Contacts of the helix formed by residues 80 - 100 (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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASN* 2.8 16.2 + - - +
79B PHE* 1.3 74.3 - - - +
81B ASP* 1.3 63.8 + - - +
82B ASP* 3.1 19.8 + - - +
83B ILE* 3.2 24.7 + - + +
84B LEU* 3.0 25.1 + - - +
327B GLY* 4.0 2.0 - - - -
328B PHE 4.0 17.9 + - - +
329B THR* 3.6 28.2 + - - +
330B GLY 5.2 0.2 + - - -
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 4.2 14.2 - - - +
30B THR* 2.6 44.3 + - - +
33B LEU* 3.5 23.2 - - + +
79B PHE 3.5 4.3 + - - +
80B ASP* 1.3 72.4 + - - +
82B ASP* 1.3 60.0 + - - +
84B LEU* 4.4 2.2 - - - -
85B ALA* 2.9 31.6 + - - +
119B LYS* 4.6 17.0 + - + +
329B THR* 4.1 5.3 + - - +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 3.1 9.2 + - - +
81B ASP* 1.3 81.0 - - - +
83B ILE* 1.3 59.7 + - + +
85B ALA* 3.5 5.4 + - - +
86B GLU* 3.0 28.2 + - - +
89B ARG* 4.6 2.4 + - - -
119B LYS* 4.7 15.8 + - - +
329B THR* 5.3 1.1 + - - -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN* 3.7 20.4 - - - +
80B ASP* 3.2 34.1 + - + +
82B ASP* 1.3 75.2 - - + +
84B LEU* 1.3 62.1 + - + +
86B GLU* 3.2 9.4 + - + +
87B ARG* 3.0 40.8 + - + +
325B ILE* 6.4 0.4 - - - -
327B GLY* 5.8 1.8 - - - -
333B HIS* 5.9 9.9 - - + +
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Residues in contact with LEU 84 (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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30B THR* 3.8 32.5 - - + +
33B LEU* 4.1 15.5 - - + -
34B GLN* 3.9 25.1 - - + -
37B LEU* 4.2 20.9 - - + +
72B ALA* 4.3 24.0 - - + +
78B ASN* 3.9 19.3 - - + +
80B ASP 3.0 23.5 + - - +
81B ASP* 3.8 5.8 - - - +
83B ILE* 1.3 75.8 - - + +
85B ALA* 1.3 63.0 + - - +
87B ARG* 3.2 8.8 + - - +
88B VAL* 3.0 26.5 + - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.5 4.6 - - + +
81B ASP 2.9 18.2 + - - +
82B ASP* 3.8 5.8 - - - +
84B LEU* 1.3 75.6 - - - +
86B GLU* 1.3 62.2 + - - +
88B VAL* 3.2 6.1 + - - +
89B ARG* 3.1 35.9 + - - +
119B LYS* 4.4 16.2 - - + -
122B MET* 3.5 30.8 - - - +
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Residues in contact with GLU 86 (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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82B ASP 3.0 18.7 + - - +
83B ILE* 3.2 10.1 + - + +
85B ALA* 1.3 75.2 - - - +
87B ARG* 1.3 59.8 + - - +
89B ARG* 3.0 37.6 + - - +
90B MET* 2.9 50.5 + - + +
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Residues in contact with ARG 87 (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* 3.7 16.8 - - + -
65B LEU* 3.3 28.2 + - - +
68B GLY* 3.4 14.3 - - - -
69B ASN* 2.7 35.4 + - - +
72B ALA* 4.2 20.0 - - - -
78B ASN* 6.0 0.2 - - - -
83B ILE* 3.0 31.4 + - + +
84B LEU* 3.6 9.2 - - - +
86B GLU* 1.3 71.7 - - - +
88B VAL* 1.3 65.9 + - - +
90B MET* 3.4 23.2 + - + +
91B THR* 2.7 30.5 + - - -
325B ILE* 4.0 7.0 - - - +
337B GLU* 3.1 31.3 + - - -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.1 7.4 - - + +
36B ALA* 4.3 4.7 - - + -
37B LEU* 3.7 37.0 - - + +
40B VAL* 4.3 9.6 - - + -
84B LEU 3.0 19.1 + - - +
85B ALA* 3.2 7.6 + - - +
87B ARG* 1.3 76.1 - - - +
89B ARG* 1.3 57.1 + - - +
91B THR* 3.2 2.4 + - - -
92B CYS* 2.9 42.1 + - - -
114B TRP* 4.3 11.4 - - + -
116B ALA 4.6 1.6 - - - +
122B MET* 3.8 31.6 - - + -
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Residues in contact with ARG 89 (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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82B ASP 4.6 2.0 + - - -
85B ALA* 3.1 23.8 + - - +
86B GLU* 3.0 53.7 + - - +
88B VAL* 1.3 75.8 - - - +
90B MET* 1.3 63.1 + - - +
92B CYS* 3.3 6.1 + - - +
93B ALA* 3.0 24.6 + - - +
116B ALA 4.3 4.3 - - - +
117B SER* 2.8 47.7 + - - +
118B GLU* 4.8 0.2 - - - +
119B LYS* 4.2 12.1 - - - +
122B MET* 3.8 9.5 - - + +
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Residues in contact with MET 90 (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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65B LEU* 4.1 17.7 - - + +
86B GLU* 2.9 36.5 + - + +
87B ARG* 3.6 46.7 - - + +
88B VAL 3.3 0.2 - - - -
89B ARG* 1.3 76.4 - - - +
91B THR* 1.3 57.5 + - - +
93B ALA* 3.4 6.7 + - - +
94B ALA* 3.0 28.9 + - - +
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.9 0.5 - - - +
