Contacts of the helix formed by residues 20 - 35 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19N PHE* 1.3 75.0 - - - +
21N GLU* 1.3 64.1 + - - +
22N THR* 3.1 12.3 + - - -
23N GLU* 3.0 60.2 + - - +
24N ILE* 3.2 12.7 + - - +
93N PRO* 4.4 18.4 - - - +
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Residues in contact with GLU 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N PHE 4.0 0.6 + - - -
20N ASP* 1.3 72.3 - - - +
22N THR* 1.3 58.5 + - - +
24N ILE* 3.2 16.2 + - + +
25N GLU* 2.9 49.3 + - + +
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Residues in contact with THR 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N ASP* 3.1 9.9 + - - -
21N GLU* 1.3 75.6 - - - +
23N GLU* 1.3 57.6 + - - +
25N GLU* 3.1 18.7 + - + +
26N ASP* 2.9 44.7 + - - +
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Residues in contact with GLU 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839M MLY 6.4 1.3 - - - -
19N PHE* 3.3 26.6 - - + -
20N ASP* 3.0 45.6 + - - +
22N THR* 1.3 78.2 - - - +
24N ILE* 1.3 55.9 + - - +
26N ASP* 3.2 13.8 + - + +
27N PHE* 3.1 50.5 + - + -
88N LEU* 5.8 1.6 - - - +
91N ALA* 5.0 12.5 - - - +
93N PRO* 5.8 4.7 - - - +
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Residues in contact with ILE 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N PHE* 3.9 36.8 - - + +
20N ASP 3.2 15.9 + - - +
21N GLU* 3.2 17.0 + - + +
23N GLU* 1.3 78.1 - - - +
25N GLU* 1.3 57.3 + - + +
27N PHE* 3.2 10.3 + - - +
28N LYS* 2.9 25.9 + - - +
77N PHE* 3.9 19.7 - - + -
81N LEU* 4.4 15.7 - - + -
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Residues in contact with GLU 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N GLU* 2.9 48.2 + - + +
22N THR* 3.1 19.7 + - + +
24N ILE* 1.3 77.4 - - + +
26N ASP* 1.3 58.3 + - - +
28N LYS* 3.2 23.8 + - - +
29N GLU* 3.0 42.5 + - - +
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Residues in contact with ASP 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835M PHE* 4.4 19.8 - - + -
839M MLY 5.1 11.4 - - - -
842M LEU* 5.6 7.7 - - + +
22N THR* 2.9 40.3 + - - +
23N GLU* 3.2 13.3 + - + +
25N GLU* 1.3 76.2 - - - +
27N PHE* 1.3 59.8 + - + +
29N GLU* 3.2 18.7 + - - +
30N ALA* 3.0 27.9 + - - +
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Residues in contact with PHE 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832M MET* 5.1 2.2 - - + -
835M PHE* 3.9 33.9 - + - -
19N PHE* 3.5 31.9 - + - -
23N GLU* 3.1 39.7 + - + -
24N ILE* 3.2 7.2 + - - +
26N ASP* 1.3 76.5 - - + +
28N LYS* 1.3 59.3 + - - +
30N ALA* 3.4 5.6 + - + +
31N PHE* 2.9 29.6 + - - +
77N PHE* 4.1 3.9 - - + -
80N PHE* 4.6 11.1 - + + -
81N LEU* 4.0 23.6 - - + -
84N PHE* 4.3 37.7 - + + -
88N LEU* 4.5 10.5 - - + -
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Residues in contact with LYS 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N ILE 2.9 12.6 + - - +
25N GLU* 3.4 26.3 + - - +
27N PHE* 1.3 75.3 - - - +
29N GLU* 1.3 79.1 + - - +
31N PHE* 3.3 6.5 + - + +
32N THR* 2.9 36.6 + - - +
77N PHE* 3.5 30.7 - - + -
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Residues in contact with GLU 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842M LEU* 5.1 18.1 - - + +
843M LYS 5.4 4.6 - - - +
25N GLU* 3.0 23.0 + - - +
26N ASP* 3.2 23.2 + - - +
28N LYS* 1.3 90.6 + - - +
30N ALA* 1.3 59.4 + - - +
32N THR* 3.2 7.7 + - - -
33N VAL* 3.0 35.2 + - + +
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Residues in contact with ALA 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835M PHE* 4.2 24.5 - - + -
838M ILE* 5.6 8.7 - - + -
842M LEU* 6.1 3.3 - - + +
26N ASP 3.0 16.1 + - - +
27N PHE* 3.8 8.7 - - + +
29N GLU* 1.3 76.2 - - - +
31N PHE* 1.3 62.6 + - - +
33N VAL* 3.2 7.4 + - - +
34N ILE* 3.1 37.1 + - + +
80N PHE* 4.9 5.6 - - + -
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Residues in contact with PHE 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N PHE 2.9 18.9 + - - +
28N LYS* 3.4 11.4 - - + +
29N GLU 3.3 0.2 - - - -
30N ALA* 1.3 76.5 - - - +
32N THR* 1.3 62.6 + - - +
34N ILE 3.4 0.7 + - - -
35N ASP* 2.9 37.2 + - + +
40N GLY* 3.1 42.8 - - - -
41N ILE 4.2 0.4 - - - -
42N ILE* 3.5 26.6 - - + +
75N ILE* 3.4 20.6 - - + -
76N ASN 3.5 10.8 - - - -
77N PHE* 3.6 28.7 - + + -
80N PHE* 3.7 24.2 - + + -
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Residues in contact with THR 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N LYS* 2.9 22.2 + - - +
29N GLU* 3.2 8.4 + - - -
31N PHE* 1.3 83.7 - - - +
33N VAL* 1.3 62.6 + - + +
35N ASP* 3.3 23.4 - - - +
36N GLN* 4.6 1.7 - - - +
38N ALA* 6.1 4.5 - - + -
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Residues in contact with VAL 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838M ILE* 4.6 13.7 - - + -
842M LEU* 5.8 9.0 - - + -
29N GLU* 3.0 20.1 + - + +
30N ALA* 3.2 7.6 + - - +
32N THR* 1.3 80.5 - - + +
34N ILE* 1.3 62.8 + - + +
36N GLN* 3.5 13.2 + - - +
50N THR* 3.4 12.6 + - + +
54N MET* 4.4 22.0 - - + -
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Residues in contact with ILE 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831M TRP* 3.1 43.3 - - + -
834M LEU* 3.7 25.1 - - + -
838M ILE* 6.2 0.2 - - + -
30N ALA* 3.1 22.8 + - + +
33N VAL* 1.3 81.1 - - + +
35N ASP* 1.3 59.3 + - - +
36N GLN 3.2 2.6 + - - -
42N ILE* 3.8 13.9 - - + -
46N ASP* 3.0 26.0 - - - +
47N LEU* 3.8 16.4 - - + -
50N THR* 3.2 25.5 + - + +
51N PHE* 6.5 0.7 - - + -
80N PHE* 4.4 9.6 - - + -
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Residues in contact with ASP 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N PHE* 2.9 24.5 + - + +
32N THR* 3.3 15.7 - - - +
33N VAL 3.5 0.2 - - - -
34N ILE* 1.3 74.1 - - - +
36N GLN* 1.3 56.2 + - - +
37N ASN* 2.9 25.5 - - - +
38N ALA* 3.0 21.5 + - - +
39N ASP 3.3 2.9 + - - -
40N GLY* 3.0 26.8 + - - -
41N ILE 3.1 26.1 + - - +
42N ILE* 3.5 10.1 - - + +
46N ASP* 3.2 10.9 - - - +
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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