Contacts of the helix formed by residues 52 - 66 (chain A) in PDB entry 2CZY
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE 4.1 1.8 - - - +
49A GLY 5.0 3.3 - - - +
50A SER 3.9 5.8 - - - +
51A ASP* 1.3 86.3 - - - +
53A ALA* 1.3 65.7 + - + +
55A TYR* 3.2 10.3 + - + +
56A ASN* 3.0 27.1 + - - +
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Residues in contact with ALA 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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51A ASP* 3.2 11.6 - - - +
52A PRO* 1.3 83.3 - - + +
54A THR* 1.3 63.4 + - - +
56A ASN* 3.4 6.3 + - - +
57A GLY* 3.0 20.6 + - - -
82A LEU* 5.3 0.5 - - - +
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Residues in contact with THR 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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44A VAL* 5.3 0.8 - - + +
48A PHE* 3.2 52.3 - - + -
51A ASP* 3.5 18.9 + - - +
52A PRO 3.2 0.6 - - - -
53A ALA* 1.3 77.5 - - - +
55A TYR* 1.3 62.6 + - - +
57A GLY 3.2 1.2 + - - -
58A PHE* 3.1 18.4 + - - +
82A LEU* 3.3 44.0 - - + +
83A PHE* 3.9 3.1 - - + -
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Residues in contact with TYR 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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41A LEU* 3.5 46.0 + - + +
44A VAL* 4.1 16.4 - - + +
45A LYS* 3.3 62.9 - - + +
48A PHE* 5.1 2.8 - - + +
51A ASP 3.9 2.8 + - - +
52A PRO* 3.2 16.1 + - + +
54A THR* 1.3 79.5 - - - +
56A ASN* 1.3 65.9 + - - +
58A PHE* 3.1 18.1 + + + +
59A LEU* 3.3 49.3 + - + +
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Residues in contact with ASN 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 PRO* 3.0 18.2 + - - +
53A ALA* 3.8 6.7 - - - +
55A TYR* 1.3 80.3 - - - +
57A GLY* 1.3 62.4 + - - +
59A LEU* 3.6 16.9 + - - +
60A GLU* 3.2 24.5 + - - +
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Residues in contact with GLY 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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53A ALA 3.0 14.4 + - - -
54A THR 3.2 4.5 + - - -
55A TYR 3.1 0.6 - - - -
56A ASN* 1.3 75.3 - - - +
58A PHE* 1.3 63.5 + - - +
60A GLU* 3.2 19.6 + - - +
61A ILE* 3.1 22.7 + - - +
78A ARG* 5.2 7.3 - - - +
82A LEU* 4.3 11.9 - - - -
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Residues in contact with PHE 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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40A TYR* 3.5 38.1 - + - -
41A LEU* 4.2 25.1 - - + -
44A VAL* 5.1 10.5 - - + -
54A THR 3.1 10.4 + - - +
55A TYR* 3.1 12.0 + + + +
57A GLY* 1.3 75.6 - - - +
59A LEU* 1.3 64.4 + - + +
61A ILE* 3.2 21.8 + - + +
62A MET* 3.2 55.1 + - + +
79A VAL* 4.3 8.5 - - + -
82A LEU* 3.9 8.4 - - + +
83A PHE* 4.3 19.1 - + + -
93A PHE* 4.1 17.3 - + - -
49B LEU* 4.8 5.2 - - + -
53B ALA* 6.0 1.1 - - + -
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Residues in contact with LEU 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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41A LEU* 4.6 8.5 - - + -
55A TYR* 3.3 49.6 + - + +
56A ASN* 3.8 17.9 - - - +
58A PHE* 1.3 77.8 - - + +
60A GLU* 1.3 53.8 + - - +
62A MET* 3.4 4.7 + - - +
63A LYS* 2.7 39.6 + - + +
53B ALA* 3.4 42.4 - - + +
54B LEU* 4.8 6.7 - - + +
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Residues in contact with GLU 60 (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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56A ASN* 3.2 15.6 + - - +
57A GLY* 3.2 14.0 + - - +
59A LEU* 1.3 76.9 - - - +
61A ILE* 1.3 52.0 + - + +
63A LYS* 4.4 6.7 - - + -
64A GLU* 2.7 62.3 + - + +
78A ARG* 4.4 20.1 + - - +
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Residues in contact with ILE 61 (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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57A GLY 3.1 20.4 - - - +
58A PHE* 3.2 25.5 + - + +
60A GLU* 1.3 77.7 - - + +
62A MET* 1.3 66.4 + - + +
64A GLU* 3.6 5.8 - - - +
65A PHE* 3.0 22.3 + - - +
70A ILE* 4.2 9.4 - - + +
74A GLY 4.6 0.4 - - - +
75A VAL* 3.2 49.4 - - + +
78A ARG* 3.5 38.8 - - + +
79A VAL* 4.3 8.1 - - + +
82A LEU* 4.7 6.5 - - + -
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Residues in contact with MET 62 (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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58A PHE* 3.2 63.8 + - + +
59A LEU* 3.9 7.2 - - - +
61A ILE* 1.3 94.9 - - + +
63A LYS* 1.3 63.4 + - - +
65A PHE* 3.0 16.9 + - - +
66A LYS 3.1 10.2 + - - -
75A VAL* 4.2 11.4 - - + -
79A VAL* 4.7 0.9 - - + -
93A PHE* 4.3 8.3 - - + -
46B LEU* 4.4 8.5 - - + +
49B LEU* 3.9 17.0 - - + +
50B ALA* 3.2 44.1 - - + +
53B ALA* 5.0 4.7 - - + -
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Residues in contact with LYS 63 (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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59A LEU* 2.7 24.4 + - + +
60A GLU* 4.0 6.3 - - + +
62A MET* 1.3 73.2 - - - +
64A GLU* 1.3 63.6 + - + +
66A LYS* 3.3 15.2 + - - +
67A SER* 3.4 19.5 + - - +
50B ALA* 4.1 2.9 - - - +
54B LEU* 3.6 42.2 - - + +
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Residues in contact with GLU 64 (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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60A GLU* 2.7 52.4 + - + +
61A ILE* 3.6 6.3 - - - +
63A LYS* 1.3 76.2 - - + +
65A PHE* 1.3 60.8 + - - +
67A SER* 3.4 19.8 + - - -
68A GLN 3.8 2.9 + - - -
69A SER* 3.8 11.4 + - - -
70A ILE* 3.4 32.1 + - + +
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Residues in contact with PHE 65 (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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61A ILE 3.0 12.1 + - - +
62A MET* 3.0 14.0 + - - +
64A GLU* 1.3 76.0 - - - +
66A LYS* 1.3 60.4 + - + +
68A GLN* 2.9 22.7 + - - +
70A ILE* 3.3 23.7 - - + +
71A ASP* 4.9 0.4 - - - -
72A THR* 4.1 21.1 - - + -
75A VAL* 3.3 26.7 - - + -
43B ALA* 4.6 9.2 - - + -
46B LEU* 3.4 49.4 - - + +
47B ILE* 3.8 23.5 - - + +
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Residues in contact with LYS 66 (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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62A MET 3.1 5.5 + - - -
63A LYS* 3.3 9.8 + - - +
65A PHE* 1.3 77.5 - - - +
67A SER* 1.3 62.5 + - - +
68A GLN* 3.0 7.8 + - - +
46B LEU 5.3 0.2 - - - +
47B ILE* 3.7 31.0 + - + +
50B ALA* 3.3 35.0 - - + -
51B ASN* 3.2 41.2 - - - +
54B LEU* 4.1 20.4 - - + -
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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