Contacts of the helix formed by residues 54 - 69 (chain A) in PDB entry 5AX3
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 THR 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A HIS* 4.7 5.8 - - - +
53A GLN* 1.3 80.1 - - - +
55A TYR* 1.3 78.9 + - + +
56A CYS 3.5 0.2 - - - -
57A GLN* 3.9 17.2 + - - +
58A ARG* 3.3 47.2 + - - +
177A GLU* 4.1 27.8 - - + +
178A TYR* 4.6 9.6 - - + -
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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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47A ILE* 5.3 1.2 - - - +
48A SER 4.9 3.1 - - - -
49A PRO* 3.6 33.5 - - + +
50A PHE 4.4 0.7 - - - +
51A GLU* 4.5 16.4 - - + -
52A HIS* 3.4 50.3 + + + +
53A GLN 3.3 0.8 - - - -
54A THR* 1.3 90.6 - - + +
56A CYS* 1.3 64.2 + - - +
57A GLN 3.1 1.2 + - - -
58A ARG* 3.3 28.3 - - - +
59A THR* 3.2 16.0 - - - +
178A TYR* 5.3 7.6 - + - -
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Residues in contact with CYS 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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49A PRO* 4.6 0.7 - - - -
50A PHE* 3.6 51.1 - - + -
52A HIS 4.0 11.3 + - - +
53A GLN 4.1 0.6 + - - +
55A TYR* 1.3 79.2 - - - +
57A GLN* 1.3 61.5 + - - +
59A THR* 3.3 10.0 - - - +
60A LEU* 3.2 26.2 + - - +
330A LYS* 4.4 17.3 - - - -
333A LEU* 3.6 30.2 - - + +
337A ILE* 3.8 3.3 - - + +
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Residues in contact with GLN 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 GLN* 3.2 44.0 + - - +
54A THR* 3.9 15.0 + - - +
55A TYR 3.1 0.6 - - - -
56A CYS* 1.3 75.9 - - - +
58A ARG* 1.3 55.1 + - - +
60A LEU* 3.0 5.0 + - - +
61A ARG* 2.6 38.7 + - - +
326A ASP* 3.8 47.2 + - + +
327A ASP 6.1 0.2 - - - -
328A LEU 5.0 3.2 + - - -
333A LEU* 3.7 17.9 - - + +
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Residues in contact with ARG 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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27A TYR* 4.1 26.3 + - + -
54A THR* 3.3 37.1 + - - +
55A TYR* 3.3 25.9 - - - +
57A GLN* 1.3 80.3 - - - +
59A THR* 1.3 60.8 + - - +
61A ARG* 4.1 1.1 - - - -
62A GLU* 2.9 24.1 + - - +
160A GLY* 3.2 41.0 + - - +
161A LEU* 4.8 16.8 - - - +
177A GLU* 4.3 15.8 - - - +
178A TYR* 4.4 30.1 + - - +
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Residues in contact with THR 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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27A TYR* 5.3 2.5 - - - -
47A ILE* 3.6 36.1 - - + +
49A PRO* 4.5 10.2 - - + +
55A TYR 3.2 17.3 - - - +
56A CYS* 3.3 15.5 - - - +
58A ARG* 1.3 78.7 - - - +
60A LEU* 1.3 63.6 + - - +
62A GLU* 3.9 7.0 - - - +
63A ILE* 2.8 46.8 + - - +
92A VAL* 5.4 3.1 - - + +
94A ILE* 4.8 3.6 - - - +
337A ILE* 3.8 11.3 - - + +
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Residues in contact with LEU 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 CYS 3.2 15.5 - - - +
57A GLN 3.0 4.6 + - - +
59A THR* 1.3 78.6 - - - +
61A ARG* 1.3 60.6 + - - +
63A ILE* 4.4 3.1 - - + -
64A LYS* 2.9 46.2 + - + +
326A ASP* 4.6 11.2 - - - +
333A LEU* 4.5 15.9 - - + +
336A LEU* 3.7 54.3 - - + +
337A ILE* 3.5 21.1 - - + -
340A GLU* 3.8 19.3 - - + -
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Residues in contact with ARG 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 GLN 2.6 19.7 + - - +
58A ARG* 3.7 5.4 - - - +
60A LEU* 1.3 75.3 - - - +
62A GLU* 1.3 59.9 + - - +
64A LYS* 4.1 12.6 - - - +
65A ILE* 3.2 43.2 + - + +
136A VAL* 5.7 1.6 - - - +
159A PHE 4.0 3.6 - - - +
160A GLY 4.0 10.5 - - - +
162A ALA 3.3 30.5 + - - +
163A ARG* 4.5 13.8 - - - +
164A VAL* 3.4 29.7 - - - +
319A PHE* 3.8 23.1 - - - -
324A GLU* 3.5 36.4 - - - +
326A ASP* 4.0 18.6 + - - -
