Contacts of the helix formed by residues 46 - 60 (chain B) in PDB entry 1UEX
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 SER 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A TYR* 3.1 25.9 - - - -
11B TYR* 4.6 3.3 + - - -
12B LYS* 4.6 10.3 + - - -
44B VAL* 3.1 13.2 - - - +
45B ASN* 1.3 80.7 - - - +
47B ARG* 1.3 64.6 + - - +
48B GLU* 3.8 12.6 + - - -
49B GLU* 3.1 26.3 + - - +
50B GLY 3.3 4.9 + - - -
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Residues in contact with ARG 47 (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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91A TYR* 3.2 43.7 + - + +
92A GLU 4.6 5.1 + - - -
93A ASN* 3.6 20.2 + - - +
46B SER* 1.3 72.8 - - - +
48B GLU* 1.3 76.3 + - + +
50B GLY* 3.3 2.8 + - - -
51B GLU* 3.2 23.1 + - + +
106B ASN* 4.8 3.9 - - - +
107B LYS* 5.4 1.6 - - - +
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Residues in contact with GLU 48 (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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11B TYR* 3.6 16.8 + - + +
12B LYS* 5.5 3.6 + - - +
46B SER* 3.8 10.4 - - - +
47B ARG* 1.3 90.9 + - + +
49B GLU* 1.3 63.3 + - - +
51B GLU* 3.5 6.9 + - - +
52B PHE* 3.2 21.0 + - - +
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Residues in contact with GLU 49 (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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11B TYR* 3.5 22.6 + - + -
12B LYS* 5.6 0.2 - - - -
14B HIS* 5.8 0.7 - - - -
16B TYR* 2.6 37.5 + - + +
43B SER 3.1 14.4 - - - +
44B VAL* 4.3 2.7 - - + -
45B ASN* 3.1 29.7 + - - +
46B SER* 3.1 22.7 + - - +
48B GLU* 1.3 75.5 - - - +
50B GLY* 1.3 65.3 + - - +
52B PHE* 3.3 2.8 + - - +
53B ILE* 3.2 31.8 + - + +
122B LYS* 2.7 19.9 + - - -
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Residues in contact with GLY 50 (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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91A TYR* 5.6 1.6 - - - -
42B MET* 6.2 0.2 - - - -
44B VAL* 3.7 24.1 - - - +
46B SER 3.3 8.3 + - - -
47B ARG 3.3 3.8 + - - -
48B GLU 3.3 0.4 - - - -
49B GLU* 1.3 80.9 - - - +
51B GLU* 1.3 55.4 + - - +
53B ILE* 3.4 5.0 + - - +
54B SER* 3.1 30.5 + - - -
106B ASN* 3.9 10.7 - - - -
108B TRP* 6.2 0.4 - - - -
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Residues in contact with GLU 51 (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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47B ARG* 3.2 15.8 + - + +
48B GLU* 3.9 7.4 - - - +
49B GLU 3.3 0.2 - - - -
50B GLY* 1.3 74.1 - - - +
52B PHE* 1.3 63.1 + - - +
54B SER* 4.0 2.2 - - - -
55B LYS* 3.2 50.1 + - - +
104B PHE 5.2 1.4 - - - +
106B ASN* 2.7 32.1 + - - +
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Residues in contact with PHE 52 (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 SER* 3.9 18.2 - - - -
10B SER 3.7 11.9 - - - -
11B TYR* 3.5 42.4 - + + -
16B TYR* 3.3 32.8 - + - -
48B GLU 3.2 12.9 + - - +
49B GLU* 3.4 9.4 - - - +
50B GLY 3.2 0.2 - - - -
51B GLU* 1.3 76.7 - - - +
53B ILE* 1.3 70.8 + - + +
55B LYS* 3.5 15.3 + - + +
56B LEU* 3.1 40.4 + - + +
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Residues in contact with ILE 53 (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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16B TYR* 4.4 22.2 - - + -
