Contacts of the helix formed by residues 18 - 34 (chain A) in PDB entry 3MWZ
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP 4.8 1.1 - - - +
17A ASP* 1.3 90.2 - - - +
19A GLU* 1.3 61.8 + - - +
20A TYR 3.2 0.9 + - - -
21A LEU* 3.3 11.9 + - + +
22A GLU* 3.2 33.2 + - - +
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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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17A ASP* 2.9 18.7 + - - +
18A PRO* 1.3 78.0 - - - +
20A TYR* 1.3 61.6 + - + +
22A GLU* 4.0 22.1 - - + +
23A MSE 2.8 46.8 + - + +
60A TYR* 4.6 1.4 + - - -
99A ARG* 2.8 46.5 + - - -
105A LYS* 5.9 0.3 + - - -
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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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12A ARG* 3.5 24.5 + - + +
13A SER 3.5 24.7 - - - -
14A ASN* 4.4 6.3 - - + +
16A ASP* 4.9 3.1 - - + +
17A ASP* 3.4 38.6 + - + +
18A PRO 3.2 1.0 - - - -
19A GLU* 1.3 78.4 - - + +
21A LEU* 1.3 57.4 + - - +
23A MSE 3.4 15.2 + - + -
24A ALA* 2.9 28.1 + - - +
47A VAL* 4.4 6.0 - - + +
50A VAL* 3.6 44.4 - - + -
52A THR* 4.4 2.0 - - + +
60A TYR* 3.9 25.2 - + - -
62A LEU* 3.6 13.8 - - + +
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP 4.7 0.6 + - - -
18A PRO* 3.3 12.4 + - + +
19A GLU 3.2 0.2 - - - -
20A TYR* 1.3 77.5 - - - +
22A GLU* 1.3 65.1 + - - +
24A ALA* 3.2 1.7 + - - +
25A HIS* 3.0 54.0 + - + +
44A VAL* 4.2 11.4 - - + +
46A GLU* 6.1 0.4 - - - -
47A VAL* 3.9 25.7 - - + +
79A LYS* 6.3 0.9 - - + +
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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 PRO* 3.2 29.0 + - + +
19A GLU* 3.2 23.6 + - + +
21A LEU* 1.3 76.7 - - - +
23A MSE 1.3 59.0 + - + +
25A HIS* 3.2 4.5 + - - +
26A TYR* 3.0 27.1 + - - +
79A LYS* 3.4 30.1 + - - +
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Residues in contact with MSE 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* 2.8 53.4 + - + +
20A TYR* 3.8 12.8 - - + +
22A GLU* 1.3 70.2 - - + +
24A ALA* 1.3 61.1 + - - +
26A TYR* 3.5 7.2 - - - +
27A ALA* 2.9 31.2 + - - +
60A TYR* 3.6 52.3 - - + -
62A LEU* 4.3 2.9 - - + -
97A ILE* 3.6 29.6 - - + +
99A ARG* 3.8 17.9 - - - -
105A LYS* 4.5 15.9 - - + -
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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 TYR 2.9 18.5 + - - +
21A LEU 3.2 6.0 + - - +
23A MSE 1.3 75.9 - - - +
25A HIS* 1.3 57.0 + - - +
27A ALA* 3.4 3.4 + - - +
28A THR* 2.9 35.0 + - - -
44A VAL* 3.6 12.3 - - + -
47A VAL* 3.9 9.6 - - + -
62A LEU* 3.8 8.7 - - + +
64A LEU* 3.7 33.2 - - + -
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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 LEU* 3.0 49.6 + - + +
22A GLU 3.2 6.9 + - - +
24A ALA* 1.3 73.9 - - - +
26A TYR* 1.3 60.2 + - - +
28A THR* 4.7 0.2 - - - -
29A SER* 2.8 37.9 + - - -
43A THR* 3.6 12.3 - - - -
44A VAL* 3.9 23.9 + - + +
77A TYR* 2.7 35.7 + - + -
79A LYS* 3.7 45.2 + - + +
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Residues in contact with TYR 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 GLU 3.0 13.7 + - - +
23A MSE 3.5 14.4 - - - +
25A HIS* 1.3 76.2 - - - +
27A ALA* 1.3 70.0 + - + +
29A SER* 3.4 4.6 + - - -
30A THR* 2.7 48.4 + - + +
97A ILE* 4.3 13.0 - - + -
105A LYS* 3.5 46.5 + - + -
