Contacts of the helix formed by residues 16 - 31 (chain A) in PDB entry 3WAL
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ARG* 1.3 76.8 - - - +
17A PHE* 1.3 60.2 + - - +
18A ALA* 3.6 7.8 + - - +
19A ASP* 3.0 35.6 + - - +
20A ARG* 2.8 28.6 + - - +
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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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16A SER* 1.3 72.7 - - - +
18A ALA* 1.3 66.7 + - - +
20A ARG* 3.2 19.1 + - - +
21A CYS* 3.0 44.4 + - - -
109A GLU* 3.8 18.6 - - + -
110A ASP* 3.7 22.9 - - + -
201A MLT 3.7 48.1 + - + +
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Residues in contact with ALA 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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16A SER* 3.2 8.1 + - - +
17A PHE* 1.3 84.6 - - + +
19A ASP* 1.3 61.5 + - - +
21A CYS* 3.3 7.5 + - - +
22A LYS* 3.0 42.6 + - - +
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Residues in contact with ASP 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* 4.5 19.1 - - + -
16A SER* 3.0 32.2 + - - +
18A ALA* 1.3 80.7 - - - +
20A ARG* 1.3 62.1 + - - +
22A LYS* 3.4 20.3 + - - +
23A GLU* 3.1 24.2 + - - +
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Residues in contact with ARG 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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11A PHE* 3.6 33.7 - - + -
12A LYS* 3.6 24.7 + - - +
15A ARG* 3.1 38.9 + - + -
16A SER* 2.8 9.3 + - - +
17A PHE* 3.5 22.7 - - - +
19A ASP* 1.3 74.5 - - - +
21A CYS* 1.3 65.4 + - - +
23A GLU* 3.1 6.9 + - - +
24A VAL* 3.1 26.0 + - - +
110A ASP* 2.8 32.8 + - + +
112A PHE* 3.7 5.7 - - + -
114A TYR* 3.5 3.8 + - - -
201A MLT 2.4 53.9 + - - -
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Residues in contact with CYS 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* 3.0 53.0 + - - -
18A ALA* 3.7 9.6 - - - +
20A ARG* 1.3 74.9 - - - +
22A LYS* 1.3 62.4 + - + +
24A VAL* 3.3 2.9 + - - +
25A GLN* 3.0 40.3 + - - +
109A GLU 4.4 2.7 - - - -
110A ASP* 3.6 22.2 - - - -
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Residues in contact with LYS 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 ALA* 3.0 29.2 + - - +
19A ASP* 3.7 21.3 + - - +
20A ARG 3.2 0.2 - - - -
21A CYS* 1.3 76.5 - - + +
23A GLU* 1.3 64.6 + - - +
25A GLN* 3.4 16.3 + - - +
26A GLN* 3.0 23.6 + - - +
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Residues in contact with GLU 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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11A PHE* 3.9 15.2 - - - -
15A ARG* 5.1 13.5 + - - +
19A ASP 3.1 13.8 + - - +
20A ARG* 3.1 10.2 + - - +
22A LYS* 1.3 79.5 - - - +
24A VAL* 1.3 61.1 + - - +
26A GLN* 3.3 14.8 + - - +
27A ILE* 3.0 37.5 + - + +
55A LYS* 2.5 48.7 + - - +
112A PHE* 4.1 6.2 - - + -
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Residues in contact with VAL 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 ARG 3.1 9.6 + - - +
21A CYS 3.3 4.0 + - - +
23A GLU* 1.3 75.3 - - - +
25A GLN* 1.4 51.0 - - - +
27A ILE* 3.0 10.3 + - - +
28A ARG* 2.9 60.0 + - + +
36A PRO* 4.1 11.8 - - + +
103A TYR* 4.3 2.2 - - - +
110A ASP 3.3 23.3 - - - +
111A GLY* 3.7 25.4 - - - +
112A PHE* 3.5 29.8 - - + -
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Residues in contact with GLN 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 CYS* 3.0 31.4 + - - +
22A LYS* 3.7 19.6 - - - +
24A VAL* 1.4 75.6 - - - +
26A GLN* 1.3 60.9 + - - +
28A ARG* 3.1 41.2 + - - +
29A ASP* 3.3 18.5 + - - -
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Residues in contact with GLN 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 LYS 3.0 16.8 + - - +
23A GLU* 3.6 12.9 + - - +
25A GLN* 1.3 78.9 - - - +
27A ILE* 1.3 61.5 + - - +
29A ASP* 3.1 8.3 + - - +
30A GLN* 2.8 52.5 + - + +
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Residues in contact with ILE 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 GLU* 3.0 37.1 + - + +
24A VAL* 3.0 7.4 + - - +
26A GLN* 1.3 77.8 - - + +
28A ARG* 1.3 60.9 + - + +
30A GLN* 4.4 1.3 - - - +
31A HIS* 2.8 53.4 + - + +
34A LYS 4.6 9.0 - - - +
36A PRO* 4.0 32.5 - - + -
55A LYS* 4.6 3.1 - - + -
57A LEU* 4.3 28.7 - - + -
112A PHE* 4.2 11.0 - - + -
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Residues in contact with ARG 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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21A CYS 5.2 0.2 + - - -
24A VAL* 2.9 38.9 + - + +
25A GLN* 3.1 44.6 - - - +
26A GLN 3.2 0.2 - - - -
27A ILE* 1.3 76.6 - - - +
29A ASP* 1.3 59.8 + - - +
31A HIS 4.8 0.2 - - - -
32A PRO* 3.3 33.8 - - - +
34A LYS 6.2 0.2 - - - -
36A PRO* 6.4 1.3 - - + -
103A TYR* 4.5 8.4 + - - +
111A GLY* 5.2 3.0 - - - -
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Residues in contact with ASP 29 (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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25A GLN 3.3 11.8 + - - +
26A GLN* 3.1 10.6 + - - +
28A ARG* 1.3 82.2 - - - +
30A GLN* 1.3 71.6 + - - +
32A PRO* 3.7 10.1 - - - +
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Residues in contact with GLN 30 (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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26A GLN* 2.8 49.3 + - + +
27A ILE* 5.0 0.2 - - - -
29A ASP* 1.3 79.7 - - - +
31A HIS* 1.3 88.1 + - + +
32A PRO* 3.6 5.0 - - - +
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Residues in contact with HIS 31 (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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27A ILE* 2.8 31.4 + - + +
28A ARG* 4.8 0.3 - - - -
30A GLN* 1.3 95.1 + - + +
32A PRO* 1.3 67.6 - - - +
33A SER 3.0 4.4 + - - -
34A LYS* 3.0 45.4 + - + +
57A LEU* 3.9 26.4 - - + +
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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