Contacts of the helix formed by residues 59 - 73 (chain B) in PDB entry 1UPX
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 ASP 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ALA* 4.1 1.6 + - - +
58B VAL* 1.3 77.8 - - - +
60B HIS* 1.3 74.8 + - - +
61B ARG* 3.2 39.7 + - + +
62B ILE* 3.0 31.2 + - + +
63B ASP* 3.8 2.3 + - - +
98B LEU* 5.7 1.8 - - + +
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL 3.6 2.0 + - - -
59B ASP* 1.3 76.4 + - - +
61B ARG* 1.3 62.5 + - - +
63B ASP* 2.9 46.5 + - + +
64B ARG* 3.0 41.1 + - + +
161B ASP* 2.9 33.4 + - - -
166B HIS* 3.4 47.2 + + + +
168B ASN* 5.6 1.1 - - - +
171B ASP* 3.9 7.2 + - - -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASP* 3.2 33.2 + - + +
60B HIS* 1.3 77.8 - - - +
62B ILE* 1.3 73.7 + - + +
64B ARG* 3.3 14.2 + - - +
65B LEU* 3.0 27.0 + - - +
94B ALA* 5.7 4.0 - - - +
97B GLU* 4.3 17.2 + - - -
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.1 17.5 - - + -
48B ALA* 4.6 1.1 - - + -
58B VAL* 3.7 23.6 - - + -
59B ASP* 3.0 20.5 + - + +
61B ARG* 1.3 92.7 - - + +
63B ASP* 1.3 65.9 + - - +
65B LEU* 3.2 7.4 + - + +
66B VAL* 3.0 23.7 + - + +
94B ALA* 4.0 27.8 - - + +
98B LEU* 4.1 33.0 - - + -
175B GLN* 4.4 11.4 - - - +
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 3.2 15.9 + - - -
58B VAL* 4.5 3.7 - - - +
59B ASP 4.1 4.0 - - - +
60B HIS* 2.9 42.5 + - + +
62B ILE* 1.3 76.5 - - - +
64B ARG* 1.3 57.0 + - - +
66B VAL* 3.3 2.6 + - - +
67B THR* 3.0 33.9 + - - +
168B ASN* 5.2 5.0 - - - +
171B ASP* 3.5 33.1 - - + +
175B GLN* 2.8 24.7 + - - +
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS* 3.0 34.0 + - + +
61B ARG* 3.6 14.4 - - - +
62B ILE 3.2 0.2 - - - -
63B ASP* 1.3 73.6 - - - +
65B LEU* 1.3 62.0 + - - +
67B THR* 3.7 7.0 - - - -
68B GLY 3.0 23.4 + - - -
158B LYS* 3.0 14.4 + - - +
161B ASP* 2.7 49.4 + - - +
164B GLY* 6.0 1.4 - - - -
166B HIS* 5.1 4.0 + - - -
337B GLU* 3.6 6.7 - - - +
338B ILE* 3.7 48.1 + - + +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.9 14.8 - - + -
61B ARG 3.0 13.6 + - - +
62B ILE* 3.2 11.4 + - + +
64B ARG* 1.3 78.1 - - - +
66B VAL* 1.3 56.3 + - - +
69B ASN* 2.9 50.5 + - - +
87B ARG* 3.3 13.6 + - - +
90B MET* 4.1 24.2 - - + +
91B THR* 3.9 20.9 - - - +
94B ALA* 3.6 31.0 - - + -
337B GLU* 5.0 0.7 - - - -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR* 4.0 16.3 - - + +
44B LEU* 3.8 26.0 - - + -
45B GLY 5.4 0.7 - - - +
62B ILE* 3.0 14.3 + - + +
63B ASP 3.3 7.2 + - - +
65B LEU* 1.3 76.4 - - - +
67B THR* 1.3 62.5 + - - +
69B ASN* 3.2 3.3 + - - +
70B LEU* 3.0 31.8 + - + +
174B MET* 4.2 11.7 - - - -
175B GLN* 4.1 26.0 - - + +
