Contacts of the helix formed by residues 94 - 109 (chain B) in PDB entry 1UK0
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 ALA 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLN* 3.2 23.3 - - - +
93B ASN* 1.3 78.7 + - - +
95B ASP* 1.4 76.3 + - - +
97B VAL 3.6 2.2 - - - +
98B GLN* 2.8 39.4 + - - +
226B THR* 6.1 2.0 - - + +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASN* 2.4 34.8 + - - +
94B ALA* 1.4 88.7 + - - +
96B SER* 1.3 67.6 + - - +
97B VAL 2.6 0.5 + - - -
98B GLN* 2.8 17.3 + - - +
99B ALA* 3.3 6.0 + - - -
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 5.2 9.7 - - - +
90B LEU 3.8 13.9 + - - -
91B LEU* 3.6 22.0 - - - -
93B ASN* 4.0 16.7 + - - -
95B ASP* 1.3 76.3 - - - +
97B VAL* 1.4 62.3 + - - +
99B ALA* 4.0 6.3 - - - +
100B LYS* 2.9 36.9 + - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.9 29.6 - - + +
55B VAL* 3.8 21.8 - - + -
56B GLN* 4.1 13.2 - - + +
91B LEU* 4.2 22.2 - - + +
93B ASN 3.7 19.7 + - - +
94B ALA* 3.3 4.5 + - - +
95B ASP 2.6 9.1 + - - -
96B SER* 1.4 74.1 - - - +
98B GLN* 1.4 52.5 - - - +
100B LYS* 3.2 6.1 + - - +
101B VAL* 2.7 49.4 + - + +
224B PRO* 4.5 5.4 - - + -
227B GLY* 5.9 0.2 - - - -
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 4.8 1.4 - - - +
94B ALA* 2.8 34.1 + - - +
95B ASP* 2.8 9.8 + - - +
97B VAL* 1.4 68.7 - - - +
99B ALA* 1.3 67.0 + - - +
100B LYS 3.1 1.6 - - - -
101B VAL* 2.6 18.4 + - + +
102B GLU* 2.6 32.5 + - + +
226B THR 4.0 14.6 + - - +
227B GLY* 3.5 25.2 - - - +
228B TYR 4.9 0.8 - - - +
276B HIS* 6.0 0.6 - - - -
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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
----------------------------------------------------------
28B TYR* 5.3 4.8 - - + +
95B ASP 3.3 8.7 + - - -
96B SER* 3.6 6.0 + - - +
98B GLN* 1.3 77.1 - - - +
100B LYS* 1.3 79.3 + - + +
102B GLU* 3.9 8.4 + - - +
103B MET* 2.9 25.9 + - - +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.9 16.0 + - - +
52B LEU* 3.8 9.9 - - + -
75B PHE* 3.7 30.1 - - + -
76B TYR* 4.3 7.9 - - - +
81B HIS* 2.8 37.6 + - - -
83B PHE* 4.4 7.2 - - + -
89B PRO* 6.4 0.9 - - + -
91B LEU* 3.6 22.4 - - + -
96B SER* 2.9 23.8 - - - +
97B VAL* 3.2 4.2 + - - +
98B GLN 3.1 0.6 - - - -
99B ALA* 1.3 87.9 - - + +
101B VAL* 1.4 64.9 + - - +
103B MET* 3.3 31.3 - - - +
104B LEU* 3.4 8.5 - - - +
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Residues in contact with VAL 101 (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 TYR* 4.0 6.3 - - + -
52B LEU* 4.1 8.5 - - + -
97B VAL* 2.7 34.7 + - + +
98B GLN* 2.6 18.1 + - - +
100B LYS* 1.4 71.8 - - - +
102B GLU* 1.4 54.5 + - + +
104B LEU* 2.7 27.9 + - - +
105B ASP* 3.6 7.9 + - - +
224B PRO* 3.8 35.7 - - + -
227B GLY* 3.3 22.7 - - - +
228B TYR* 3.2 31.0 - - + +
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Residues in contact with GLU 102 (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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28B TYR* 6.2 0.4 - - + -
98B GLN* 2.6 36.1 + - + +
99B ALA* 3.9 6.0 + - - +
101B VAL* 1.4 67.6 - - + +
103B MET* 1.3 57.7 + - - +
104B LEU 3.0 1.9 + - - -
105B ASP* 3.1 12.4 - - - +
106B ASN* 2.8 49.5 + - - +
