Contacts of the helix formed by residues 9 - 25 (chain A) in PDB entry 4XZC
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 THR 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ALA* 3.6 0.8 - - - +
8A ASN* 1.3 89.5 - - + +
10A LYS* 1.3 54.0 + - - +
11A LYS* 3.1 12.9 + - - +
12A GLU* 2.9 32.1 + - + +
13A TYR* 2.7 35.5 + - - +
82A TRP* 3.9 9.8 - - - -
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Residues in contact with LYS 10 (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 THR* 1.3 73.4 - - - +
11A LYS* 1.3 58.3 + - - +
13A TYR* 3.9 2.2 - - - +
14A ASP* 2.9 47.4 + - - +
78A TYR* 3.5 22.3 + - - +
82A TRP* 3.7 26.9 - - + -
141A ILE* 3.8 44.1 + - + +
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Residues in contact with LYS 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 THR* 3.0 11.0 + - - +
10A LYS* 1.3 78.1 - - - +
12A GLU* 1.3 64.2 + - + +
14A ASP* 3.0 21.9 + - + +
15A GLU* 3.0 36.3 + - + +
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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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6A LYS 4.4 3.6 - - - +
7A ALA* 3.5 9.4 - - - +
8A ASN* 2.5 52.8 + - - +
9A THR* 2.9 24.5 + - + +
11A LYS* 1.3 74.3 - - + +
13A TYR* 1.3 62.6 + - - +
15A GLU* 3.2 19.8 + - - +
16A TRP* 3.0 21.1 + - - +
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Residues in contact with TYR 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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5A ILE* 3.7 16.2 - - + -
7A ALA* 3.3 12.7 - - + +
9A THR 2.7 22.3 + - - +
10A LYS* 3.9 2.7 - - - +
12A GLU* 1.3 72.2 - - - +
14A ASP* 1.3 59.8 + - - +
16A TRP* 3.0 27.0 + + + +
17A PHE* 2.9 44.2 + + + -
77A ILE 4.1 0.3 + - - -
78A TYR* 2.9 56.6 + + - -
81A GLY* 3.2 26.5 - - - -
82A TRP* 3.4 36.6 - + + -
85A CYS* 3.9 9.4 - - + -
141A ILE* 5.3 0.4 - - + -
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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* 2.9 42.2 + - - +
11A LYS* 3.0 11.9 + - + +
13A TYR* 1.3 74.8 - - - +
15A GLU* 1.3 61.8 + - + +
17A PHE* 3.1 15.6 + - - +
18A LYS* 3.2 18.4 + - - +
78A TYR* 2.7 32.2 + - - -
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Residues in contact with GLU 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 LYS* 3.0 40.8 + - + +
12A GLU* 3.5 22.7 - - - +
13A TYR 3.2 0.2 - - - -
14A ASP* 1.3 77.6 - - + +
16A TRP* 1.3 61.7 + - - +
18A LYS* 4.8 1.3 - - - +
19A PRO* 3.3 18.7 - - - +
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Residues in contact with TRP 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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4A GLN* 3.2 24.5 + - - +
5A ILE* 3.8 26.9 - - + -
6A LYS* 4.3 12.3 - - + +
12A GLU 3.0 11.5 + - - +
13A TYR* 3.0 46.3 + + + +
15A GLU* 1.3 77.4 - - - +
17A PHE* 1.3 71.0 + + - +
19A PRO* 3.3 16.2 - - - +
20A TYR* 3.4 54.3 + + + +
77A ILE* 6.2 0.2 - - + -
81A GLY* 4.9 2.0 - - - -
396A VAL* 4.8 2.2 - - + -
401A PRO* 3.7 30.6 - - + +
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Residues in contact with PHE 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 TYR* 2.9 39.4 + - + +
14A ASP* 3.1 5.3 + - - +
16A TRP* 1.3 92.4 - + + +
18A LYS* 1.3 60.5 + - - +
20A TYR* 3.6 5.6 - + - -
21A ALA* 2.7 45.7 + - + +
26A LEU* 3.7 22.9 - - + -
34A ALA* 6.1 1.6 - - + -
77A ILE* 4.2 12.6 - - + -
78A TYR* 3.4 54.7 - + + -
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Residues in contact with LYS 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 ASP 3.2 14.3 + - - +
15A GLU* 4.8 1.3 - - - +
17A PHE* 1.3 80.0 - - - +
19A PRO* 1.4 72.6 - - + +
21A ALA* 3.5 3.1 + - - +
22A GLU* 3.2 57.3 + - + +
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Residues in contact with PRO 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 GLU 3.3 18.2 - - - +
16A TRP* 3.3 15.3 - - - +
18A LYS* 1.4 95.9 - - + +
20A TYR* 1.3 54.5 + - - +
22A GLU* 3.3 14.5 + - + +
23A LYS* 2.9 30.3 + - - +
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Residues in contact with TYR 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 TRP* 3.4 52.9 - + + +
17A PHE* 3.2 12.6 + + - +
19A PRO* 1.3 81.7 - - - +
21A ALA* 1.3 64.7 + - - +
23A LYS* 3.1 7.3 + - - +
24A THR* 3.0 51.1 + - + +
26A LEU* 5.5 0.2 - - + -
36A PHE* 4.6 1.2 - - - -
77A ILE* 3.6 26.3 - - + +
396A VAL* 4.0 6.8 - - + +
401A PRO* 2.8 42.3 + - + -
402A GLU* 3.9 19.1 - - - +
404A ALA* 3.5 15.8 - - - +
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Residues in contact with ALA 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 PHE* 2.7 48.1 + - + +
18A LYS* 4.0 4.5 - - - +
20A TYR* 1.3 74.2 - - - +
22A GLU* 1.3 63.0 + - + +
24A THR* 3.6 7.6 + - - -
25A HIS* 3.2 18.5 + - - -
26A LEU* 3.7 20.9 + - + +
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Residues in contact with GLU 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 LYS* 3.2 49.8 + - + +
19A PRO* 3.5 15.6 - - - +
21A ALA* 1.3 81.5 - - + +
23A LYS* 1.3 60.8 + - - +
25A HIS* 3.3 22.9 + - - +
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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 PRO 2.9 14.2 + - - +
20A TYR* 3.1 10.9 + - - +
22A GLU* 1.3 77.7 - - - +
24A THR* 1.3 60.5 + - + +
25A HIS* 3.3 26.1 + - - -
402A GLU* 3.1 39.8 + - + +
25B HIS* 5.2 0.3 - - - -
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Residues in contact with THR 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 TYR* 3.0 50.3 + - + +
21A ALA* 3.6 6.9 + - - -
23A LYS* 1.3 76.5 - - + +
25A HIS* 1.3 74.1 + - - +
26A LEU* 3.7 15.4 - - - +
36A PHE* 3.5 25.4 - - - -
402A GLU* 4.5 9.2 - - + -
405A VAL* 3.8 27.0 - - + +
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Residues in contact with HIS 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 ALA 3.2 9.1 + - - -
22A GLU 3.3 15.0 + - - -
23A LYS* 3.3 21.9 + - - -
24A THR* 1.3 80.0 - - - +
26A LEU* 1.3 64.0 + - - +
27A LYS* 3.5 26.1 + - - +
36A PHE* 4.6 4.2 - - - -
23B LYS 5.8 0.4 - - - -
25B HIS* 2.5 54.5 + + - -
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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