Contacts of the helix formed by residues 50 - 63 (chain A) in PDB entry 1UH6
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP 4.1 8.3 - - - +
49A ASP* 1.3 76.4 - - - +
51A ILE* 1.3 67.4 + - - +
52A GLY* 3.5 8.8 + - - -
53A ASP* 2.9 19.7 + - - +
54A LEU* 2.7 20.9 + - - +
80A ASP 3.8 16.7 + - - +
81A HIS 5.5 2.7 - - - -
82A VAL 4.3 3.1 - - - -
83A SER* 3.9 26.7 - - - +
84A LEU* 5.0 0.9 - - - -
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Residues in contact with ILE 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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50A THR* 1.3 73.0 - - - +
52A GLY* 1.3 54.7 + - - +
54A LEU* 2.9 15.9 + - + +
55A LYS* 2.5 83.5 + - + +
71A LEU* 4.6 9.9 - - + -
78A PHE* 3.7 34.3 - - + -
79A LYS 3.4 20.9 - - - +
80A ASP* 4.9 0.2 - - - -
82A VAL 3.4 18.2 + - - +
83A SER* 4.5 0.6 - - - +
84A LEU* 3.8 21.5 - - + +
87A TYR* 4.5 0.4 - - + -
89A ILE* 4.9 2.5 - - + -
95A LEU* 5.8 1.3 - - + -
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Residues in contact with GLY 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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50A THR* 3.1 6.7 + - - -
51A ILE* 1.3 81.6 - - - +
53A ASP* 1.3 62.6 + - - +
55A LYS* 3.1 10.2 + - - +
56A LYS* 2.8 31.0 + - - +
66A TRP* 4.3 13.3 - - - -
80A ASP* 4.4 17.1 - - - +
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Residues in contact with ASP 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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12A SER* 3.6 25.1 + - - -
49A ASP* 3.7 29.1 - - + +
50A THR* 2.9 24.0 + - - +
52A GLY* 1.3 74.2 - - - +
54A LEU* 1.3 62.7 + - - +
56A LYS* 3.2 20.5 + - - +
57A LEU* 3.2 24.5 + - - +
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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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31A VAL* 3.8 27.8 - - + -
33A CYS* 5.8 0.9 - - - -
43A VAL* 4.2 11.7 - - + -
45A CYS* 3.1 43.1 - - + -
49A ASP* 4.7 2.0 - - + +
50A THR 2.7 16.5 + - - +
51A ILE* 3.2 24.0 - - + +
53A ASP* 1.3 70.8 - - - +
55A LYS* 1.3 67.0 + - + +
57A LEU* 2.8 20.4 + - + +
58A ILE* 2.9 27.2 + - + +
71A LEU* 5.8 3.1 - - + -
84A LEU* 4.5 14.4 - - + -
89A ILE* 5.6 0.9 - - + -
95A LEU* 5.7 3.4 - - + -
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Residues in contact with LYS 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 ILE* 2.5 50.2 + - + +
52A GLY* 3.4 8.5 - - - +
54A LEU* 1.3 72.6 - - + +
56A LYS* 1.3 55.0 + - - +
58A ILE* 3.1 9.7 + - + -
59A ALA 2.7 31.0 + - - -
66A TRP* 4.0 19.5 - - + +
69A ILE* 3.0 40.9 + - + +
70A VAL* 4.4 3.4 - - - +
71A LEU* 3.4 37.1 - - + +
78A PHE 3.6 17.4 + - - -
79A LYS 4.7 1.8 + - - -
80A ASP* 5.4 3.0 - - + +
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Residues in contact with LYS 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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10A HIS* 4.5 20.2 - - - +
12A SER* 5.9 1.4 + - - -
52A GLY 2.8 18.0 + - - +
53A ASP* 3.2 23.0 + - - +
54A LEU 3.0 0.2 - - - -
55A LYS* 1.3 77.0 - - - +
57A LEU* 1.3 53.3 + - + +
59A ALA* 3.2 3.5 + - - +
60A ALA* 2.8 33.8 + - - +
66A TRP* 3.3 56.1 - - + +
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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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43A VAL* 4.1 14.1 - - + -
44A LYS 3.7 22.7 - - - +
45A CYS* 4.3 13.9 - - + -
49A ASP* 4.4 10.3 - - - +
53A ASP 3.2 11.6 + - - +
54A LEU* 2.8 14.8 + - + +
56A LYS* 1.3 74.9 - - + +
58A ILE* 1.3 50.9 + - - +
60A ALA* 2.5 15.5 + - + +
61A GLN* 2.5 39.9 + - + +
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Residues in contact with ILE 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 CYS* 3.3 34.8 - - + -
41A VAL* 5.3 0.9 - - + -
43A VAL* 4.0 18.1 - - + +
54A LEU* 2.9 41.2 + - + +
55A LYS* 3.4 13.5 - - - +
57A LEU* 1.3 75.1 - - - +
59A ALA* 1.3 52.6 + - - +
61A GLN* 2.8 10.3 + - - -
62A THR* 2.5 55.8 + - + +
64A THR* 4.8 0.2 - - - +
69A ILE* 3.8 18.8 - - + -
71A LEU* 4.4 11.9 - - + -
97A LEU* 4.7 9.4 - - + -
99A TYR* 5.8 0.4 - - + -
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Residues in contact with ALA 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 LYS 2.7 13.1 + - - +
56A LYS 3.5 4.5 - - - +
58A ILE* 1.3 73.8 - - - +
60A ALA* 1.3 54.4 + - - +
63A GLY* 2.6 36.4 + - - -
64A THR* 2.6 36.3 - - - +
66A TRP* 3.2 16.2 - - + +
69A ILE* 3.0 21.0 - - + +
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Residues in contact with ALA 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 LYS 2.8 13.1 + - - +
57A LEU* 2.5 29.3 + - + +
59A ALA* 1.3 72.0 - - - +
61A GLN* 1.3 62.3 + - + +
63A GLY* 4.0 4.6 + - - -
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Residues in contact with GLN 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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41A VAL* 5.1 4.3 - - + +
42A ARG 3.2 24.9 + - - -
43A VAL* 3.9 24.3 - - + +
57A LEU* 2.5 14.4 + - + +
58A ILE 2.8 7.1 + - - +
60A ALA* 1.3 77.5 - - + +
62A THR* 1.3 65.6 + - + +
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Residues in contact with THR 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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37A LEU* 6.5 1.3 - - + -
41A VAL* 3.6 37.9 - - + -
58A ILE* 2.5 40.7 + - + +
61A GLN* 1.3 75.1 - - + +
63A GLY* 1.3 57.0 + - - +
64A THR* 2.7 32.1 + - - -
97A LEU* 5.1 1.3 - - + -
99A TYR* 4.8 12.1 - - - +
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Residues in contact with GLY 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 ALA 2.6 23.0 + - - -
60A ALA 4.4 4.9 - - - -
61A GLN 3.4 0.8 - - - -
62A THR* 1.3 75.8 - - - +
64A THR* 1.3 60.2 + - - +
65A ARG* 3.7 17.8 + - - -
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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