Contacts of the helix formed by residues 50 - 65 (chain A) in PDB entry 5C5A
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 MET 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A THR* 3.0 28.6 + - + +
28A VAL* 4.2 17.1 - - + +
49A THR* 1.3 72.5 - - - +
51A LYS* 1.3 63.4 + - - +
53A VAL* 3.2 5.2 + - - -
54A LEU* 2.9 33.9 + - + +
100A TYR* 4.1 24.2 - - + +
103A ILE* 3.8 29.8 - - + -
104A TYR* 3.6 45.5 - - + +
107A LEU* 4.3 4.7 - - + -
204A IOD 4.1 5.3 - - + +
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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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49A THR* 3.7 9.6 - - - +
50A MET* 1.3 79.3 - - - +
52A GLU* 1.3 64.5 + - - +
54A LEU* 3.5 12.2 + - + +
55A PHE* 3.0 23.6 + - - +
204A IOD 3.6 24.8 - - + +
32B PRO* 4.0 29.5 - - + +
33B LEU* 4.3 24.0 - - + +
206B IOD 4.0 14.4 - - + -
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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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45A LYS* 2.8 33.1 + - - -
48A TYR* 3.3 16.2 - - + -
49A THR* 3.0 39.7 + - - +
51A LYS* 1.3 77.2 - - - +
53A VAL* 1.3 59.4 + - - +
55A PHE* 3.3 5.4 + - - +
56A TYR* 2.9 43.8 + - + -
31B LYS* 2.7 38.9 + - - +
206B IOD 4.3 10.5 - - + -
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.0 13.9 - - + -
30A PRO* 6.0 0.9 - - + -
34A LEU* 4.5 14.1 - - + -
38A LEU* 4.3 23.3 - - + +
48A TYR* 3.8 20.6 - - + -
49A THR 3.0 16.4 + - - +
50A MET* 3.2 10.1 + - - +
52A GLU* 1.3 76.1 - - - +
54A LEU* 1.3 64.5 + - - +
56A TYR* 3.3 1.4 + - - +
57A LEU* 2.9 43.4 + - + +
103A ILE* 4.1 20.0 - - + -
107A LEU* 4.9 1.8 - - + -
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Residues in contact with LEU 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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50A MET* 2.9 28.8 + - + +
51A LYS* 3.7 11.2 - - + +
53A VAL* 1.3 76.8 - - - +
55A PHE* 1.3 64.2 + - - +
57A LEU* 3.3 2.4 + - - -
58A GLY 3.0 18.4 + - - -
99A ILE* 4.1 0.9 - - + -
100A TYR* 3.5 33.4 - - + +
103A ILE* 3.5 26.7 - - + -
201A NUT 3.2 60.8 - - + -
203A CL 4.4 7.2 - - + -
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Residues in contact with PHE 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 3.0 17.9 + - - +
52A GLU* 3.6 4.0 - - - +
53A VAL 3.3 0.2 - - - -
54A LEU* 1.3 75.7 - - - +
56A TYR* 1.3 68.0 + + - +
58A GLY* 3.2 3.3 + - - -
59A GLN* 3.0 60.0 + - + +
201A NUT 4.9 0.7 - - - +
203A CL 3.9 15.1 - - + +
29B ARG* 3.4 26.9 - - + -
30B PRO 3.3 17.7 - - - -
31B LYS* 3.3 28.5 - - + -
32B PRO* 3.7 25.8 - - + -
108B VAL* 3.9 16.6 - - + -
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Residues in contact with TYR 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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38A LEU* 3.7 28.5 - - + -
41A VAL* 3.8 21.3 - - + +
42A GLY* 3.4 22.1 - - - -
43A ALA* 3.2 18.4 + - + +
48A TYR* 4.3 14.8 - + - -
52A GLU* 2.9 32.6 + - + +
55A PHE* 1.3 82.5 - + - +
57A LEU* 1.3 61.2 + - - +
59A GLN* 3.2 2.5 + - - +
60A TYR* 2.8 30.1 + - - +
31B LYS* 2.9 43.0 + - + +
105B ARG* 3.5 9.5 + - - -
107B LEU 4.8 3.0 + - - -
108B VAL* 4.0 20.2 - - + -
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Residues in contact with LEU 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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34A LEU* 4.2 14.4 - - + -
37A LEU* 3.7 35.4 - - + -
38A LEU* 5.0 1.1 - - + -
53A VAL* 2.9 31.3 + - + +
54A LEU 3.7 3.4 - - - +
