Contacts of the helix formed by residues 55 - 77 (chain G) in PDB entry 1U3H
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 55 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E SER* 4.4 7.9 - - - +
102E THR* 3.1 33.9 - - + +
105E ARG* 4.4 9.4 + - - -
54G PHE* 1.3 87.8 - - - +
56G PRO* 1.3 66.6 - - - +
57G GLN* 2.9 21.4 + - - +
58G GLY* 2.9 18.9 + - - -
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Residues in contact with PRO 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G VAL* 3.9 26.2 - - + +
39G LYS* 3.9 22.4 - - + +
40G GLU* 3.7 6.3 - - - +
41G THR* 3.3 28.9 - - - +
54G PHE 3.3 4.2 - - - +
55G ASP* 1.3 87.3 - - - +
57G GLN* 1.3 65.0 + - - +
58G GLY 2.9 2.2 - - - -
59G GLY* 2.8 13.0 + - - -
60G LEU* 3.0 15.9 + - + +
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Residues in contact with GLN 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E THR* 4.4 12.3 - - + -
103E TYR* 5.3 4.0 - - + +
48F TYR* 3.2 20.3 + - - +
50F TYR* 2.8 40.7 + - - +
56F GLU* 3.2 29.0 + - - +
39G LYS* 4.8 3.8 - - - +
55G ASP* 2.9 18.7 + - - +
56G PRO* 1.3 77.5 - - - +
58G GLY* 1.3 63.4 + - - +
60G LEU* 3.1 18.1 + - - +
61G GLN* 2.8 27.1 + - - +
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Residues in contact with GLY 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E SER* 4.9 2.2 - - - -
101E GLY* 3.9 23.1 - - - -
102E THR* 4.5 3.4 - - - +
54G PHE* 3.8 13.5 - - - -
55G ASP* 2.9 12.4 + - - -
57G GLN* 1.3 80.2 - - - +
59G GLY* 1.3 59.7 + - - +
61G GLN* 3.6 2.0 + - - +
62G ASN* 2.7 33.8 + - - -
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Residues in contact with GLY 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G TYR* 3.5 35.0 - - - -
34G VAL* 4.5 4.0 - - - -
36G LEU* 4.7 2.9 - - - -
54G PHE* 3.8 6.6 - - - -
56G PRO 2.8 10.5 + - - -
58G GLY* 1.3 77.3 - - - +
60G LEU* 1.3 54.4 + - - -
61G GLN 3.5 0.2 + - - -
62G ASN 3.5 1.0 + - - -
63G ILE* 2.9 37.8 + - - +
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Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F TYR* 4.0 9.1 - - + -
56F GLU* 3.8 4.0 - - - +
34G VAL* 5.1 2.5 - - + -
36G LEU* 3.5 45.5 - - + +
39G LYS* 3.6 40.6 - - + -
56G PRO 3.0 15.4 + - - +
57G GLN* 3.1 35.2 + - - +
59G GLY* 1.3 73.3 - - - +
61G GLN* 1.3 64.8 + - - +
63G ILE* 3.3 7.4 + - + +
64G ALA* 3.1 22.5 + - - +
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Residues in contact with GLN 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E GLY 3.9 18.6 - - - +
31F ASN* 3.3 6.6 - - - +
50F TYR* 3.0 42.5 - - + +
97F ALA* 3.1 36.0 - - - +
98F GLY* 3.3 32.2 + - - +
57G GLN 2.8 20.5 + - - +
58G GLY 3.8 4.9 - - - +
60G LEU* 1.3 71.7 - - - +
62G ASN* 1.3 61.7 + - - +
64G ALA* 3.0 18.6 + - - +
65G THR* 3.2 9.1 + - - +
3I GLN* 4.7 7.2 - - - +
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Residues in contact with ASN 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E GLY 4.7 0.2 - - - +
11G VAL* 3.8 12.7 - - + +
22G TYR* 3.6 31.8 + - + -
58G GLY* 2.7 25.7 + - - -
61G GLN* 1.3 75.9 - - - +
63G ILE* 1.3 63.9 + - - +
65G THR* 3.3 10.1 + - - -
66G GLY 3.1 15.6 + - - -