18B VAL* 5.3 1.6 - - + -
42B MET* 3.4 54.5 - - + -
43B SER 5.1 0.2 - - - +
44B VAL* 4.0 12.6 - - + -
49B GLU* 3.2 19.7 + - + +
50B GLY 3.7 5.6 - - - +
51B GLU 3.3 0.2 - - - -
52B PHE* 1.3 86.6 - - + +
54B SER* 1.3 55.6 + - - +
56B LEU* 2.8 11.3 + - + +
57B ALA* 2.7 34.7 + - + +
66B VAL* 5.1 4.0 - - + -
101B ALA* 6.2 0.2 - - + -
120B VAL* 4.1 18.6 - - + -
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Residues in contact with SER 54 (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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50B GLY 3.1 11.8 + - - -
51B GLU* 4.0 7.2 - - - -
53B ILE* 1.3 80.5 - - - +
55B LYS* 1.3 52.5 + - - +
57B ALA* 4.5 0.2 - - - -
58B LEU* 2.7 39.9 + - - +
101B ALA* 5.8 2.4 - - - +
102B GLU 3.8 3.1 + - - -
103B SER* 3.3 33.3 + - - -
106B ASN* 2.8 34.8 + - - +
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Residues in contact with LYS 55 (chain B).
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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51B GLU* 3.2 46.8 + - - +
52B PHE* 3.8 14.6 - - + +
54B SER* 1.3 78.3 - - - +
56B LEU* 1.3 53.8 + - - +
58B LEU* 4.5 1.1 - - - -
59B GLU* 2.6 64.9 + - - +
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Residues in contact with LEU 56 (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 SER* 3.1 38.8 - - - +
16B TYR* 3.8 28.7 - - + +
17B LYS* 5.1 0.4 - - - -
18B VAL* 4.3 16.1 - - + +
52B PHE* 3.1 27.7 + - + +
53B ILE* 2.8 12.7 + - + +
55B LYS* 1.3 79.9 - - - +
57B ALA* 1.3 61.1 + - - +
59B GLU* 4.9 1.1 - - - -
60B LYS* 3.4 45.7 + - - +
61B MET* 3.9 3.6 + - - +
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Residues in contact with ALA 57 (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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18B VAL* 3.8 30.5 - - + +
53B ILE* 2.7 19.3 + - + +
54B SER* 4.5 0.2 - - - -
56B LEU* 1.3 74.1 - - - +
58B LEU* 1.3 54.0 + - - +
61B MET* 3.4 6.9 - - - +
62B ARG 3.0 8.3 + - - -
63B ILE* 2.7 34.6 + - + +
66B VAL* 4.4 7.6 - - + -
103B SER* 3.4 20.2 - - - +
120B VAL* 5.0 1.8 - - + -
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Residues in contact with LEU 58 (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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54B SER 2.7 22.4 + - - +
55B LYS* 4.3 0.9 - - - +
57B ALA* 1.3 72.7 - - - +
59B GLU* 1.3 67.8 + - - +
62B ARG* 2.7 31.2 + - - +
63B ILE 3.6 18.1 + - - +
64B VAL* 4.6 3.1 - - + -
103B SER* 3.5 25.1 - - - +
104B PHE* 4.3 24.0 - - + -
678C SER* 4.1 25.4 - - - -
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Residues in contact with GLU 59 (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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55B LYS* 2.6 69.6 + - - +
56B LEU* 4.5 0.7 - - - +
58B LEU* 1.3 84.0 - - - +
60B LYS* 1.3 66.8 + - + +
61B MET 3.3 0.2 + - - -
62B ARG* 3.4 19.9 + - - -
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Residues in contact with LYS 60 (chain B).
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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7B ASP 5.6 4.4 + - - -
9B SER* 3.4 19.8 + - - -
56B LEU* 3.4 34.1 + - + +
59B GLU* 1.3 84.0 - - + +
61B MET* 1.3 68.5 + - + +
62B ARG* 4.3 9.9 + - - +
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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