56A TYR* 1.3 76.4 - - - +
58A GLY* 1.3 63.3 + - - +
60A TYR* 3.2 6.3 + - + +
61A ILE* 3.0 29.5 + - + +
82A LEU* 4.0 18.2 - - + -
85A LEU* 5.8 0.2 - - + -
86A PHE* 4.3 8.3 - - + -
103A ILE* 3.6 38.6 - - + -
201A NUT 4.0 12.1 - - + -
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Residues in contact with GLY 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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54A LEU 3.0 13.8 + - - -
55A PHE 3.7 1.8 - - - -
57A LEU* 1.3 77.6 - - - +
59A GLN* 1.3 56.7 + - - +
61A ILE* 3.2 1.4 + - - -
62A MET* 3.0 24.8 + - - +
201A NUT 3.2 55.1 - - - +
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Residues in contact with GLN 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 VAL* 4.1 14.4 - - + -
55A PHE* 3.0 49.8 + - + +
56A TYR* 3.2 4.4 + - - +
58A GLY* 1.3 72.4 - - - +
60A TYR* 1.3 60.9 + - - +
62A MET* 3.6 4.7 - - - +
63A THR* 2.9 36.2 + - - +
201A NUT 2.9 39.6 + - - -
29B ARG* 2.9 35.9 + - - +
108B VAL* 3.5 20.8 - - + +
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Residues in contact with TYR 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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37A LEU* 3.7 45.5 - - + -
40A SER* 3.6 24.9 - - - -
41A VAL* 4.0 12.0 - - + +
56A TYR 2.8 17.4 + - - +
57A LEU* 3.2 6.7 + - + +
59A GLN* 1.3 76.6 - - - +
61A ILE* 1.3 67.6 + - + +
63A THR* 3.3 4.2 + - + -
64A LYS* 3.0 60.3 + - + +
66A LEU* 4.0 10.5 - - + -
80A ASP* 2.6 29.4 + - - -
81A LEU* 3.9 13.1 - - + +
82A LEU* 4.0 7.4 - - + -
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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 LEU* 3.0 15.4 + - + +
58A GLY 3.2 6.0 + - - +
60A TYR* 1.3 76.8 - - + +
62A MET* 1.3 58.3 + - - +
64A LYS 3.5 0.2 + - - -
65A ARG* 2.9 24.3 + - - -
66A LEU* 3.1 29.1 + - + -
67A TYR* 3.9 9.6 - - + +
75A VAL* 4.0 14.8 - - + -
82A LEU* 3.6 30.1 - - + -
91A PHE* 4.0 9.9 - - + -
201A NUT 3.8 59.9 - - + -
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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 GLY 3.0 19.6 + - - +
59A GLN* 3.6 9.0 - - - +
60A TYR 3.2 0.2 - - - -
61A ILE* 1.3 77.7 - - - +
63A THR* 1.3 60.4 + - - +
65A ARG* 2.9 34.4 + - - -
67A TYR* 3.8 34.5 + - + +
72A GLN* 5.0 7.4 - - - +
201A NUT 3.6 55.0 - - + +
29B ARG* 4.1 26.9 - - - +
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Residues in contact with THR 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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40A SER 6.2 0.2 - - - +
41A VAL* 4.6 10.3 - - + +
59A GLN* 2.9 24.8 + - - +
60A TYR* 3.3 8.0 + - + -
62A MET* 1.3 75.7 - - - +
64A LYS* 1.3 67.4 - - + +
65A ARG* 3.7 9.2 + - - +
108B VAL* 6.0 1.7 - - - +
109B VAL 5.1 1.7 + - - -
111B ASN* 3.3 40.3 + - - +
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Residues in contact with LYS 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 TYR* 3.0 53.8 + - + +
63A THR* 1.3 85.0 - - + +
65A ARG* 1.3 72.5 + - - +
66A LEU* 3.3 19.3 + - + +
80A ASP* 2.9 23.6 + - - +
81A LEU* 5.5 0.8 - - - +
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Residues in contact with ARG 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 2.9 7.7 + - - -
62A MET 2.9 21.5 + - - -
63A THR 3.7 8.3 + - - +
64A LYS* 1.3 80.8 - - - +
66A LEU* 1.3 63.3 + - - +
67A TYR* 3.2 43.7 + - + +
69A GLU* 5.6 2.0 - - - -
111B ASN* 3.0 46.2 + - - +
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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