106A SER* 3.5 24.1 - - - -
107A ILE* 3.6 27.5 + - + +
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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 MSE 2.9 17.0 + - - +
24A ALA 3.9 2.7 - - - +
26A TYR* 1.3 76.3 - - + +
28A THR* 1.3 58.4 + - - +
30A THR* 3.9 0.7 - - - -
31A TRP* 2.9 34.0 + - - +
95A THR* 3.9 26.0 - - + +
97A ILE* 3.9 13.2 - - + -
107A ILE* 3.8 19.4 - - + +
110A PHE* 3.7 10.5 - - + -
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Residues in contact with THR 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 2.9 18.1 + - - -
25A HIS* 4.1 1.6 - - - -
27A ALA* 1.3 77.6 - - - +
29A SER* 1.3 57.9 + - - +
31A TRP* 4.1 1.9 - - + +
32A SER* 2.8 31.8 + - - -
42A ASP* 3.5 35.0 - - + +
43A THR* 3.8 13.9 - - - +
44A VAL* 3.5 8.6 - - - +
64A LEU* 3.4 21.1 - - - +
66A VAL* 3.9 11.7 - - + +
77A TYR* 5.5 0.2 - - - -
110A PHE* 3.6 14.3 - - + -
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Residues in contact with SER 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 HIS 2.8 23.4 + - - -
26A TYR* 3.4 6.1 + - - -
28A THR* 1.3 77.3 - - - +
30A THR* 1.3 66.6 + - - +
32A SER* 3.4 7.1 + - - -
33A ALA* 3.2 24.8 + - - +
41A PHE* 3.6 12.0 - - - -
42A ASP 4.3 3.3 + - - -
77A TYR* 3.5 43.2 - - - +
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Residues in contact with THR 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 TYR* 2.7 39.1 + - + -
29A SER* 1.3 77.7 + - - +
31A TRP* 1.3 66.8 + - - +
33A ALA* 3.5 9.1 + - - +
34A GLN* 3.5 30.1 + - - +
107A ILE* 3.8 22.2 - - + -
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Residues in contact with TRP 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 2.9 18.9 + - - +
28A THR 4.1 2.5 - - - +
30A THR* 1.3 77.5 - - - +
32A SER* 1.3 85.3 + - - +
34A GLN* 2.9 23.8 + - - +
35A GLN* 3.0 60.6 + - + +
38A LYS* 5.7 0.7 - - - -
42A ASP* 3.5 11.2 - - + -
66A VAL* 5.8 0.2 - - + -
91A ARG* 3.4 30.5 - - - -
107A ILE* 4.6 5.1 - - + +
110A PHE* 3.4 61.9 + + + -
112A CYS* 4.1 13.0 - - + -
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Residues in contact with SER 32 (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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28A THR 2.8 24.6 + - - -
29A SER* 3.4 8.3 + - - -
31A TRP* 1.3 93.6 - - - +
33A ALA* 1.3 60.2 + - - +
35A GLN* 3.2 19.4 + - - +
38A LYS* 3.6 19.7 - - - +
41A PHE* 3.7 5.6 - - - -
42A ASP* 3.0 40.1 + - - -
73A LEU* 4.4 2.7 - - - -
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Residues in contact with ALA 33 (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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29A SER 3.2 17.6 + - - +
30A THR* 3.7 8.3 - - - +
31A TRP 3.2 0.2 - - - -
32A SER* 1.3 76.6 + - - +
34A GLN* 1.3 60.2 + - + +
35A GLN 3.4 2.3 + - - +
41A PHE* 4.1 9.0 - - + -
73A LEU* 3.7 29.2 - - + +
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Residues in contact with GLN 34 (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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30A THR* 3.5 28.8 - - + +
31A TRP* 2.9 18.7 + - - +
33A ALA* 1.3 77.7 - - + +
35A GLN* 1.3 70.3 + - - +
36A PRO* 3.8 6.6 - - - +
107A ILE* 5.9 0.9 - - - +
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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