Contacts of the helix formed by residues 81 - 100 (chain B) in PDB entry 4UY1
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 ASN 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY 3.5 16.2 - - - +
63A GLU* 2.8 34.7 + - - +
81A ASN* 3.4 17.2 - - - +
83A CYS* 3.8 17.6 - - - +
79B ALA* 3.4 4.3 + - - +
80B GLU* 1.3 77.0 - - - +
82B LYS* 1.3 61.6 + - - +
83B CYS* 2.9 8.9 + - - +
84B GLN* 2.9 35.3 + - - +
85B GLU* 3.5 24.6 + - - +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY 4.5 2.6 + - - -
81B ASN* 1.3 74.1 - - - +
83B CYS* 1.3 61.3 + - - +
85B GLU* 3.2 27.6 + - + +
86B LEU* 2.9 42.2 + - + +
89B LYS* 5.6 4.5 - - - +
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Residues in contact with CYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 3.7 20.4 - - - +
56B ALA 5.3 1.1 - - - -
57B GLY 4.1 2.5 - - - -
58B CYS* 2.0 53.8 - - + -
63B GLU* 3.5 19.7 - - - +
81B ASN* 2.9 9.2 + - - +
82B LYS* 1.3 78.8 - - - +
84B GLN* 1.3 57.1 + - - +
86B LEU* 3.2 2.6 + - - +
87B LEU* 2.8 36.1 + - - +
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 4.4 4.8 + - - +
63B GLU* 4.3 9.9 + - + +
64B ARG 3.6 25.5 + - - +
65B TYR* 3.9 20.2 - - + +
66B SER 5.0 0.5 + - - -
78B PRO 4.1 3.8 - - - +
79B ALA* 3.7 11.4 - - + -
80B GLU* 2.9 55.2 + - - +
81B ASN* 2.9 27.7 + - - +
83B CYS* 1.3 71.2 - - - +
85B GLU* 1.3 65.2 + - - +
87B LEU* 4.1 4.4 - - - +
88B CYS* 3.0 27.9 + - - +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B CYS* 5.3 2.9 - - - +
79B ALA* 3.4 25.9 - - + +
81B ASN 3.5 10.9 + - - +
82B LYS* 3.2 36.8 + - + +
83B CYS 3.3 0.2 - - - -
84B GLN* 1.3 76.8 - - - +
86B LEU* 1.3 64.0 + - - +
88B CYS* 4.0 3.6 - - - +
89B LYS* 3.1 48.6 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B CYS* 5.7 1.8 - - - +
52B ARG* 5.0 1.1 - - + +
53B ALA* 4.0 32.8 - - + +
56B ALA* 4.3 13.5 - - + -
58B CYS* 4.1 15.9 - - - -
82B LYS* 2.9 25.9 + - + +
83B CYS* 3.2 8.7 + - - +
85B GLU* 1.3 76.6 - - - +
87B LEU* 1.3 64.1 + - + +
89B LYS* 3.0 20.1 + - + +
90B CYS* 3.0 29.8 + - - -
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Residues in contact with LEU 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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1B GLY 4.5 1.1 - - - +
50B TYR* 4.8 5.8 - - + -
53B ALA* 3.8 21.8 - - + -
58B CYS* 4.7 4.0 - - + -
59B SER 3.8 2.7 - - - +
60B PRO* 3.4 49.4 - - + +
63B GLU* 3.6 39.3 - - + +
65B TYR* 3.8 18.4 - - + -
83B CYS 2.8 23.6 + - - +
84B GLN* 4.1 1.1 - - - +
86B LEU* 1.3 72.9 - - - +
88B CYS* 1.3 63.0 + - - +
90B CYS* 3.3 6.1 + - - +
91B ASP* 3.1 28.8 + - - +
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Residues in contact with CYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 5.4 0.2 - - - -
65B TYR* 3.4 39.8 - - + -
66B SER 4.5 1.1 - - - +
67B TRP* 4.0 7.6 - - - -
74B VAL* 4.4 6.1 - - - -
76B CYS* 2.0 55.4 - - + -
77B GLY 5.4 0.2 - - - +
84B GLN 3.0 18.6 + - - +
85B GLU* 4.0 2.2 - - - +
87B LEU* 1.3 78.0 - - - +
89B LYS* 1.3 54.4 - - - +
91B ASP* 4.0 0.3 - - - +
92B GLN* 2.8 33.8 + - - +
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Residues in contact with LYS 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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49B CYS* 4.9 2.0 - - - -
76B CYS* 4.0 4.2 - - + -
82B LYS* 5.6 4.0 - - - +
85B GLU* 3.1 39.2 + - - +
86B LEU* 3.0 20.5 + - + +
88B CYS* 1.3 75.9 - - - +
90B CYS* 1.3 63.9 + - - +
92B GLN* 3.9 15.1 - - - +
93B GLU* 2.9 27.5 + - - +
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Residues in contact with CYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 3.2 13.5 - - + -
49B CYS* 2.0 68.0 - - + -
50B TYR* 3.8 20.4 - - + -
53B ALA* 5.1 4.3 - - - -
86B LEU* 3.0 23.8 + - - -
87B LEU* 3.6 8.3 - - - +
89B LYS* 1.3 76.1 - - - +
91B ASP* 1.3 58.0 + - - +
93B GLU* 3.5 5.9 + - - +
94B ILE 3.1 21.7 + - - -
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Residues in contact with ASP 91 (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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1B GLY 4.1 2.4 + - - +
5B LEU* 3.5 19.3 + - + +
8B THR* 3.6 17.6 + - - +
46B HIS* 2.8 14.4 + - - -
50B TYR* 2.6 30.8 + - - -
65B TYR* 2.8 36.4 + - - +