2I SER 4.5 3.4 + - - -
3I GLN* 3.4 31.8 + - - +
4I TYR* 3.0 42.1 + - + +
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 4.1 14.6 - - + -
12G VAL 4.6 1.3 - - - +
13G TYR* 3.5 24.9 - - + -
20G GLY* 4.6 2.7 - - - -
21G GLN 3.8 38.6 - - - +
22G TYR* 4.1 6.5 - - + -
36G LEU* 3.8 30.5 - - + -
59G GLY 2.9 25.7 + - - +
60G LEU* 3.6 10.1 - - + +
61G GLN 3.2 0.2 - - - -
62G ASN* 1.3 75.4 - - - +
64G ALA* 1.3 60.8 + - - +
66G GLY* 3.0 15.8 + - - -
67G LYS 3.0 10.6 + - - -
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Residues in contact with ALA 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ASN* 5.4 0.8 + - - -
50F TYR* 3.6 39.2 - - + +
97F ALA* 5.8 1.3 - - + -
60G LEU 3.1 10.3 + - - +
61G GLN* 3.0 12.7 + - - +
63G ILE* 1.3 80.8 - - - +
65G THR* 1.3 56.1 + - - +
67G LYS* 3.4 13.4 + - + +
68G HIS* 3.1 23.6 + - - +
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Residues in contact with THR 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ASN* 5.3 0.4 - - - +
97F ALA* 3.4 29.4 + - - +
61G GLN 3.2 8.0 + - - -
62G ASN* 3.5 12.9 + - - -
63G ILE 3.1 0.6 - - - -
64G ALA* 1.3 74.1 - - - +
66G GLY* 1.3 56.7 + - - +
68G HIS* 3.1 7.0 + - - +
69G ASN* 2.7 51.4 + - - +
4I TYR* 3.2 35.3 + - + +
5I ARG 3.9 7.6 - - - -
6I PRO* 3.9 8.2 - - + +
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Residues in contact with GLY 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 4.4 2.5 - - - -
13G TYR* 3.8 16.8 - - - -
62G ASN 3.1 8.1 + - - -
63G ILE 3.0 8.1 + - - -
65G THR* 1.3 75.8 - - - +
67G LYS* 1.3 58.2 + - - +
69G ASN 4.4 0.2 - - - -
70G LEU* 2.8 33.8 + - - +
9H VAL* 3.5 4.3 - - - +
4I TYR* 3.4 22.8 - - - -
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Residues in contact with LYS 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ALA* 3.0 35.1 - - + +
13G TYR* 3.3 43.5 - - + +
18G ASP* 3.6 18.8 + - - +
63G ILE 3.0 7.2 + - - +
64G ALA* 3.4 14.8 - - + +
66G GLY* 1.3 76.1 - - - +
68G HIS* 1.3 53.1 + - - +
70G LEU* 2.6 24.1 - - - +
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Residues in contact with HIS 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ASN* 5.8 2.7 - - - -
30F ASN* 3.3 34.2 + - - +
64G ALA 3.1 14.2 + - - +
65G THR* 3.1 8.5 + - - +
67G LYS* 1.3 76.2 - - - +
69G ASN* 1.3 79.0 + - - +
70G LEU 2.8 10.2 - - - +
72G VAL* 3.3 25.7 + - + +
6I PRO* 3.6 18.4 - - + +
7I SER 3.3 27.2 + - - -
8I GLN* 4.5 9.6 + - - -
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Residues in contact with ASN 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G THR* 2.7 23.1 + - - +
66G GLY 4.2 1.1 - - - +
68G HIS* 1.3 71.1 - - - +
70G LEU* 1.3 63.1 + - - +
72G VAL* 3.0 4.8 + - - -
73G LEU* 2.8 41.1 + - + +
9H VAL* 4.2 2.7 - - + -
30H TYR* 4.6 1.8 - - - -
37H TYR* 4.7 5.2 - - - +
61H TYR* 4.3 2.5 + - - -
4I TYR* 3.4 37.1 - - - +
5I ARG 2.8 23.4 + - - -
6I PRO* 3.4 3.1 - - - +
7I SER* 3.0 35.0 + - - -
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Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G TYR* 3.6 25.4 - - + +
14G GLN* 3.7 14.6 - - - -
15G SER* 3.6 25.8 - - - +
