Contacts of the helix formed by residues 69 - 84 (chain A) in PDB entry 1UA4
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU* 5.5 3.3 - - - +
59A TYR* 4.9 0.2 - - - -
67A ILE* 3.4 8.5 - - - +
68A ASN* 1.3 89.4 - - + +
70A VAL* 1.3 64.2 + - - +
71A SER* 2.9 23.6 + - - +
72A GLN* 3.0 28.2 + - - +
73A LEU* 3.1 16.8 + - - +
96A VAL* 3.5 10.5 - - - +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 3.7 22.7 - - + -
69A THR* 1.3 71.9 - - - +
71A SER* 1.3 66.5 + - - +
73A LEU* 3.1 7.8 + - + +
74A LEU* 2.9 28.5 + - + +
95A PRO 5.5 0.7 - - - +
96A VAL* 3.8 11.6 - - + +
99A TYR* 3.7 59.7 - - + -
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 4.0 19.5 + - - +
55A GLU* 3.1 44.1 + - - +
56A VAL* 3.8 22.4 - - - +
59A TYR* 3.9 6.1 - - - -
69A THR* 2.9 17.0 + - - -
70A VAL* 1.3 79.3 - - - +
72A GLN* 1.3 56.8 + - - +
75A GLY* 2.9 26.7 + - - -
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Residues in contact with GLN 72 (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 TYR* 3.4 48.3 + - + +
64A PRO* 4.3 9.4 - - + +
66A LYS 3.3 12.8 - - - +
67A ILE* 4.2 9.4 - - + -
68A ASN* 2.7 38.1 + - - +
69A THR* 3.0 36.1 + - - +
70A VAL 3.1 0.2 - - - -
71A SER* 1.3 76.9 + - - +
73A LEU* 1.3 56.5 - - - +
75A GLY 3.9 0.2 - - - -
76A SER* 2.8 37.0 + - - -
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Residues in contact with LEU 73 (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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67A ILE* 3.8 30.7 - - + +
69A THR 3.1 11.1 + - - +
70A VAL* 3.1 9.1 + - - +
72A GLN* 1.3 77.5 - - - +
74A LEU* 1.3 63.5 + - + +
76A SER* 3.3 3.5 + - - -
77A ILE* 3.0 34.1 + - + +
96A VAL* 4.1 7.4 - - + -
99A TYR* 4.2 20.4 - - + -
100A MET* 3.6 47.1 - - + -
103A TRP* 4.4 10.5 - - + -
179A TYR* 4.3 12.3 - - + +
198A PHE* 4.3 7.9 - - + -
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Residues in contact with LEU 74 (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 LEU* 4.0 9.7 - - + +
47A ARG* 3.3 41.3 - - + +
48A ILE* 3.7 17.6 - - + +
51A ALA* 3.8 13.2 - - + -
56A VAL* 4.0 13.3 - - + +
70A VAL* 2.9 23.7 + - + +
73A LEU* 1.3 81.7 - - + +
75A GLY* 1.3 58.3 + - - +
77A ILE* 3.3 9.5 + - + +
78A LEU* 2.9 28.1 + - - +
99A TYR* 4.0 5.6 - - + +
103A TRP* 3.8 35.9 - - + -
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Residues in contact with GLY 75 (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 VAL* 3.3 28.7 - - - +
59A TYR* 4.1 6.1 - - - -
60A SER* 3.2 16.8 - - - -
71A SER 2.9 17.1 + - - -
72A GLN 3.9 0.9 - - - -
74A LEU* 1.3 75.0 - - - +
76A SER* 1.3 60.4 + - - +
78A LEU* 3.3 1.8 + - - -
79A TRP 2.8 22.0 + - - -
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Residues in contact with SER 76 (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 TYR* 4.6 0.4 - - - +
63A LEU* 3.4 16.8 - - - +
64A PRO* 3.5 6.9 - - - +
67A ILE* 4.2 1.5 - - - +
72A GLN 2.8 22.3 + - - -
73A LEU 3.6 3.4 - - - -
74A LEU 3.3 0.2 - - - -
75A GLY* 1.3 73.6 - - - +
77A ILE* 1.3 66.8 + - - +
79A TRP* 3.1 15.8 + - - +
80A SER* 3.2 5.4 + - - -
89A LEU* 3.4 19.6 - - - +
198A PHE* 3.4 40.1 - - - -
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Residues in contact with ILE 77 (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 LEU* 3.7 27.1 - - + -
44A LEU* 4.4 8.5 - - + -
73A LEU* 3.0 22.1 + - + +
74A LEU* 3.5 13.9 - - + +
75A GLY 3.3 0.2 - - - -
76A SER* 1.3 77.0 - - - +
