Contacts of the helix formed by residues 10 - 25 (chain A) in PDB entry 1GNU
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 PRO 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LYS 5.2 0.4 - - - +
8A GLU 4.3 4.3 - - - +
9A HIS* 1.3 86.8 - - + +
11A PHE* 1.3 66.7 + - - +
12A GLU* 4.4 5.6 - - + +
13A LYS* 3.0 30.2 + - + +
14A ARG* 3.1 10.1 + - - +
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Residues in contact with PHE 11 (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 3.5 1.8 + - - -
10A PRO* 1.3 71.9 - - - +
12A GLU* 1.3 64.2 + - + +
14A ARG* 3.1 34.3 + - - +
15A ARG* 2.8 70.6 + - + -
101A GLU* 3.6 30.7 - - + -
102A ASP* 3.6 23.1 - - + -
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Residues in contact with GLU 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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10A PRO* 3.1 5.0 + - + +
11A PHE* 1.3 82.4 - - + +
13A LYS* 1.3 58.8 + - - +
15A ARG* 2.2 45.0 + - - +
16A SER* 3.0 29.8 + - - -
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Residues in contact with LYS 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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9A HIS* 5.2 6.5 - - + -
10A PRO* 3.0 28.6 + - + +
12A GLU* 1.3 78.0 - - - +
14A ARG* 1.3 63.7 + - + +
16A SER* 2.8 21.4 + - - +
17A GLU* 3.1 13.2 + - - +
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Residues in contact with ARG 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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5A TYR* 3.8 25.8 - - + +
6A LYS* 3.3 44.2 + - - +
9A HIS* 3.0 36.2 + - + -
10A PRO 3.1 13.2 + - - +
11A PHE* 3.6 37.9 - - - +
13A LYS* 1.3 72.0 - - - +
15A ARG* 1.3 68.0 + - - +
17A GLU* 3.2 4.4 + - - -
18A GLY 2.9 19.4 + - - -
100A GLU* 4.8 1.2 + - - -
102A ASP* 2.7 41.2 + - + +
104A PHE* 3.5 11.6 - - + -
106A TYR* 3.4 9.9 + - - -
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Residues in contact with ARG 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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11A PHE* 2.8 46.7 + - + +
12A GLU* 2.2 37.2 + - - +
14A ARG* 1.3 80.0 - - - +
16A SER* 1.3 63.1 + - - +
18A GLY* 3.9 0.3 - - - -
19A GLU* 3.0 44.1 + - - +
101A GLU* 3.7 18.6 - - - +
102A ASP* 3.5 13.3 - - - +
103A PHE* 4.3 7.4 - - + -
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.0 16.8 + - - -
13A LYS* 2.8 28.6 + - - +
15A ARG* 1.3 78.6 - - - +
17A GLU* 1.3 61.5 + - - +
19A GLU* 3.6 5.5 + - - +
20A LYS* 3.2 24.1 + - - +
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Residues in contact with GLU 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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5A TYR* 3.7 10.4 + - - -
9A HIS* 6.1 0.2 - - - -
13A LYS 3.1 13.8 + - - +
14A ARG* 3.7 7.7 - - - +
15A ARG 3.1 0.2 - - - -
16A SER* 1.3 78.6 + - - +
18A GLY* 1.3 62.2 + - - +
20A LYS* 3.2 10.3 + - + +
21A ILE* 3.0 46.8 + - + +
48A LYS* 2.5 40.0 + - - +
104A PHE* 4.0 10.3 - - + -
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Residues in contact with GLY 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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14A ARG 2.9 11.1 + - - -
17A GLU* 1.3 78.1 - - - +
19A GLU* 1.3 62.4 + - - +
21A ILE* 3.3 5.2 + - - +
22A ARG* 3.0 30.1 + - - +
30A PRO* 5.0 1.6 - - - -
102A ASP 3.6 16.4 - - - -
103A PHE* 3.8 11.9 - - - -
104A PHE* 3.8 13.2 - - - -
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Residues in contact with GLU 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 ARG* 3.0 35.7 + - - +
16A SER* 4.0 5.8 - - - +
18A GLY* 1.3 77.7 - - - +
20A LYS* 1.3 56.6 + - - +
22A ARG* 3.5 3.9 + - - +
23A LYS* 2.9 31.0 + - - +
103A PHE* 3.2 37.0 - - + +
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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 SER 3.2 15.9 + - - +
17A GLU* 3.6 10.5 - - + +
19A GLU* 1.3 78.4 - - - +
21A ILE* 1.3 63.5 + - + +
23A LYS* 3.2 24.6 + - - +
24A LYS* 2.9 60.0 + - + +
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Residues in contact with ILE 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 GLU* 3.0 49.3 + - + +
18A GLY* 3.8 4.0 - - - +
19A GLU 3.2 0.2 - - - -
20A LYS* 1.3 80.4 - - + +
22A ARG* 1.3 56.4 + - - +
24A LYS* 4.6 0.4 - - - -
25A TYR* 2.7 49.6 + - + +
28A ARG* 5.2 0.9 - - + +
30A PRO* 4.1 28.3 - - + -
48A LYS* 5.5 2.5 - - + -
50A LEU* 3.3 39.5 - - + -
104A PHE* 4.4 5.4 - - + -
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Residues in contact with ARG 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 GLY 3.0 20.3 + - - +
19A GLU* 3.9 4.9 - - - +
21A ILE* 1.3 77.2 - - - +
23A LYS* 1.3 64.4 + - - +
25A TYR 4.5 2.5 - - - -
26A PRO* 3.3 47.7 + - - +
27A ASP 5.0 0.2 - - - -
28A ARG 2.8 29.1 + - - -
29A VAL* 4.6 5.9 - - - +
30A PRO* 3.9 12.1 - - + -
53A SER* 5.8 1.8 - - - -
95A TYR* 3.4 49.4 - - - +
96A GLN* 5.3 9.7 - - - +
103A PHE* 4.6 4.5 - - + +
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Residues in contact with LYS 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 GLU 2.9 16.3 + - - +
20A LYS* 3.2 35.6 + - - +
22A ARG* 1.3 80.9 - - - +
24A LYS* 1.3 74.8 + - - +
26A PRO* 3.6 9.0 - - - +
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Residues in contact with LYS 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* 2.9 45.2 + - + +
23A LYS* 1.3 92.6 - - - +
25A TYR* 1.3 105.3 + - + +
26A PRO* 3.3 7.7 - - - +
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Residues in contact with TYR 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 ILE* 2.7 36.9 + - + +
22A ARG* 4.2 0.7 - - - +
24A LYS* 1.3 117.1 + - + +
26A PRO* 1.3 59.5 - - - +
27A ASP 3.0 6.3 - - - -
28A ARG* 2.8 46.0 + - + +
50A LEU* 4.1 22.7 - - + -
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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