Contacts of the helix formed by residues 16 - 27 (chain A) in PDB entry 1UCP
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 THR 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASN 4.6 7.0 - - - +
15A LEU* 1.3 76.1 - - - +
17A ALA* 1.3 54.8 + - - +
18A GLU* 3.7 7.8 + - - +
19A GLU* 3.3 29.2 + - + +
20A LEU* 2.7 37.1 + - - +
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Residues in contact with ALA 17 (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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16A THR* 1.3 73.7 - - - +
18A GLU* 1.3 57.2 + - - +
20A LEU* 3.6 5.5 + - - +
21A LYS* 3.0 32.0 + - - +
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Residues in contact with GLU 18 (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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16A THR* 3.3 8.1 + - - +
17A ALA* 1.3 76.0 - - - +
19A GLU* 1.3 71.3 + - + +
21A LYS* 3.3 14.0 + - + +
22A LYS* 3.1 34.5 + - + +
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Residues in contact with GLU 19 (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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15A LEU* 4.0 22.5 - - + +
16A THR* 3.3 31.0 + - + +
18A GLU* 1.3 81.3 - - + +
20A LEU* 1.3 51.8 + - - +
22A LYS* 3.3 2.5 + - - +
23A PHE* 2.7 34.6 + - - +
76A MET* 3.1 26.5 - - + +
78A LEU* 5.0 11.8 - - - +
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Residues in contact with LEU 20 (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 LEU* 3.3 46.4 - - + +
15A LEU* 3.5 30.3 - - + +
16A THR 2.7 24.9 + - - +
17A ALA* 4.0 5.6 - - - +
19A GLU* 1.3 69.8 - - - +
21A LYS* 1.3 57.6 + - - +
23A PHE* 4.0 5.8 - - + -
24A LYS* 2.9 56.6 + - - +
48A ASP* 6.1 1.3 - - - -
49A ALA* 5.6 8.1 - - + +
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Residues in contact with LYS 21 (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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17A ALA* 3.0 17.5 + - - +
18A GLU* 3.3 17.3 + - + +
20A LEU* 1.3 76.4 - - - +
22A LYS* 1.3 68.0 + - + +
24A LYS* 3.3 7.5 + - - +
25A LEU* 3.1 38.5 + - + +
45A LEU* 5.1 13.3 - - + +
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Residues in contact with LYS 22 (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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18A GLU* 3.1 23.3 + - + +
19A GLU* 4.7 1.6 - - - +
21A LYS* 1.3 83.8 - - + +
23A PHE* 1.3 49.8 + - - +
25A LEU* 3.2 16.9 + - + +
26A LYS* 2.8 46.8 + - + +
76A MET* 3.4 25.8 - - + -
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Residues in contact with PHE 23 (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 LEU* 3.6 35.7 - - + -
15A LEU* 4.2 7.9 - - + -
19A GLU 2.7 22.2 + - - +
20A LEU* 3.6 10.1 - - + +
22A LYS* 1.3 71.2 - - - +
24A LYS* 1.3 57.2 + - + +
26A LYS* 3.0 2.1 + - - +
27A LEU* 2.8 69.4 + - + +
52A LEU* 3.9 8.7 - - + -
68A LEU* 5.2 0.2 - - + -
69A THR* 4.0 24.7 - - + -
72A VAL* 3.8 26.9 - - + -
73A LEU* 3.6 31.9 - - + -
76A MET* 3.2 13.3 - - + -
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Residues in contact with LYS 24 (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 LEU* 5.9 2.0 - - - -
20A LEU* 2.9 46.4 + - + +
21A LYS 3.6 3.8 - - - +
23A PHE* 1.3 78.1 - - + +
25A LEU* 1.3 61.3 + - - +
27A LEU* 3.8 7.3 - - + +
28A LEU 4.1 1.6 + - - -
41A ARG* 3.9 9.7 - - - +
44A LEU* 3.0 56.5 + - + +
45A LEU* 3.7 36.9 + - + +
47A MET 2.8 27.7 + - - -
48A ASP* 4.4 8.8 - - - +
52A LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 25 (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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21A LYS* 3.1 36.6 + - + +
22A LYS* 3.5 16.6 - - + +
24A LYS* 1.3 75.5 - - - +
26A LYS* 1.3 58.6 + - + +
28A LEU* 2.9 10.9 + - - +
29A SER* 2.9 27.6 + - - -
41A ARG* 3.7 30.5 - - + -
45A LEU* 5.6 1.3 - - + -
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Residues in contact with LYS 26 (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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22A LYS* 2.8 35.1 + - + +
23A PHE* 3.5 6.3 - - - +
25A LEU* 1.3 67.3 - - + +
27A LEU* 1.3 56.8 + - - +
28A LEU 3.0 4.7 + - - -
29A SER* 2.9 30.7 + - - +
30A VAL* 3.2 19.8 + - - +
72A VAL* 3.6 15.7 - - + -
75A ASP* 2.7 49.2 + - + +
76A MET* 3.7 24.0 - - + +
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Residues in contact with LEU 27 (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 PHE* 2.8 53.3 + - + +
24A LYS* 4.1 4.3 - - + -
26A LYS* 1.3 69.9 - - - +
28A LEU* 1.3 58.2 + - - +
29A SER 3.7 0.2 - - - -
30A VAL* 4.6 6.3 - - - +
32A LEU* 5.9 3.6 - - - +
38A ARG* 5.4 6.1 - - - +
39A ILE 4.8 4.2 + - - +
44A LEU* 3.4 31.0 - - + -
52A LEU* 3.5 30.1 - - + -
56A LEU* 4.8 5.2 - - + -
60A TYR* 5.4 3.6 + - - -
68A LEU* 3.4 35.8 - - + +
72A VAL* 3.5 9.4 - - + +
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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
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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