40B VAL* 3.6 41.7 - - + +
41B THR 4.1 0.4 - - - +
44B LEU* 4.0 16.4 - - + -
65B LEU* 3.9 11.1 - - - +
69B ASN* 2.8 31.3 + - - +
87B ARG 2.7 21.2 + - - -
88B VAL 3.6 3.6 - - - -
90B MET* 1.3 75.2 - - - +
92B CYS* 1.3 60.0 + - - +
94B ALA* 3.3 1.6 + - - +
95B LYS* 2.9 30.1 + - + +
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Residues in contact with CYS 92 (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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40B VAL* 4.0 18.2 - - - -
88B VAL* 2.9 27.3 + - - +
89B ARG* 3.7 6.3 - - - +
91B THR* 1.3 77.8 - - - +
93B ALA* 1.3 61.7 + - - +
95B LYS* 3.5 11.0 + - - +
96B LYS* 3.1 25.3 + - - +
114B TRP* 3.8 7.9 - - - -
115B GLU* 3.6 44.2 - - + +
116B ALA 4.1 9.0 - - - +
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Residues in contact with ALA 93 (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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89B ARG 3.0 17.1 + - - +
90B MET* 3.7 7.2 - - - +
92B CYS* 1.3 76.5 - - - +
94B ALA* 1.3 62.9 + - - +
96B LYS* 3.5 6.5 + - - +
97B GLU* 3.2 23.5 + - - +
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Residues in contact with ALA 94 (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* 4.4 4.7 - - + -
61B ARG* 5.7 3.8 - - - +
62B ILE* 4.0 18.9 - - + +
65B LEU* 3.6 23.6 - - + -
90B MET 3.0 17.9 + - - +
91B THR 3.3 2.2 + - - +
93B ALA* 1.3 76.8 - - - +
95B LYS* 1.3 56.4 + - - +
97B GLU* 3.4 11.1 + - - +
98B LEU* 3.0 30.1 + - - +
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Residues in contact with LYS 95 (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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40B VAL* 3.7 37.2 - - - +
43B GLY 4.2 0.9 - - - -
44B LEU* 3.7 26.0 - - + +
47B ILE* 3.6 15.2 - - + +
91B THR 2.9 16.7 + - - +
92B CYS* 3.6 14.5 + - - +
94B ALA* 1.3 75.1 - - - +
96B LYS* 1.3 67.6 + - - +
98B LEU* 4.4 1.3 - - - -
99B ALA* 3.0 26.3 + - - +
111B ALA 3.3 17.8 + - - +
112B ALA 2.9 30.1 + - - +
113B LEU 3.8 1.6 + - - -
114B TRP 2.6 30.0 + - - +
115B GLU* 4.9 1.2 - - - +
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Residues in contact with LYS 96 (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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92B CYS 3.1 17.5 + - - +
93B ALA* 3.7 6.5 - - - +
95B LYS* 1.3 80.3 - - - +
97B GLU* 1.3 63.1 + - - +
99B ALA* 3.5 5.7 + - - +
100B ALA* 3.4 18.9 + - - +
112B ALA 5.9 0.4 - - - -
115B GLU* 3.6 32.4 + - - +
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Residues in contact with GLU 97 (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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61B ARG* 4.3 16.7 + - - -
93B ALA 3.2 10.8 + - - +
94B ALA* 3.6 12.2 - - - +
96B LYS* 1.3 80.8 - - - +
98B LEU* 1.3 64.3 + - + +
100B ALA* 3.4 18.9 + - + +
101B SER* 3.9 5.9 + - - -
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Residues in contact with LEU 98 (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* 3.6 25.4 - - + -
47B ILE* 3.6 12.7 - - + +
48B ALA* 4.1 23.6 - - + -
51B LEU* 3.6 27.2 - - + +
58B VAL* 4.5 9.9 - - + -
59B ASP* 5.7 1.6 - - + +
62B ILE* 4.1 26.0 - - + -
94B ALA 3.0 17.0 + - - +
95B LYS* 3.9 2.7 - - - +
97B GLU* 1.3 78.3 - - + +
99B ALA* 1.3 63.2 + - - +
101B SER* 3.0 24.3 + - - +
102B LEU 3.8 1.6 + - - -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.8 22.4 - - + -
95B LYS 3.0 18.2 + - - +
96B LYS* 3.9 6.1 - - - +
97B GLU 3.3 0.2 - - - -
98B LEU* 1.3 77.0 - - - +
100B ALA* 1.3 62.3 + - - +
102B LEU* 3.1 23.5 + - - +
105B LYS* 3.4 11.4 - - + +
108B LEU* 4.3 18.6 - - + -
112B ALA 5.8 0.4 - - - +
113B LEU* 6.0 2.5 - - + -
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Residues in contact with ALA 100 (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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96B LYS 3.4 9.3 + - - +
97B GLU* 3.4 14.5 + - + +
98B LEU 3.1 0.6 - - - -
99B ALA* 1.3 78.8 - - - +
101B SER* 1.3 56.7 + - - +
102B LEU 3.3 0.4 - - - +
105B LYS* 3.3 24.3 + - - +
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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
------------------------------------------------------------
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