66G GLY 2.8 19.0 + - - +
67G LYS 2.6 24.7 - - - +
68G HIS 2.8 7.1 - - - +
69G ASN* 1.3 74.9 - - - +
71G GLY* 1.3 59.1 + - - +
73G LEU* 4.7 0.4 - - - +
74G THR* 3.4 17.7 - - - +
7H PHE* 4.0 4.0 - - + -
8H VAL 3.5 24.2 - - - +
9H VAL* 3.4 29.0 - - + +
32H TYR* 4.4 2.5 - - + -
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Residues in contact with GLY 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G HIS 4.5 0.2 - - - -
69G ASN 3.3 0.4 + - - -
70G LEU* 1.3 73.8 - - - +
72G VAL* 1.3 61.7 + - - +
73G LEU 3.3 0.4 - - - -
74G THR* 3.1 25.5 + - - +
75G LYS* 3.1 23.9 + - - +
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Residues in contact with VAL 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G HIS* 3.3 27.8 + - + +
69G ASN* 3.0 10.7 + - - +
70G LEU 3.2 1.4 + - - -
71G GLY* 1.3 76.8 - - - +
73G LEU* 1.3 66.4 + - + +
75G LYS* 3.9 2.9 - - - +
76G ARG* 3.0 41.0 + - - +
7I SER* 3.7 37.5 - - - +
8I GLN* 4.5 15.5 - - + +
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Residues in contact with LEU 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ASN* 2.8 25.0 + - + +
72G VAL* 1.3 91.4 - - + +
74G THR* 1.3 58.1 + - - +
76G ARG* 4.0 15.2 - - - +
77G SER* 2.9 32.9 + - - -
9H VAL* 4.5 5.2 - - + -
32H TYR* 3.5 22.0 - - + -
37H TYR* 3.4 48.9 - - + +
53H LEU* 3.4 28.9 - - + -
57H ASP* 5.0 0.4 - - - +
7I SER* 4.2 9.6 - - - +
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Residues in contact with THR 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G SER* 5.4 0.3 + - - -
70G LEU* 3.4 20.4 - - - +
71G GLY* 3.1 26.0 + - - +
72G VAL 3.3 0.6 - - - -
73G LEU* 1.3 79.0 - - - +
75G LYS* 1.3 52.0 + - - +
77G SER* 3.0 4.0 + - - -
79G SER* 2.7 42.3 + - - +
7H PHE* 3.9 39.9 - - + +
32H TYR* 3.3 10.3 + - - -
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Residues in contact with LYS 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G GLY 3.1 18.4 + - - +
72G VAL* 3.9 2.7 - - - +
74G THR* 1.3 74.7 - - - +
76G ARG* 1.3 56.6 + - - +
77G SER 3.0 1.6 - - - -
78G ASN* 2.6 32.9 + - - +
79G SER* 4.5 2.5 - - - +
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Residues in contact with ARG 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G VAL* 3.0 38.1 + - + +
73G LEU* 4.0 17.7 - - - +
75G LYS* 1.3 77.4 - - - +
77G SER* 1.3 57.1 + - - +
78G ASN* 3.0 12.4 + - - -
37H TYR* 4.8 0.2 - - - -
52H GLU* 6.1 0.7 - - - +
53H LEU* 2.8 43.9 + - + +
54H GLY* 4.2 1.6 - - - -
56H PRO* 4.0 29.6 - - + +
57H ASP* 2.7 42.4 + - - -
7I SER* 4.1 3.0 + - - -
8I GLN* 5.1 6.3 - - - +
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Residues in contact with SER 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G LEU 2.9 14.6 + - - -
74G THR 3.0 12.5 + - - -
75G LYS 3.0 0.4 + - - -
76G ARG* 1.3 75.3 - - - +
78G ASN* 1.3 70.3 + - - +
80G THR* 2.9 40.3 + - - -
32H TYR* 3.3 28.4 + - - -
53H LEU* 4.5 14.6 - - - +
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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
------------------------------------------------------------
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