Contacts of the helix formed by residues 80 - 101 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ASN* 2.8 15.8 + - - +
79A PHE* 1.3 74.1 - - - +
81A ASP* 1.3 64.0 + - - +
82A ASP* 3.1 21.5 + - - +
83A ILE* 3.1 25.3 + - + +
84A LEU* 3.0 24.8 + - - +
327A GLY* 4.0 2.8 + - - -
328A PHE 4.1 16.8 + - - +
329A THR* 3.7 27.5 + - - +
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Residues in contact with ASP 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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29A GLU* 4.1 14.4 - - - +
30A THR* 2.6 45.0 + - - +
33A LEU* 3.5 21.8 - - + +
79A PHE 3.5 3.0 + - - +
80A ASP* 1.3 73.1 + - - +
82A ASP* 1.3 58.8 + - - +
84A LEU* 4.4 2.0 - - - -
85A ALA* 2.9 32.6 + - - +
119A LYS* 4.5 16.0 + - - +
329A THR* 4.2 4.6 + - - +
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Residues in contact with ASP 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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80A ASP* 3.1 10.3 + - - +
81A ASP* 1.3 79.3 - - - +
83A ILE* 1.3 64.9 + - + +
85A ALA* 3.6 4.4 + - - +
86A GLU* 3.1 23.6 + - - +
89A ARG* 4.9 1.6 + - - -
119A LYS* 4.7 11.7 + - - +
329A THR* 5.4 0.4 + - - -
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Residues in contact with ILE 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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78A ASN* 3.8 19.7 - - - +
80A ASP* 3.1 33.6 + - + +
82A ASP* 1.3 77.2 - - + +
84A LEU* 1.3 60.4 + - + +
86A GLU* 3.2 7.6 + - + +
87A ARG* 2.9 42.7 + - + +
327A GLY* 5.8 2.0 - - - -
333A HIS* 5.9 10.3 - - + +
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Residues in contact with LEU 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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30A THR* 3.7 33.2 - - + +
33A LEU* 4.0 15.7 - - + +
34A GLN* 3.9 23.1 - - + -
37A LEU* 4.3 13.7 - - + +
72A ALA* 4.3 29.2 - - + +
78A ASN* 3.9 20.4 - - - +
80A ASP 3.0 22.8 + - - +
81A ASP* 3.8 6.1 - - - +
83A ILE* 1.3 76.7 - - + +
85A ALA* 1.3 62.2 + - - +
87A ARG* 3.1 9.2 + - - +
88A VAL* 3.0 26.0 + - - +
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Residues in contact with ALA 85 (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 LEU* 4.3 12.4 - - + +
81A ASP 2.9 17.7 + - - +
82A ASP* 3.9 5.6 - - - +
84A LEU* 1.3 76.4 - - - +
86A GLU* 1.3 61.9 + - - +
88A VAL* 3.2 5.2 + - - +
89A ARG* 3.1 41.2 + - - +
119A LYS* 4.5 11.0 - - + -
122A MET* 3.6 23.2 - - - +
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Residues in contact with GLU 86 (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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82A ASP 3.1 18.3 + - - +
83A ILE* 3.7 7.2 - - + +
85A ALA* 1.3 78.3 - - - +
87A ARG* 1.3 57.1 + - + +
89A ARG* 3.1 36.8 + - - +
90A MET* 2.9 61.5 + - + +
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Residues in contact with ARG 87 (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* 3.7 17.0 - - + -
65A LEU* 3.4 19.6 + - - +
68A GLY* 3.4 13.6 - - - -
69A ASN* 2.7 42.5 + - - +
72A ALA* 4.3 19.7 - - - -
83A ILE* 2.9 31.6 + - + +
84A LEU* 3.1 8.9 + - - +
86A GLU* 1.3 76.5 - - + +
88A VAL* 1.3 57.8 - - - +
90A MET* 3.4 25.1 + - + +
91A THR* 2.7 33.1 + - - -
325A ILE* 4.5 4.6 - - - +
337A GLU* 3.1 29.5 + - - -
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Residues in contact with VAL 88 (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 LEU* 4.0 8.1 - - + +
36A ALA* 4.3 6.3 - - + -
37A LEU* 3.8 36.1 - - + +
40A VAL* 4.4 8.2 - - + +
84A LEU 3.0 19.3 + - - +
85A ALA* 3.2 7.8 + - - +
87A ARG* 1.3 76.0 - - - +
89A ARG* 1.3 56.9 + - - +
91A THR* 3.3 4.0 + - - -
92A CYS* 2.9 41.6 + - - -
114A TRP* 4.7 9.2 - - + -
116A ALA 4.8 0.7 - - - +
122A MET* 3.8 33.4 - - + -
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Residues in contact with ARG 89 (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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82A ASP 4.9 1.4 + - - -
85A ALA* 3.1 23.9 + - - +
86A GLU* 3.1 52.3 + - - +
88A VAL* 1.3 75.7 - - - +
90A MET* 1.3 58.5 + - - +
92A CYS* 3.3 6.6 + - - +
93A ALA* 2.9 30.5 + - - +
116A ALA 4.3 7.6 - - - +
117A SER* 2.7 35.5 + - - +
118A GLU* 4.9 0.2 - - - +
119A LYS* 4.2 11.7 - - - +
122A MET* 3.7 12.6 - - + +
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Residues in contact with MET 90 (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 LEU* 4.0 24.0 - - + +
86A GLU* 2.9 42.2 + - + +
87A ARG* 3.8 36.8 - - + +
89A ARG* 1.3 74.6 - - - +
91A THR* 1.3 58.3 + - - +
93A ALA* 3.4 6.3 + - - +
94A ALA* 3.0 29.6 + - - +
