Contacts of the helix formed by residues 15 - 31 (chain A) in PDB entry 4WB7
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY 3.7 1.4 + - - -
14A ALA* 1.3 77.5 - - - +
16A ASP* 1.3 66.8 + - - +
17A GLU* 3.7 6.6 + - - +
18A GLU* 3.0 35.5 + - - +
19A ILE* 3.0 23.9 + - - +
60A ARG* 4.9 0.2 - - - +
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Residues in contact with ASP 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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15A SER* 1.3 76.1 - - - +
17A GLU* 1.3 59.3 + - + +
19A ILE* 3.3 11.1 + - - +
20A LYS* 2.9 29.2 + - - +
54A LEU 5.1 2.6 - - - +
55A SER* 5.5 7.6 - - - +
57A PRO* 5.4 9.9 - - - +
60A ARG* 4.1 14.0 + - - -
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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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15A SER* 3.3 6.7 + - - +
16A ASP* 1.3 78.0 - - + +
18A GLU* 1.3 61.9 + - - +
20A LYS* 3.2 38.2 + - - +
21A ARG* 2.8 43.0 + - - +
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Residues in contact with GLU 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 LEU* 3.8 8.7 - - + +
13A GLY 4.7 0.5 - - - +
14A ALA* 3.4 17.0 - - + -
15A SER* 3.0 38.5 + - - +
17A GLU* 1.3 76.3 - - - +
19A ILE* 1.3 53.6 + - - +
21A ARG* 3.3 24.7 + - - +
22A ALA* 2.8 36.6 + - - +
25A ARG* 4.9 0.5 + - - -
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Residues in contact with ILE 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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5A TYR* 5.3 0.4 - - + -
8A LEU* 4.4 7.5 - - + +
10A LEU* 3.7 23.1 - - + -
14A ALA* 4.2 6.1 - - + +
15A SER 3.0 17.1 + - - +
16A ASP* 3.5 10.5 - - - +
18A GLU* 1.3 73.6 - - - +
20A LYS* 1.3 60.2 + - - +
22A ALA* 3.8 1.0 - - - +
23A TYR* 2.9 30.1 + - - +
51A TYR* 4.0 19.3 - - + -
54A LEU* 3.6 36.3 - - + +
55A SER* 4.2 11.7 - - - -
60A ARG* 3.5 34.8 - - - +
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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 ASP* 2.9 15.7 + - - +
17A GLU* 3.2 43.0 + - - +
19A ILE* 1.3 77.6 - - - +
21A ARG* 1.3 62.5 + - - +
23A TYR* 3.3 2.8 + - - +
24A ARG* 3.1 44.1 + - + +
51A TYR* 4.2 23.3 - - + +
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Residues in contact with ARG 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* 2.8 29.9 + - - +
18A GLU* 3.8 34.5 + - - +
20A LYS* 1.3 73.8 - - - +
22A ALA* 1.3 58.6 + - - +
24A ARG* 3.4 7.7 + - - +
25A ARG* 3.0 58.0 + - + +
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Residues in contact with ALA 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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8A LEU* 3.4 26.9 - - + +
10A LEU* 3.7 18.8 - - + -
18A GLU 2.8 21.6 + - - +
19A ILE 3.8 3.1 - - - +
21A ARG* 1.3 71.5 - - - +
23A TYR* 1.3 65.5 - - - +
25A ARG* 3.5 18.8 - - - +
26A GLN* 2.9 28.9 + - - +
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Residues in contact with TYR 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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8A LEU* 4.3 11.3 - - + +
19A ILE 2.9 17.7 + - - +
20A LYS 3.7 2.9 - - - +
22A ALA* 1.3 77.2 - - - +
24A ARG* 1.3 70.6 + - + +
26A GLN* 3.4 0.9 + - - +
27A ALA* 2.8 46.9 + - + +
44A PHE* 4.9 11.9 + + - -
47A ILE* 3.4 25.6 - - + -
48A ALA* 3.8 24.0 - - + +
51A TYR* 3.6 46.7 - + + -
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Residues in contact with ARG 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* 3.1 33.0 + - + +
21A ARG* 3.8 6.3 - - - +
23A TYR* 1.3 88.5 - - + +
25A ARG* 1.3 64.0 + - + +
27A ALA* 3.3 4.9 + - - +
28A LEU* 3.1 32.3 + - + +
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Residues in contact with ARG 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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8A LEU 4.1 9.5 + - - -
9A GLY* 5.0 6.1 + - - -
10A LEU* 5.6 1.2 - - - +
18A GLU 4.9 0.8 + - - -
21A ARG* 3.0 51.8 + - + +
22A ALA* 3.5 28.8 + - - +
24A ARG* 1.3 78.1 - - - +
26A GLN* 1.3 74.0 + - - +
27A ALA 3.3 0.2 + - - -
28A LEU* 3.6 9.4 + - - +
29A ARG* 3.4 18.0 + - - +
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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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7A THR 4.0 18.0 + - - +
8A LEU* 4.0 18.8 - - - +
9A GLY* 6.0 0.4 - - - -
22A ALA* 2.9 20.0 + - - +
25A ARG* 1.3 90.3 + - + +
27A ALA* 1.3 61.8 + - - +
29A ARG* 3.2 38.8 + - - +
30A TYR* 3.2 41.0 + - - -
47A ILE* 3.6 23.5 - - + +
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Residues in contact with ALA 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 TYR* 2.8 47.0 + - + +
24A ARG* 3.6 5.6 - - - +
25A ARG 3.2 0.2 - - - -
26A GLN* 1.3 73.8 - - - +
28A LEU* 1.3 67.6 + - + +
30A TYR 2.9 12.6 + - - -
31A HIS* 3.0 12.8 + - + -
44A PHE* 3.3 25.0 - - + -
47A ILE* 4.4 4.5 - - - +
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Residues in contact with LEU 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 ARG* 3.1 21.3 + - + +
25A ARG* 3.8 7.9 - - - +
27A ALA* 1.3 77.5 - - + +
29A ARG* 1.3 62.2 + - - +
30A TYR 3.4 0.7 + - - -
31A HIS* 3.5 25.5 + - + +
34A LYS* 4.6 19.8 - - + +
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Residues in contact with ARG 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 ARG 3.4 9.4 + - - +
26A GLN* 3.2 42.4 + - - +
27A ALA 3.0 0.6 + - - -
28A LEU* 1.3 79.8 - - - +
30A TYR* 1.3 93.4 + - + +
34A LYS 4.9 0.9 - - - +
35A ASN* 2.8 27.3 + - - +
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Residues in contact with TYR 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* 3.2 26.2 + - - -
27A ALA 2.9 4.7 + - - -
29A ARG* 1.3 121.3 + - + +
31A HIS* 1.3 66.1 + - - +
32A PRO* 3.3 5.5 - - - +
35A ASN* 4.0 22.4 - - - +
37A GLU* 5.9 1.3 - - - -
40A ALA* 3.7 28.4 - - + +
41A GLU* 4.9 0.9 + - - -
43A LYS* 3.4 45.2 + - + +
44A PHE* 3.6 25.6 - - + +
47A ILE* 3.4 21.1 - - + -
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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 ALA* 3.0 8.0 + - + +
28A LEU* 3.5 28.0 + - + +
29A ARG 3.6 0.2 - - - -
30A TYR* 1.3 75.5 - - - +
32A PRO* 1.3 68.1 - - + +
33A ASP* 2.8 40.4 + - - -
34A LYS* 2.8 36.2 + - + +
35A ASN* 2.8 14.4 + - - +
44A PHE* 3.6 22.8 - + - -
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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