178B LEU* 3.8 27.4 - - + -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASP 3.0 19.3 + - - +
64B ARG* 3.2 6.8 + - - +
66B VAL* 1.3 75.5 - - - +
68B GLY* 1.3 64.0 + - - +
70B LEU* 3.5 1.6 + - - +
71B PHE* 3.0 26.2 + - - +
154B ALA* 3.9 26.6 - - - +
157B ALA* 4.6 6.7 - - + -
158B LYS* 3.1 27.4 + - - +
161B ASP* 5.4 1.0 + - - -
171B ASP* 4.1 12.1 - - - +
174B MET* 3.9 28.7 - - + -
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG 3.0 11.8 + - - -
67B THR* 1.3 79.3 + - - +
69B ASN* 1.3 54.8 + - - +
71B PHE* 3.8 0.6 - - - -
72B ALA* 2.9 31.5 + - - +
87B ARG* 3.4 18.8 - - - -
158B LYS* 3.6 21.5 - - - -
325B ILE* 3.7 10.0 - - - +
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.6 18.9 - - + +
38B ILE* 5.1 1.3 - - + -
41B THR* 2.9 32.2 + - + +
44B LEU* 5.3 0.6 - - - +
65B LEU* 2.9 29.7 + - - +
66B VAL* 3.2 4.9 + - - +
68B GLY* 1.3 76.8 - - - +
70B LEU* 1.3 63.9 + - - +
72B ALA* 3.3 9.5 + - - +
73B THR* 3.3 19.2 - - - +
87B ARG* 2.7 37.2 + - - +
91B THR* 2.8 30.2 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.7 23.3 - - + -
41B THR* 4.5 9.0 - - + -
66B VAL* 3.0 25.9 + - + +
69B ASN* 1.3 77.8 - - - +
71B PHE* 1.3 60.8 + - - +
73B THR* 2.8 22.5 + - - -
74B ILE* 3.4 9.3 + - - +
147B THR* 5.1 4.0 - - + +
150B LEU* 3.9 12.6 - - + +
151B LYS* 3.9 21.7 - - + +
154B ALA* 3.7 28.9 - - + -
174B MET* 4.0 16.4 - - + -
178B LEU* 4.2 27.4 - - + -
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B THR 3.0 18.4 + - - +
68B GLY* 3.9 1.6 - - - +
70B LEU* 1.3 77.1 - - - +
72B ALA* 1.3 61.7 + - - +
74B ILE* 3.0 30.7 + - + -
77B ALA* 3.4 8.6 - - + +
151B LYS 5.1 0.4 - - - -
154B ALA* 4.9 0.4 - - - +
155B ALA* 3.6 40.6 - - + +
158B LYS* 4.1 20.4 - - + -
159B HIS* 3.6 28.9 - + - -
306B THR* 3.8 17.0 - - + -
307B ASN* 3.4 24.0 - - - -
325B ILE* 3.6 27.1 - - + -
489B LYS* 4.2 3.4 - - - -
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLN* 4.0 6.9 + - - -
37B LEU* 4.6 1.1 - - + -
68B GLY 2.9 19.9 + - - +
69B ASN 3.6 6.1 - - - +
70B LEU 3.2 0.2 - - - -
71B PHE* 1.3 75.5 - - - +
73B THR* 1.3 60.1 + - - +
74B ILE 3.4 0.6 + - - -
77B ALA* 4.2 0.7 - - - -
78B ASN* 3.4 28.4 + - + +
84B LEU* 4.3 14.6 - - + +
87B ARG* 4.2 20.0 - - - -
325B ILE* 4.1 22.6 - - + +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 2.9 22.5 + - - -
34B GLN* 3.5 40.4 - - + +
37B LEU* 4.0 14.8 - - + -
38B ILE* 3.4 20.8 - - + +
69B ASN 3.3 13.9 - - - +
70B LEU 2.8 16.2 + - - -
72B ALA* 1.3 76.7 - - - +
74B ILE* 1.3 61.9 + - - +
151B LYS* 3.0 28.0 + - - -
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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