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Residues in contact with THR 91 (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* 3.9 0.5 - - - +
40A VAL* 3.7 40.6 - - + +
41A THR 4.1 0.7 - - - +
44A LEU* 4.0 17.0 - - + -
65A LEU* 3.9 11.2 - - - +
69A ASN* 2.8 31.3 + - - +
87A ARG 2.7 22.0 + - - -
88A VAL 3.6 3.4 - - - -
89A ARG 3.2 0.2 - - - -
90A MET* 1.3 74.5 - - - +
92A CYS* 1.3 65.7 + - - +
94A ALA* 3.3 1.4 + - - +
95A LYS* 2.9 24.7 + - - +
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Residues in contact with CYS 92 (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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40A VAL* 4.0 17.7 - - - -
88A VAL* 2.9 28.8 + - - +
89A ARG* 3.3 6.0 + - - +
91A THR* 1.3 75.5 - - - +
93A ALA* 1.3 62.5 + - - +
95A LYS* 3.4 9.9 + - - +
96A LYS* 3.0 28.0 + - - +
114A TRP* 4.0 7.6 - - - -
115A GLU* 3.7 41.1 - - + +
116A ALA 4.0 11.4 - - - +
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Residues in contact with ALA 93 (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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89A ARG 2.9 17.1 + - - +
90A MET* 3.7 7.0 - - - +
92A CYS* 1.3 76.3 - - - +
94A ALA* 1.3 64.0 + - - +
96A LYS* 3.7 9.6 - - - +
97A GLU* 3.1 35.9 + - - +
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Residues in contact with ALA 94 (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* 4.5 4.3 - - + -
62A ILE* 4.1 17.3 - - + +
65A LEU* 3.6 23.3 - - + -
90A MET 3.0 18.4 + - - +
91A THR 3.8 1.6 - - - +
93A ALA* 1.3 77.2 - - - +
95A LYS* 1.3 57.6 + - - +
97A GLU* 3.4 12.3 + - - +
98A LEU* 3.0 30.5 + - - +
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Residues in contact with LYS 95 (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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40A VAL* 3.7 37.5 - - - +
43A GLY 4.2 0.9 - - - -
44A LEU* 3.7 27.1 - - + +
47A ILE* 3.5 14.3 - - + +
91A THR 2.9 16.3 + - - +
92A CYS* 3.7 13.9 + - - +
94A ALA* 1.3 75.6 - - - +
96A LYS* 1.3 62.0 + - - +
98A LEU* 4.3 1.3 - - - -
99A ALA* 2.9 31.9 + - - +
111A ALA 3.2 16.5 + - - +
112A ALA 2.8 28.0 + - - +
113A LEU 3.9 2.0 + - - -
114A TRP 2.7 29.2 + - - +
115A GLU* 4.9 1.4 - - - +
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Residues in contact with LYS 96 (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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92A CYS 3.0 18.3 + - - +
93A ALA* 3.7 9.0 - - - +
95A LYS* 1.3 79.0 - - + +
97A GLU* 1.3 62.5 + - + +
99A ALA* 3.4 5.6 + - - +
100A ALA* 3.2 21.5 + - - +
112A ALA 5.9 0.4 - - - -
115A GLU* 2.9 41.5 + - - +
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Residues in contact with GLU 97 (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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93A ALA* 3.1 25.1 + - + +
94A ALA* 3.7 8.5 - - - +
96A LYS* 1.3 75.1 - - + +
98A LEU* 1.3 65.9 + - + +
100A ALA* 3.3 20.2 + - - +
101A SER* 3.6 6.8 + - - -
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Residues in contact with LEU 98 (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* 3.7 25.1 - - + -
47A ILE* 3.5 14.9 - - + +
48A ALA* 4.2 12.8 - - + -
51A LEU* 3.7 27.3 - - + +
58A VAL* 4.5 9.4 - - + -
59A ASP 5.8 0.7 - - - +
62A ILE* 4.0 30.1 - - + -
94A ALA 3.0 18.9 + - - +
95A LYS* 3.9 2.7 - - - +
97A GLU* 1.3 76.0 - - + +
99A ALA* 1.3 63.0 - - - +
101A SER* 2.4 28.0 + - - +
102A LEU 3.5 2.9 + - - -
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Residues in contact with ALA 99 (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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47A ILE* 3.6 22.8 - - + +
95A LYS 2.9 19.1 + - - +
96A LYS* 3.8 6.7 - - - +
98A LEU* 1.3 77.2 - - - +
100A ALA* 1.3 62.5 + - - +
102A LEU* 3.1 22.2 + - - +
105A LYS* 3.4 14.5 - - + +
108A LEU* 4.5 13.5 - - + -
112A ALA 5.6 1.3 - - - +
113A LEU* 5.8 3.4 - - + -
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Residues in contact with ALA 100 (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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96A LYS 3.2 13.4 + - - +
97A GLU* 3.4 13.7 - - - +
98A LEU 3.2 0.4 - - - -
99A ALA* 1.3 76.6 - - - +
101A SER* 1.3 59.8 + - - +
102A LEU 3.6 6.3 + - - +
105A LYS* 4.2 10.9 + - - +
254B GLY 6.1 0.7 - - - +
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Residues in contact with SER 101 (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* 3.1 18.6 - - - +
56A LYS* 3.3 25.6 - - - +
97A GLU 3.6 6.0 + - - -
98A LEU* 2.4 26.0 + - - +
100A ALA* 1.3 76.9 - - - +
102A LEU* 1.3 63.9 + - - +
103A THR* 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