Contacts of the helix formed by residues 20 - 35 (chain B) in PDB entry 1MVW
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 ASP 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PHE* 1.3 74.8 - - - +
21B GLU* 1.3 63.6 + - - +
22B THR* 3.1 12.1 + - - -
23B GLU* 3.0 62.5 + - - +
24B ILE* 3.2 12.5 + - - +
93B PRO* 4.4 19.0 - - + +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE 4.0 0.4 + - - -
20B ASP* 1.3 72.9 - - - +
22B THR* 1.3 58.6 + - - +
24B ILE* 3.2 16.1 + - + +
25B GLU* 2.9 50.4 + - + +
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASP* 3.1 9.4 + - - -
21B GLU* 1.3 76.5 - - - +
23B GLU* 1.3 57.2 + - - +
25B GLU* 3.1 17.0 + - + +
26B ASP* 2.9 46.3 + - - +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.3 26.1 - - + -
20B ASP* 3.0 44.9 + - - +
22B THR* 1.3 78.1 - - - +
24B ILE* 1.3 56.3 + - - +
26B ASP* 3.2 13.6 + - - +
27B PHE* 3.1 51.3 + - + -
88B LEU* 5.8 1.4 - - - +
91B ALA* 5.0 12.6 - - - +
93B PRO* 5.8 4.9 - - - +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.9 36.1 - - + +
20B ASP 3.2 15.0 + - - +
21B GLU* 3.2 17.5 + - + +
23B GLU* 1.3 78.0 - - - +
25B GLU* 1.3 56.3 + - + +
27B PHE* 3.2 10.4 + - - +
28B LYS* 2.9 26.6 + - - +
77B PHE* 3.9 19.0 - - + -
81B LEU* 4.4 15.7 - - + -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU* 2.9 47.9 + - + +
22B THR* 3.1 18.6 + - + +
24B ILE* 1.3 76.3 - - + +
26B ASP* 1.3 59.7 + - - +
28B LYS* 3.2 23.8 + - - +
29B GLU* 3.0 41.3 + - - +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A PHE* 5.2 15.3 - - + -
839A MLY 5.6 8.0 - - - -
22B THR* 2.9 40.0 + - - +
23B GLU* 3.2 13.2 + - + +
25B GLU* 1.3 76.7 - - - +
27B PHE* 1.3 61.8 + - + +
29B GLU* 3.2 19.7 + - - +
30B ALA* 3.0 28.3 + - - +
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A MET* 5.8 6.7 - - + -
835A PHE* 5.9 8.1 - + - -
19B PHE* 3.5 32.5 - + - -
23B GLU* 3.1 36.9 + - + -
24B ILE* 3.2 7.2 + - - +
26B ASP* 1.3 81.6 - - + +
28B LYS* 1.3 57.0 + - - +
30B ALA* 3.4 9.4 + - + +
31B PHE* 2.9 29.5 + - - +
77B PHE* 4.1 3.9 - - + -
80B PHE* 4.6 11.2 - + + -
81B LEU* 4.0 23.8 - - + -
84B PHE* 4.3 37.7 - + + -
88B LEU* 4.5 11.2 - - + -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE 2.9 13.1 + - - +
25B GLU* 3.2 26.3 + - - +
27B PHE* 1.3 74.7 - - - +
29B GLU* 1.3 79.7 + - - +
31B PHE* 3.3 6.6 + - + +
32B THR* 2.9 37.4 + - - +
77B PHE* 3.5 29.6 - - + -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLU* 3.0 23.2 + - - +
26B ASP* 3.3 24.1 - - - +
28B LYS* 1.3 89.8 + - - +
30B ALA* 1.3 58.3 + - - +
32B THR* 3.2 8.3 + - - -
33B VAL* 3.0 35.2 + - + +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A PHE* 4.7 20.4 - - + -
26B ASP 3.0 15.9 + - - +
27B PHE* 3.8 12.6 - - + +
29B GLU* 1.3 75.6 - - - +
31B PHE* 1.3 64.2 + - - +
33B VAL* 3.2 8.2 + - - +
34B ILE* 3.1 38.8 + - + +
80B PHE* 4.9 5.2 - - + -
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE 2.9 19.1 + - - +
28B LYS* 3.4 11.7 - - + +
30B ALA* 1.3 77.4 - - - +
32B THR* 1.3 62.6 + - - +
34B ILE 3.4 0.7 + - - -
35B ASP* 2.9 37.5 + - + +
40B GLY* 3.1 43.1 - - - -
41B ILE 4.2 0.4 - - - -
42B ILE* 3.5 25.5 - - + +
75B ILE* 3.4 19.5 - - + -
76B ASN 3.5 10.8 - - - -
77B PHE* 3.6 29.8 - + + -
80B PHE* 3.7 24.4 - + + -
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS* 2.9 22.8 + - - +
29B GLU* 3.2 8.2 + - - -
31B PHE* 1.3 82.4 - - - +
33B VAL* 1.3 63.8 + - + +
35B ASP* 3.3 22.9 - - - +
36B GLN* 4.6 1.9 - - - +
38B ALA* 6.1 4.5 - - + -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A LEU* 5.4 1.3 - - + -
838A ILE* 6.1 3.4 - - + -
29B GLU* 3.0 19.4 + - + +
30B ALA* 3.2 8.5 + - - +
32B THR* 1.3 80.3 - - + +
34B ILE* 1.3 62.6 + - + +
36B GLN* 3.5 13.6 + - - +
50B THR* 3.4 13.7 + - + +
54B MET* 4.4 22.4 - - + -
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A TRP* 5.4 0.7 - - + -
831A TRP* 2.7 68.4 - - + +
834A LEU* 6.1 0.4 - - + -
30B ALA* 3.1 22.3 + - + +
33B VAL* 1.3 81.7 - - + +
35B ASP* 1.3 58.7 + - - +
36B GLN 3.2 2.6 + - - -
42B ILE* 3.8 16.8 - - + -
46B ASP* 3.0 25.3 - - - +
47B LEU* 3.8 13.2 - - + -
50B THR* 3.2 10.9 + - + -
80B PHE* 4.4 22.7 - - + -
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Residues in contact with ASP 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PHE* 2.9 24.5 + - + +
32B THR* 3.3 16.3 + - - +
33B VAL 3.5 0.2 - - - -
34B ILE* 1.3 74.3 - - - +
36B GLN* 1.3 56.5 + - - +
37B ASN* 2.9 25.5 - - - +
38B ALA* 3.0 21.7 + - - +
39B ASP 3.3 2.9 + - - -
40B GLY* 3.0 26.4 + - - -
41B ILE 3.1 25.2 + - - +
42B ILE* 3.5 9.9 - - + -
46B ASP* 3.2 11.3 - - - +
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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