78A LEU* 1.3 57.2 + - - +
80A SER* 3.2 5.7 + - - -
81A ILE* 3.0 34.2 + - + +
103A TRP* 3.9 25.8 - - + -
179A TYR* 3.5 34.3 - - + -
181A PHE* 4.6 1.5 - - + -
198A PHE* 3.7 25.6 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 6.1 0.4 - - + -
48A ILE* 4.6 9.6 - - + -
56A VAL* 4.1 11.9 - - + -
57A ILE* 3.8 26.5 - - + -
60A SER* 3.6 20.6 - - - +
74A LEU 2.9 17.2 + - - +
75A GLY* 3.6 6.3 - - - +
77A ILE* 1.3 74.6 - - - +
79A TRP* 1.3 59.4 + - - +
81A ILE* 4.0 19.3 - - + -
82A ARG* 2.9 49.1 + - + +
187A VAL* 4.2 21.3 - - + -
188A PHE* 5.9 0.9 - - + -
190A PHE* 4.1 20.2 - - + -
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Residues in contact with TRP 79 (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 SER* 3.4 15.7 - - - +
61A GLU 4.4 1.2 + - - -
62A GLU* 4.8 0.2 - - - +
63A LEU* 3.4 55.2 - - + +
75A GLY 2.8 13.4 + - - +
76A SER 3.2 10.3 - - - +
78A LEU* 1.3 78.9 - - - +
80A SER* 1.3 71.5 + - - +
83A ARG* 3.1 78.2 + - - +
85A LYS* 4.0 24.0 - - + -
86A ALA 4.1 5.8 - - - -
87A ALA* 3.7 19.1 - - + -
269A PHE* 5.0 3.6 - + - -
294A VAL* 4.7 12.6 - - + -
313A LEU* 5.3 11.0 - - + -
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Residues in contact with SER 80 (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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76A SER 3.2 2.8 + - - -
77A ILE 3.2 9.0 + - - -
79A TRP* 1.3 83.4 - - - +
81A ILE* 1.3 53.5 + - - +
84A GLY* 2.7 33.6 + - - -
85A LYS 2.9 29.7 + - - +
87A ALA* 3.6 25.3 + - - +
181A PHE* 3.5 17.1 - - - -
197A ARG 3.8 2.4 + - - -
198A PHE* 3.8 14.9 - - - +
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Residues in contact with ILE 81 (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 LEU* 4.3 2.2 - - + -
44A LEU* 3.7 20.0 - - + -
77A ILE* 3.0 26.2 + - + +
78A LEU* 3.6 21.5 - - + +
80A SER* 1.3 77.9 - - - +
82A ARG* 1.3 64.4 + - - +
83A ARG 3.3 0.3 + - - -
84A GLY 3.3 0.9 + - - -
181A PHE* 3.6 26.2 - - + -
185A PHE* 3.7 35.9 - - + +
187A VAL* 3.8 8.1 - - + -
190A PHE* 5.1 4.7 - - + -
191A GLU 4.7 2.0 - - - -
192A ALA* 3.2 43.0 - - + +
193A PRO* 3.3 3.5 - - - +
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Residues in contact with ARG 82 (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 ILE* 4.3 4.2 + - - +
60A SER* 2.9 38.6 + - - -
61A GLU* 3.6 26.1 + - - +
78A LEU* 2.9 31.3 + - + +
79A TRP 3.9 3.6 - - - +
81A ILE* 1.3 73.6 - - - +
83A ARG* 1.3 67.1 + - + +
190A PHE* 3.4 53.9 - - + -
191A GLU 4.4 6.2 - - - +
193A PRO* 3.4 15.6 - - - +
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Residues in contact with ARG 83 (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 SER 2.9 24.0 + - - -
61A GLU* 3.2 28.1 + - - +
79A TRP* 3.1 63.0 + - - +
81A ILE 3.3 0.2 - - - -
82A ARG* 1.3 85.6 - - + +
84A GLY* 1.3 65.5 + - - +
85A LYS* 3.3 35.1 + - + +
193A PRO* 3.4 12.9 - - - +
313A LEU* 5.6 11.4 - - - +
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Residues in contact with GLY 84 (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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80A SER 2.7 17.2 + - - -
81A ILE 3.3 6.3 + - - -
83A ARG* 1.3 75.7 - - - +
85A LYS* 1.3 58.6 + - - +
181A PHE* 4.5 1.8 - - - -
193A PRO* 3.6 13.9 - - - +
194A ARG* 3.6 40.0 + - - +
196A ASN* 3.0 18.0 + - - -
316A ASP* 4.8 0.2 - - - +
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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