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Residues in contact with GLU 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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27A TYR* 3.2 39.3 + - - +
45A LYS* 5.3 1.6 - - - +
58A ARG 2.9 18.6 + - - +
59A THR* 3.9 5.7 - - - +
61A ARG* 1.3 76.1 - - - +
63A ILE* 1.3 63.9 + - - +
66A LEU* 3.1 55.5 + - + +
75A ILE* 5.8 0.2 - - - +
94A ILE* 3.8 22.1 - - - +
96A GLN* 4.9 6.7 + - - +
157A CYS* 5.3 2.3 - - - +
158A ASP 4.2 7.3 + - - -
159A PHE* 3.7 31.9 + - + +
401A 5ID 6.3 0.3 - - - +
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Residues in contact with ILE 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 THR* 2.8 39.4 + - - +
60A LEU* 3.9 4.9 - - - +
62A GLU* 1.3 76.7 - - - +
64A LYS* 1.3 63.1 + - - +
66A LEU 4.1 0.3 - - - -
67A LEU* 3.1 47.4 + - + +
77A ILE* 4.2 16.6 - - + +
80A ILE* 4.2 17.5 - - + -
92A VAL* 4.4 21.3 - - + -
94A ILE* 4.5 12.3 - - + -
337A ILE* 4.5 19.3 - - + -
340A GLU* 4.2 19.5 - - + +
341A THR* 4.7 2.2 - - - +
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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 LEU* 2.9 34.7 + - + +
61A ARG* 4.1 22.4 - - - +
63A ILE* 1.3 76.9 - - - +
65A ILE* 1.3 63.4 + - - +
67A LEU* 3.1 12.2 + - - +
68A ARG* 3.2 30.7 - - - +
319A PHE* 4.6 8.3 - - + -
323A MET* 3.5 45.4 + - + +
324A GLU* 4.4 6.1 + - + +
336A LEU* 6.0 5.1 - - - +
340A GLU* 3.3 48.2 + - + +
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Residues in contact with ILE 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 ARG* 3.2 34.5 + - + +
62A GLU* 4.3 2.5 - - - +
64A LYS* 1.3 74.8 - - - +
66A LEU* 1.3 60.4 + - + +
67A LEU 3.2 0.3 + - - -
68A ARG* 3.2 2.1 + - - -
69A PHE* 3.0 61.7 + - + +
136A VAL* 3.8 17.7 - - + -
159A PHE* 4.5 18.6 - - + +
162A ALA* 3.7 29.6 - - + -
319A PHE* 4.2 25.8 - - + -
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Residues in contact with LEU 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 GLU* 3.1 52.7 + - + +
65A ILE* 1.3 80.4 - - + +
67A LEU* 1.3 61.5 + - - +
69A PHE* 3.5 17.0 - - + +
74A ILE* 4.2 6.3 - - + -
75A ILE* 3.4 38.0 - - + +
76A GLY* 4.7 3.6 - - - -
77A ILE* 3.9 38.3 + - + +
96A GLN* 4.4 4.7 - - - +
159A PHE* 3.5 32.3 - - + -
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Residues in contact with LEU 67 (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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63A ILE* 3.1 36.6 + - + +
64A LYS 3.1 5.1 + - - +
65A ILE 3.1 0.6 - - - -
66A LEU* 1.3 80.0 - - - +
68A ARG* 1.3 64.9 + - + +
69A PHE 3.4 2.9 + - - +
70A ARG* 5.5 2.6 - - - +
77A ILE* 4.6 17.3 - - + +
80A ILE* 4.8 3.6 - - + -
340A GLU* 3.7 32.8 - - - +
343A ARG* 4.6 31.3 + - - +
344A PHE* 3.4 33.2 - - + -
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Residues in contact with ARG 68 (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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64A LYS* 3.2 27.6 + - - +
65A ILE 3.2 4.3 + - - +
67A LEU* 1.3 79.8 - - + +
69A PHE* 1.3 67.1 + - + +
70A ARG* 4.2 2.1 + - - +
130A TYR* 4.5 4.2 + - - -
319A PHE* 4.1 30.1 - - + -
323A MET* 5.1 15.1 - - - +
340A GLU* 3.0 38.9 + - - -
343A ARG* 4.0 21.6 - - - +
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Residues in contact with PHE 69 (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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65A ILE* 3.0 41.1 + - + +
66A LEU* 3.5 17.0 - - + +
67A LEU 3.4 2.0 - - - +
68A ARG* 1.3 89.3 - - + +
70A ARG* 1.3 69.3 + - - +
74A ILE* 4.1 29.6 - - + -
75A ILE 5.8 0.4 - - - +
130A TYR* 3.8 18.4 - + + -
131A ILE* 3.8 33.4 - - + -
134A ALA* 3.9 28.9 - - + -
136A VAL* 4.5 9.2 - - + -
159A PHE* 5.2 1.3 - + - -
315A ALA* 5.9 0.4 - - + -
319A PHE* 4.5 13.7 - + - -
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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