Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 1UFX
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 GLU 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLY 5.6 0.2 - - - +
26A GLY* 3.9 7.4 - - - -
27A ALA* 4.8 11.7 - - + +
28A ASN* 4.1 20.3 + - + +
67A GLY 5.2 0.9 - - - +
68A LYS* 1.3 73.7 - - - +
70A HIS* 1.3 68.7 + - - +
71A ARG* 4.2 8.1 - - + +
72A GLU* 2.7 27.0 + - + +
73A ALA* 3.0 10.0 + - - +
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Residues in contact with HIS 70 (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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23A ILE* 2.8 63.6 + - + +
24A GLU* 3.4 6.4 + - - +
25A GLY 3.4 23.1 + - - +
26A GLY* 3.6 10.8 - - - -
34A PRO* 4.8 5.4 - - + -
68A LYS 3.8 0.2 + - - -
69A GLU* 1.3 70.2 - - - +
71A ARG* 1.3 72.9 + - + +
73A ALA* 3.1 10.5 + - - +
74A ALA* 3.0 27.1 + - + +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 2.8 10.7 + - + +
70A HIS* 1.3 87.3 - - + +
72A GLU* 1.3 79.1 + - - +
73A ALA 3.0 0.9 + - - -
74A ALA* 3.0 19.5 + - + +
75A ARG* 3.3 30.4 + - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 3.6 34.5 + - + +
69A GLU* 2.7 29.1 + - + +
71A ARG* 1.3 91.7 + - - +
73A ALA* 1.3 59.7 + - - +
75A ARG* 3.5 17.8 + - - +
76A ILE* 3.3 27.7 + - + +
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Residues in contact with ALA 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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23A ILE* 4.2 5.4 - - + -
34A PRO* 4.1 13.5 - - + -
65A LEU* 3.5 41.3 - - + -
68A LYS* 5.1 1.9 - - + +
69A GLU 3.0 9.4 + - - +
70A HIS* 3.3 10.3 - - - +
72A GLU* 1.3 73.5 - - - +
74A ALA* 1.3 59.3 + - - +
75A ARG 2.9 1.3 - - - -
76A ILE* 2.7 24.4 + - - +
77A ILE* 2.9 16.9 + - + +
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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
----------------------------------------------------------
23A ILE* 4.5 6.2 - - + +
70A HIS* 3.0 22.3 + - + +
71A ARG* 3.0 15.2 + - - +
73A ALA* 1.3 75.4 - - - +
75A ARG* 1.3 60.3 + - - +
77A ILE* 3.8 11.0 + - - +
78A ALA* 3.2 24.4 + - - +
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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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71A ARG* 3.3 26.5 + - - +
72A GLU* 3.6 22.9 + - - +
73A ALA 2.9 0.6 - - - -
74A ALA* 1.3 77.8 - - - +
76A ILE* 1.3 61.7 + - + +
78A ALA* 3.4 5.6 + - - +
79A GLU* 2.9 56.1 + - + +
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Residues in contact with ILE 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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60A VAL* 4.3 20.4 - - + +
61A ASN* 6.2 0.2 - - + -
63A LEU* 4.2 37.7 - - + -
64A THR 5.2 2.2 - - - +
65A LEU* 3.4 28.0 - - + -
68A LYS* 4.5 21.8 - - + -
72A GLU* 3.3 21.7 + - + +
73A ALA* 2.7 12.1 + - - +
75A ARG* 1.3 75.9 - - + +
77A ILE* 1.3 62.7 + - - +
79A GLU* 3.4 8.0 + - - +
80A ALA* 3.3 18.9 + - - +
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Residues in contact with ILE 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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19A LEU* 3.7 17.9 - - + -
21A ILE* 3.9 20.6 - - + -
23A ILE* 4.4 10.1 - - + -
57A ILE* 4.2 18.2 - - + -
60A VAL* 3.9 29.2 - - + -
65A LEU* 5.0 1.6 - - + -
73A ALA* 2.9 25.2 + - + +
74A ALA* 4.1 8.1 - - - +
76A ILE* 1.3 73.9 - - + +
78A ALA* 1.3 66.2 + - - +
80A ALA* 2.9 19.9 + - - +
81A PHE 3.3 4.2 + - - -
89A ILE* 3.5 5.5 - - + +
91A PHE* 3.5 28.9 - - + -
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Residues in contact with ALA 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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19A LEU* 5.6 2.5 - - - -
74A ALA 3.2 17.7 + - - +
75A ARG* 3.7 6.3 - - - +
77A ILE* 1.3 79.2 - - - +
79A GLU* 1.3 57.9 + - - +
81A PHE* 2.8 27.0 + - - +
82A LYS* 3.1 31.8 + - - +
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Residues in contact with GLU 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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75A ARG* 2.9 42.7 + - + +
76A ILE* 3.5 9.4 - - - +
77A ILE 3.2 0.2 - - - -
78A ALA* 1.3 76.7 - - - +
80A ALA* 1.3 61.7 + - - +
81A PHE 3.3 0.2 + - - -
82A LYS* 3.5 25.6 + - - +
83A THR* 3.4 22.5 + - - +
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Residues in contact with ALA 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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14A LYS* 3.0 15.6 + - - -
60A VAL* 4.6 0.2 - - + -
61A ASN* 3.3 38.6 - - + +
76A ILE 3.3 8.5 + - - +
77A ILE* 2.9 13.3 + - - +
79A GLU* 1.3 78.6 - - - +
81A PHE* 1.3 55.6 + - - +
83A THR* 3.0 23.0 - - - +
86A ARG* 4.6 1.6 - - - +
88A TYR 4.2 2.3 - - - +
89A ILE* 3.7 12.6 - - + -
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Residues in contact with PHE 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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12A VAL 6.0 0.2 - - - -
14A LYS* 3.4 50.9 - - + +
16A ALA 3.9 13.9 - - - -
17A ALA 4.1 6.5 - - - -
18A THR* 4.0 8.7 - - + -
19A LEU* 3.5 42.6 - - + -
44A SER* 3.8 15.0 - - - -
77A ILE 3.3 3.2 + - - +
78A ALA* 2.8 14.6 + - - +
80A ALA* 1.3 76.7 - - - +
82A LYS* 1.3 66.6 + - + +
83A THR 3.1 6.9 - - - +
89A ILE* 3.6 21.3 - - + -
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Residues in contact with LYS 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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78A ALA* 3.1 33.9 + - - +
79A GLU* 3.8 33.9 - - - +
81A PHE* 1.3 74.3 - - + +
83A THR* 1.3 72.6 + - - +
84A LYS* 4.1 8.7 - - - +
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Residues in contact with THR 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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14A LYS* 4.3 1.6 - - - +
79A GLU 3.4 8.2 + - - +
80A ALA* 3.0 32.5 - - - +
81A PHE 3.1 9.0 - - - +
82A LYS* 1.3 89.7 - - - +
84A LYS* 1.3 61.6 + - - +
85A ASP* 2.7 32.6 + - - +
86A ARG* 4.0 35.9 + - + +
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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