Contacts of the helix formed by residues 43 - 54 (chain K) 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 43 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37K ASN* 3.2 19.2 + - - -
39K ASP* 5.1 0.7 - - - +
41K ILE* 3.2 8.4 + - + +
42K ILE* 1.3 76.3 - - - +
44K LYS* 1.3 58.1 - - - +
45K ASP* 3.0 30.2 + - - +
46K ASP* 2.8 37.9 + - - +
47K LEU* 3.2 15.9 + - - +
68K ILE* 4.8 2.7 - - - -
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Residues in contact with LYS 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K ASP* 1.3 74.5 - - - +
45K ASP* 1.3 59.8 + - - +
47K LEU* 3.3 13.6 + - - +
48K ARG* 3.0 49.4 + - - +
61K ASN* 3.6 37.3 - - - +
64K LEU* 3.7 16.1 - - + +
65K ASP* 3.4 27.9 + - - +
68K ILE* 3.7 17.4 - - + +
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Residues in contact with ASP 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K ASP* 3.0 19.8 + - - +
44K LYS* 1.3 79.1 + - - +
46K ASP* 1.3 58.1 + - - +
48K ARG* 3.2 28.7 + - - +
49K GLU* 2.9 49.7 + - - +
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Residues in contact with ASP 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K ILE 3.0 17.5 - - - +
35K ASP* 3.2 10.2 - - - +
36K GLN* 3.0 30.6 + - - +
37K ASN* 3.1 24.6 + - - +
42K ILE* 3.9 7.2 - - + -
43K ASP* 2.8 41.1 + - - +
45K ASP* 1.3 76.5 - - - +
47K LEU* 1.3 57.4 + - - +
49K GLU* 3.3 3.0 + - - +
50K THR* 2.8 35.2 + - - -
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Residues in contact with LEU 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831J TRP* 2.4 53.6 - - + -
34K ILE* 3.8 5.6 - - + -
42K ILE* 3.7 11.0 - - + +
43K ASP 3.2 15.0 + - - +
44K LYS* 3.4 15.7 - - - +
46K ASP* 1.3 76.9 - - - +
48K ARG* 1.3 57.9 + - - +
50K THR* 3.3 1.9 + - - -
51K PHE* 3.0 42.1 + - + -
64K LEU* 3.6 24.2 - - + +
67K MET* 4.5 7.0 - - + -
68K ILE* 4.0 23.6 - - + -
75K ILE* 6.3 1.1 - - + -
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Residues in contact with ARG 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K LYS* 3.0 47.8 + - - +
45K ASP* 3.4 31.7 + - - +
47K LEU* 1.3 76.3 - - - +
49K GLU* 1.3 62.7 + - + +
51K PHE* 3.3 6.2 + - - +
52K ALA* 2.9 29.7 + - + +
59K VAL* 4.1 20.2 - - + +
61K ASN* 3.8 19.4 - - - +
64K LEU* 3.8 15.6 - - + +
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Residues in contact with GLU 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K GLN* 3.0 26.6 + - - +
45K ASP* 2.9 39.6 + - + +
46K ASP* 3.9 2.6 + - - +
48K ARG* 1.3 81.8 - - + +
50K THR* 1.3 60.1 + - - +
52K ALA* 3.9 6.9 - - - +
53K ALA* 3.2 26.7 + - - +
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Residues in contact with THR 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834J LEU* 4.4 13.5 - - + -
33K VAL* 3.9 13.7 - - + +
34K ILE* 3.2 34.6 + - + -
36K GLN* 3.0 21.0 + - - +
46K ASP 2.8 18.4 + - - -
47K LEU 3.7 3.6 - - - -
49K GLU* 1.3 73.8 - - - +
51K PHE* 1.3 64.8 + - - +
53K ALA* 3.2 4.5 + - - +
54K MET* 3.1 45.9 + - + +
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Residues in contact with PHE 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830J PRO* 5.0 5.6 - - + -
831J TRP* 5.6 4.3 - + - -
834J LEU* 2.5 41.5 - - + -
34K ILE* 6.5 0.7 - - + -
47K LEU* 3.0 31.8 + - + +
48K ARG 3.7 3.4 - - - +
50K THR* 1.3 77.4 - - + +
52K ALA* 1.3 56.3 + - - +
54K MET* 3.0 18.9 + - + +
55K GLY 3.1 0.9 + - - -
56K ARG* 2.8 52.6 + - + +
59K VAL* 3.6 24.9 - - + -
63K GLU* 5.7 0.4 - - - -
64K LEU* 3.7 17.9 - - + -
67K MET* 3.8 33.0 - - + -
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Residues in contact with ALA 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48K ARG* 2.9 19.5 + - + +
49K GLU* 4.0 8.1 - - - +
51K PHE* 1.3 74.9 - - - +
53K ALA* 1.3 57.2 + - - +
55K GLY* 3.1 18.7 + - - -
56K ARG 3.4 17.4 + - - +
57K LEU* 5.4 6.7 - - + -
59K VAL* 5.5 0.4 - - + -
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Residues in contact with ALA 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K GLN* 4.5 7.4 - - - +
49K GLU 3.2 18.7 + - - +
50K THR* 3.2 8.2 + - - +
52K ALA* 1.3 76.9 - - - +
54K MET* 1.3 69.8 + - + +
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Residues in contact with MET 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834J LEU* 5.1 7.4 - - + -
837J MLY 6.3 3.1 - - + -
838J ILE* 2.4 49.1 - - + -
841J LEU* 5.6 7.6 - - + -
33K VAL* 4.4 9.2 - - + -
50K THR* 3.1 28.0 - - + +
51K PHE* 3.0 12.4 + - + +
53K ALA* 1.3 85.7 - - + +
55K GLY* 1.3 58.8 + - - +
56K ARG* 3.7 5.3 - - + +
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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