228B TYR* 5.9 4.7 - - + -
246B TYR* 5.8 6.0 - - - -
248B HIS* 5.9 2.8 - - - -
502B FRM 6.5 1.3 - - - -
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Residues in contact with MET 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.3 47.2 - - + -
30B ILE* 3.7 35.9 - - - -
75B PHE* 4.9 2.2 - - + -
79B ILE* 4.1 12.8 - - + -
81B HIS* 4.7 5.4 - - - -
99B ALA 2.9 19.2 + - - +
100B LYS* 3.3 27.8 - - + +
102B GLU* 1.3 75.4 - - - +
104B LEU* 1.3 84.8 + - + +
105B ASP 3.5 0.2 - - - -
106B ASN* 3.8 1.8 - - - +
107B LEU* 3.1 29.2 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.5 27.4 - - + +
48B ALA* 3.5 39.7 - - + +
49B TYR* 3.2 32.5 - - + +
52B LEU* 3.6 19.7 - - + -
75B PHE* 4.2 4.9 - - + -
79B ILE* 4.5 12.3 - - + -
100B LYS 3.4 7.9 - - - +
101B VAL 2.7 11.5 + - - +
103B MET* 1.3 89.9 - - + +
105B ASP* 1.3 54.3 + - - +
107B LEU* 3.6 14.0 + - + -
108B LEU* 2.8 35.2 + - - +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR* 2.3 35.7 + - - -
101B VAL 3.6 7.6 - - - +
102B GLU* 3.1 14.5 - - - +
104B LEU* 1.3 66.1 - - - +
106B ASN* 1.4 60.4 + - - +
107B LEU 3.0 2.2 - - - -
108B LEU* 2.6 34.0 + - - +
109B ASP 3.3 6.8 + - - -
207B ASN* 4.3 0.3 - - - +
219B ALA* 4.5 0.9 - - - +
228B TYR* 2.8 39.3 + - - -
502B FRM 3.7 50.5 + - + +
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Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.2 27.2 + - - +
102B GLU* 2.8 33.9 + - - +
103B MET 3.8 1.8 - - - +
105B ASP* 1.4 79.4 - - - +
107B LEU* 1.4 55.2 + - - +
110B ILE* 3.5 22.9 - - - +
204B ARG* 3.2 39.4 + - - +
207B ASN* 3.4 21.7 + - - +
248B HIS* 4.9 6.0 + - - -
502B FRM 4.1 15.3 - - - -
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Residues in contact with LEU 107 (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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25B MET* 3.3 39.3 - - + -
28B TYR* 4.5 8.3 - - + -
30B ILE* 3.6 24.2 - - + -
35B MET* 5.8 0.4 - - + -
40B LEU* 4.2 12.8 - - + +
45B ILE* 3.5 19.6 - - + +
79B ILE* 5.0 4.3 - - + -
103B MET* 3.1 25.7 + - - +
104B LEU* 3.7 20.2 - - + -
105B ASP 2.8 1.6 + - - -
106B ASN* 1.4 69.7 - - - +
108B LEU* 1.3 57.2 - - - +
109B ASP 3.5 2.5 - - - -
110B ILE* 3.6 17.2 - - + +
111B GLU* 2.7 30.8 + - - +
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Residues in contact with LEU 108 (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 SER 4.9 0.2 - - - +
42B LYS* 4.8 16.8 - - + +
45B ILE* 3.9 23.8 - - + -
46B GLN* 5.7 2.2 - - + -
49B TYR* 3.7 13.2 - - + +
104B LEU 2.8 17.9 + - - +
105B ASP 2.6 16.7 + - - +
107B LEU* 1.3 70.0 - - - +
109B ASP* 1.4 60.2 + - - +
111B GLU* 3.6 16.0 + - + +
112B VAL* 3.7 9.9 + - - +
217B ARG* 5.5 1.7 + - - -
220B PRO* 3.5 35.4 - - + -
502B FRM 3.7 28.5 - - + -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP 3.3 6.1 + - - -
108B LEU* 1.4 74.8 - - - +
110B ILE* 1.3 55.6 + - - +
112B VAL* 2.4 29.9 + - - +
113B ALA 2.9 12.1 + - - -
206B THR 3.7 2.8 - - - +
207B ASN* 2.7 50.6 - - - +
210B GLY* 4.0 5.7 - - - -
211B ILE* 3.7 13.0 - - - +
217B ARG* 3.1 30.6 + - - -
502B FRM 3.5 22.4 - - - +
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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