Contacts of the helix formed by residues 46 - 59 (chain A) in PDB entry 2MW5
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 HIS 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR 4.8 4.7 + - - -
45A THR* 1.3 79.9 + - - +
47A LEU* 1.3 65.7 + - - +
48A LYS* 3.1 10.6 + - + +
49A LYS* 3.3 18.3 + - - +
50A LEU* 4.1 2.4 + - - +
76A ASP 4.0 7.0 - - - +
77A ASN* 3.1 42.5 + - - +
78A HIS 3.3 5.6 - - - +
79A THR* 3.6 20.5 - - + +
82A GLU* 4.9 1.3 + - - -
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Residues in contact with LEU 47 (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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46A HIS* 1.3 69.2 - - - +
48A LYS* 1.3 58.8 + - - +
49A LYS 3.2 0.4 - - - -
50A LEU* 3.0 35.0 + - + +
51A LYS* 2.8 29.6 + - - +
67A PHE* 3.8 19.2 - - + -
74A ILE* 4.0 15.0 - - + -
75A ALA 4.5 1.8 - - - +
76A ASP* 3.1 26.7 + - - +
78A HIS* 2.9 24.1 + - + +
79A THR 3.7 2.9 - - - +
80A PRO* 3.6 29.8 - - + -
85A MET* 3.8 24.2 - - + -
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Residues in contact with LYS 48 (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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46A HIS* 3.1 6.9 - - + +
47A LEU* 1.3 76.0 - - - +
49A LYS* 1.3 61.1 + - - +
51A LYS* 3.3 9.8 + - + +
52A GLU* 3.0 18.7 + - - +
62A MET* 3.5 22.8 - - + +
76A ASP* 3.0 27.8 + - + +
77A ASN* 3.6 36.3 + - - +
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Residues in contact with LYS 49 (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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45A THR* 5.3 9.9 - - + -
46A HIS* 3.3 11.1 + - - +
47A LEU 3.2 0.8 - - - -
48A LYS* 1.3 78.7 - - - +
50A LEU* 1.3 58.9 + - - +
52A GLU* 2.9 38.3 + - - +
53A SER* 2.9 39.6 + - - +
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Residues in contact with LEU 50 (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 ILE* 6.2 1.8 - - + -
27A LEU* 4.8 14.6 - - + -
29A VAL* 4.3 26.5 - - + -
39A PHE* 6.4 2.0 - - + -
41A VAL* 6.2 4.5 - - + -
46A HIS 4.1 2.3 + - - +
47A LEU* 3.0 34.4 + - + +
49A LYS* 1.3 75.0 - - - +
51A LYS* 1.3 61.2 + - - +
53A SER* 3.1 11.1 + - - +
54A TYR* 2.8 29.3 + - + +
67A PHE* 3.6 24.0 - - + -
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Residues in contact with LYS 51 (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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47A LEU 2.8 12.4 + - - +
48A LYS* 3.4 8.5 - - + +
50A LEU* 1.3 76.8 - - - +
52A GLU* 1.3 61.2 + - - +
54A TYR* 4.0 1.3 - - - +
55A CYS* 3.1 30.7 + - - -
62A MET* 3.3 42.0 - - + +
63A ASN* 4.7 4.5 - - - +
65A LEU* 2.9 30.2 + - + +
66A ARG* 3.8 6.2 - - - +
67A PHE* 3.5 18.5 - - + -
76A ASP* 2.9 38.3 + - + +
96A GLU* 3.0 23.8 + - - -
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Residues in contact with GLU 52 (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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48A LYS 3.0 12.6 + - - +
49A LYS* 2.9 44.6 + - - +
51A LYS* 1.3 76.5 - - - +
53A SER* 1.3 57.2 + - - +
55A CYS* 3.2 3.6 + - - +
56A GLN* 2.9 56.6 + - + +
62A MET* 3.8 34.1 - - + +
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Residues in contact with SER 53 (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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39A PHE* 5.7 11.7 - - - -
49A LYS* 2.9 30.6 + - - +
50A LEU* 3.1 13.8 + - - +
52A GLU* 1.3 76.4 + - - +
54A TYR* 1.3 63.1 + - - +
56A GLN* 3.4 19.0 + - - +
57A ARG* 3.3 18.2 + - - +
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Residues in contact with TYR 54 (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 VAL* 3.7 31.2 - - + -
31A GLY* 3.0 24.0 + - - -
33A ASP* 2.9 34.2 + - - +
50A LEU* 2.8 21.7 + - + +
51A LYS 4.0 3.1 - - - +
53A SER* 1.3 72.3 - - - +
55A CYS* 1.3 65.2 + - - +
57A ARG* 2.9 61.8 + - + +
58A GLN* 3.6 4.5 + - - +
65A LEU* 3.5 22.0 - - + -
67A PHE* 4.1 9.9 - + + -
93A VAL* 3.8 30.1 - - + -
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Residues in contact with CYS 55 (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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51A LYS* 3.1 27.1 + - - +
52A GLU 3.2 4.0 + - - +
54A TYR* 1.3 74.4 - - - +
56A GLN* 1.3 57.8 + - - +
58A GLN* 3.1 3.4 + - - +
59A GLY 2.9 22.0 + - - -
60A VAL* 3.1 34.8 + - + +
61A PRO 3.5 16.8 - - - +
62A MET* 3.6 20.9 - - - -
64A SER* 4.2 1.8 - - - -
65A LEU* 3.9 34.1 - - - -
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Residues in contact with GLN 56 (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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52A GLU* 2.9 43.2 + - + +
53A SER* 3.5 21.3 + - - +
54A TYR 3.2 0.2 - - - -
55A CYS* 1.3 78.5 - - + +
57A ARG* 1.3 59.3 + - - +
59A GLY* 3.2 14.0 + - - +
60A VAL 4.7 3.6 - - - +
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Residues in contact with ARG 57 (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 VAL* 3.2 21.0 + - - +
33A ASP* 4.2 9.0 - - - +
35A SER* 3.1 44.9 + - - +
37A ILE* 3.0 52.9 + - + +
53A SER 3.3 8.5 + - - +
54A TYR* 2.9 63.8 + - + +
56A GLN* 1.3 74.9 - - - +
58A GLN* 1.3 61.9 + - + +
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Residues in contact with GLN 58 (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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33A ASP* 2.9 38.4 + - - +
54A TYR* 4.0 9.3 - - + +
55A CYS 3.1 8.1 + - - +
57A ARG* 1.3 81.4 - - + +
59A GLY* 1.3 60.0 + - - +
60A VAL* 3.6 27.7 - - + +
64A SER* 5.4 0.3 - - - -
65A LEU* 3.7 31.3 - - - +
93A VAL* 5.1 2.8 - - - +
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Residues in contact with GLY 59 (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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55A CYS 2.9 4.2 + - - -
56A GLN* 3.2 13.4 + - - -
58A GLN* 1.3 80.5 - - - +
60A VAL* 1.3 60.5 + - - +
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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