87B LEU* 3.1 12.0 + - - +
88B CYS 4.0 0.2 - - - +
90B CYS* 1.3 73.2 - - - +
92B GLN* 1.3 66.3 + - - +
94B ILE* 3.3 9.4 - - - +
95B ALA* 3.0 24.8 + - - +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 4.7 1.2 + - - +
74B VAL* 2.7 51.5 + - + +
76B CYS* 3.8 11.5 - - - -
88B CYS 2.8 22.5 + - - +
89B LYS* 3.9 13.5 - - - +
91B ASP* 1.3 72.2 - - - +
93B GLU* 1.3 56.1 + - - +
95B ALA* 3.4 6.3 + - - +
96B ASN* 2.9 49.2 + - - +
1126B DMS 2.9 24.0 + - - +
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Residues in contact with GLU 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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45B GLY* 4.8 7.8 - - - +
46B HIS* 5.4 1.2 + - - -
49B CYS* 4.2 22.5 - - - +
89B LYS 2.9 19.1 + - - +
90B CYS 3.6 4.0 - - - +
92B GLN* 1.3 78.5 - - - +
94B ILE* 1.3 58.1 + - - +
96B ASN* 3.3 8.1 + - - +
97B CYS* 2.9 32.5 + - + +
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Residues in contact with ILE 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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5B LEU* 3.9 13.9 - - + -
9B VAL* 4.2 6.7 - - + -
42B CYS* 3.6 22.9 - - + +
43B CYS* 4.2 10.5 - - - -
46B HIS* 3.7 46.2 - - + +
90B CYS 3.1 7.7 + - - +
91B ASP 3.3 11.0 - - - +
93B GLU* 1.3 77.6 - - - +
95B ALA* 1.3 56.7 + - - +
97B CYS* 3.3 4.2 + - - +
98B LEU* 2.8 52.2 + - + +
1129B TJM 3.7 31.9 - - + -
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Residues in contact with ALA 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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8B THR* 3.5 30.1 - - - +
9B VAL* 4.1 13.2 - - + +
12B VAL* 3.6 18.5 - - + +
13B GLY 4.5 1.2 - - - +
74B VAL* 4.6 0.7 - - + -
91B ASP 3.0 17.5 + - - +
92B GLN* 3.4 8.7 - - - +
93B GLU 3.3 0.2 - - - -
94B ILE* 1.3 78.8 - - - +
96B ASN* 1.3 61.7 + - - +
98B LEU* 3.6 3.1 + - - +
99B ALA* 3.1 23.9 + - - +
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Residues in contact with ASN 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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12B VAL* 4.3 15.5 - - - +
73B SER* 5.7 1.9 - - - -
74B VAL* 5.3 3.8 + - - +
92B GLN* 2.9 38.7 + - - +
93B GLU* 3.8 6.6 - - - +
95B ALA* 1.3 73.5 - - - +
97B CYS* 1.3 67.2 + - - +
99B ALA* 3.5 13.7 + - - +
100B GLN* 3.0 27.8 + - - +
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Residues in contact with CYS 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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41B TRP 5.0 0.2 - - - -
42B CYS* 2.1 53.4 - - + -
93B GLU* 2.9 20.2 + - + +
94B ILE* 3.4 7.4 - - - +
96B ASN* 1.3 79.9 - - - +
98B LEU* 1.3 60.8 + - - +
100B GLN* 3.3 18.6 + - - +
101B THR* 3.5 12.0 - - - +
1132B PEG 3.5 20.8 - - - +
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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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9B VAL* 4.5 9.9 - - + -
13B GLY 4.6 2.2 - - - +
14B PRO* 4.2 0.9 - - - +
15B ARG* 3.5 8.5 + - - -
20B TYR* 3.7 49.8 - - + +
39B ILE* 3.8 21.1 - - + +
42B CYS* 3.6 22.2 - - + -
43B CYS* 4.9 1.3 - - - -
94B ILE* 2.8 35.4 + - + +
95B ALA* 4.1 3.6 - - - +
97B CYS* 1.3 68.6 - - - +
99B ALA* 1.3 64.8 + - - +
100B GLN 3.0 2.7 - - - -
101B THR* 2.5 25.7 + - - +
1129B TJM 3.9 23.1 - - + -
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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
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12B VAL* 3.4 26.2 - - + +
13B GLY 3.3 24.4 + - - +
14B PRO* 3.9 11.7 - - + +
95B ALA 3.1 7.7 + - - +
96B ASN* 3.7 8.1 - - - +
97B CYS 3.3 0.4 - - - -
98B LEU* 1.3 77.3 - - - +
100B GLN* 1.3 58.9 + - + +
101B THR 3.3 4.7 + - - +
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Residues in contact with GLN 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 ASN* 3.0 27.2 + - - +
97B CYS* 3.3 10.6 + - - +
98B LEU 3.0 1.0 - - - -
99B ALA* 1.3 80.0 - - + +
101B THR* 1.3 59.6 + - - +
102B GLU* 5.9 0.3 - - - +
1132B PEG 3.8 31.6 + - - +
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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
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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