - - - +
86A ASP* 2.3 41.5 - - - +
89A LEU* 4.0 2.0 - - + -
-15B ALA 3.0 22.4 + - - +
-14B HIS* 3.8 17.5 - - + -
-13B HIS* 2.8 31.6 + - - +
-12B HIS* 3.2 6.8 - - - -
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 3.7 9.6 - - - +
25A VAL* 3.1 42.9 + - - +
26A LEU 3.7 0.7 - - - +
27A GLU* 1.3 78.2 - - + +
29A GLN* 1.3 62.0 + - - +
30A ASP 4.5 2.9 - - - +
31A ILE* 3.8 36.0 - - + +
35A LYS* 5.1 5.7 - - - +
-13B HIS* 4.8 5.6 - - - +
-12B HIS* 3.0 13.4 + - - -
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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