Contacts of the helix formed by residues 70 - 82 (chain A) in PDB entry 1U5H
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASN* 3.7 9.3 - - + +
67A ALA* 2.7 34.5 + - + +
68A GLY 3.2 6.7 - - - +
69A GLY* 1.3 81.7 - - - +
71A ALA* 1.3 62.7 + - - +
72A ASP* 3.7 7.6 + - - -
73A GLN* 3.1 28.6 + - - +
74A ALA* 3.4 10.4 + - - +
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLY 3.9 1.8 + - - -
70A THR* 1.3 69.9 - - - +
72A ASP* 1.3 65.9 + - - +
74A ALA* 3.2 5.8 + - - +
75A ARG* 3.1 43.6 + - + +
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Residues in contact with ASP 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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41A GLU* 6.2 0.3 - - - +
44A LYS* 3.8 22.2 - - - +
48A ARG* 2.8 27.6 + - - +
66A ASN* 3.6 23.1 - - + +
70A THR* 3.2 6.4 + - - +
71A ALA* 1.3 78.6 - - - +
73A GLN* 1.3 56.6 + - - +
75A ARG* 3.1 5.0 + - - +
76A ASP* 2.8 35.0 + - - +
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Residues in contact with GLN 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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65A ILE* 3.5 21.0 - - + +
66A ASN* 3.1 23.9 - - - +
67A ALA 3.4 19.3 - - - +
68A GLY* 3.5 10.1 + - - -
69A GLY 4.7 3.2 - - - +
70A THR* 3.1 14.5 + - - +
72A ASP* 1.3 76.5 - - - +
74A ALA* 1.3 57.8 + - - +
76A ASP* 3.1 10.5 + - - +
77A LEU* 2.9 38.0 + - + +
90A LEU* 3.5 19.9 - - - +
98A GLN 5.5 0.3 - - - +
101A GLU* 4.5 14.5 + - - +
102A LEU* 3.9 16.3 - - - +
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Residues in contact with ALA 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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70A THR 3.4 6.9 + - - +
71A ALA* 3.2 11.4 + - - +
72A ASP 3.2 0.4 - - - -
73A GLN* 1.3 80.1 - - - +
75A ARG* 1.3 82.5 + - - +
77A LEU* 3.3 8.7 + - - +
78A GLU* 3.1 28.3 + - - +
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Residues in contact with ARG 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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48A ARG* 3.4 40.1 - - - +
71A ALA* 3.1 38.9 + - + +
72A ASP* 3.6 4.0 - - - +
74A ALA* 1.3 92.3 - - - +
76A ASP* 1.3 61.0 + - - +
78A GLU* 3.0 43.9 + - - +
79A ALA* 3.1 18.0 + - - +
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Residues in contact with ASP 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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35A LEU* 3.4 28.5 - - + +
48A ARG* 2.7 38.7 + - - +
51A LEU* 5.1 0.2 - - - +
65A ILE* 3.6 13.5 - - + -
66A ASN* 2.7 44.2 + - - +
72A ASP 2.8 14.4 + - - +
73A GLN* 3.1 7.7 + - - +
75A ARG* 1.3 76.2 - - - +
77A LEU* 1.3 58.9 + - - +
79A ALA* 3.2 3.5 + - - +
80A LEU* 2.9 30.4 + - - +
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Residues in contact with LEU 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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65A ILE* 4.2 27.8 - - + -
73A GLN* 2.9 30.9 + - + +
74A ALA* 3.3 6.9 + - - +
76A ASP* 1.3 77.2 - - - +
78A GLU* 1.3 62.1 + - - +
80A LEU* 3.2 9.2 + - + +
81A ALA* 3.2 19.2 + - - +
88A VAL* 5.0 0.2 - - + -
101A GLU 5.4 3.4 - - - +
102A LEU* 3.9 20.6 - - + -
105A ARG* 3.8 40.6 + - - +
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Residues in contact with GLU 78 (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 ARG* 3.1 15.8 + - - -
74A ALA* 3.1 14.5 + - - +
75A ARG* 3.0 47.7 + - - +
77A LEU* 1.3 77.6 - - + +
79A ALA* 1.3 61.7 + - - +
81A ALA* 3.2 17.0 - - - +
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Residues in contact with ALA 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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48A ARG* 3.7 42.8 - - + +
51A LEU* 4.5 7.4 - - + -
52A ARG* 3.6 22.8 + - - +
75A ARG 3.1 11.3 + - - +
76A ASP* 3.2 7.6 + - - +
78A GLU* 1.3 76.3 - - - +
80A LEU* 1.3 62.4 + - - +
81A ALA 3.2 1.0 + - - -
82A GLY 3.2 9.9 + - - -
83A THR* 3.7 11.5 - - - +
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Residues in contact with LEU 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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51A LEU* 3.8 21.8 - - + -
63A VAL* 3.8 28.3 - - + -
65A ILE* 5.2 2.5 - - + -
76A ASP 2.9 14.6 + - - +
77A LEU* 3.5 12.1 - - + +
78A GLU 3.2 0.2 - - - -
79A ALA* 1.3 77.3 - - - +
81A ALA* 1.3 63.8 + - - +
83A THR* 2.7 36.8 + - - +
85A TYR* 4.2 17.5 - - + +
86A THR 6.0 0.7 - - - -
88A VAL* 3.5 27.1 - - + -
105A ARG* 3.4 27.8 - - + +
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Residues in contact with ALA 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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52A ARG* 4.7 2.2 - - - +
77A LEU 3.2 9.9 + - - +
78A GLU* 3.2 16.6 - - - +
80A LEU* 1.3 77.9 - - - +
82A GLY* 1.3 57.1 + - - +
83A THR 3.4 8.3 + - - +
105A ARG* 5.4 2.6 - - - +
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Residues in contact with GLY 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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52A ARG* 3.6 36.8 + - - +
79A ALA 3.2 4.8 + - - -
80A LEU 3.1 1.4 - - - -
81A ALA* 1.3 77.8 - - - +
83A THR* 1.3 62.1 + - - +
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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