Contacts of the helix formed by residues 31 - 40 (chain A) in PDB entry 1UI5
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU 5.9 0.4 - - - +
29A SER 4.0 10.1 - - - +
30A THR* 1.3 76.6 - - - +
32A LEU* 1.3 64.6 + - - +
33A SER* 3.6 9.9 + - - -
34A GLU* 3.2 35.9 + - - +
35A ILE* 3.1 29.0 + - - +
53A LYS* 4.6 4.7 - - - +
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Residues in contact with LEU 32 (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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31A THR* 1.3 73.4 - - - +
33A SER* 1.3 57.5 + - - +
35A ILE* 3.4 6.1 + - + +
36A VAL* 3.0 34.0 + - - +
43A LYS* 4.0 15.7 - - - +
46A LEU* 4.2 16.3 - - + +
47A TYR* 4.1 31.4 - - + +
51A ALA 5.0 0.2 - - - +
52A ALA* 4.7 6.5 - - - -
53A LYS* 4.0 34.4 - - + +
56A LEU* 4.0 26.7 - - + -
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Residues in contact with SER 33 (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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31A THR* 3.2 9.2 + - - -
32A LEU* 1.3 76.2 - - - +
34A GLU* 1.3 65.1 + - - +
36A VAL* 3.6 6.2 + - - +
37A ALA* 3.0 26.0 + - - +
43A LYS* 3.8 19.9 + - - +
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Residues in contact with GLU 34 (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 LEU* 4.0 19.9 - - + +
25A ARG* 6.1 0.7 - - - +
29A SER 3.7 9.9 - - - +
30A THR* 3.3 25.6 + - - +
31A THR* 3.2 27.3 + - - +
33A SER* 1.3 77.9 - - - +
35A ILE* 1.3 62.9 + - - +
37A ALA* 3.1 6.3 + - - +
38A HIS* 2.9 24.4 + - - +
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Residues in contact with ILE 35 (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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14A ILE* 4.1 32.8 - - + +
17A ALA* 3.9 1.4 - - + +
18A ALA* 4.1 21.1 - - + +
21A LEU* 3.7 13.5 - - + -
22A PHE* 4.2 7.9 - - + -
30A THR* 3.7 23.1 - - + -
31A THR 3.1 22.0 + - - +
32A LEU* 3.7 12.3 - - + +
33A SER 3.3 0.2 - - - -
34A GLU* 1.3 76.1 - - - +
36A VAL* 1.3 59.1 + - + +
38A HIS* 3.4 1.6 + - - +
39A ALA* 2.9 28.5 + - + +
46A LEU* 4.4 8.5 - - + -
53A LYS* 5.0 2.7 - - + -
56A LEU* 4.0 21.8 - - + -
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Residues in contact with VAL 36 (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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14A ILE* 6.1 0.7 - - + -
32A LEU 3.0 21.1 + - - +
33A SER* 4.0 6.1 - - - +
35A ILE* 1.3 75.7 - - - +
37A ALA* 1.3 59.8 + - + +
39A ALA* 3.6 0.6 + - - -
40A GLY* 3.0 21.3 + - - -
41A VAL* 3.1 36.5 + - + +
42A THR* 3.8 23.1 - - - +
43A LYS* 4.0 19.5 - - + +
46A LEU* 3.8 26.7 - - + -
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Residues in contact with ALA 37 (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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33A SER 3.0 18.1 + - - +
34A GLU* 3.7 4.7 - - - +
36A VAL* 1.3 76.9 - - + +
38A HIS* 1.3 66.7 + - - +
40A GLY* 3.3 11.8 + - - -
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Residues in contact with HIS 38 (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* 3.7 22.8 - - + -
20A ASP* 3.1 36.5 + - + +
21A LEU* 4.1 22.2 - - + +
24A ARG* 4.6 3.9 + - - -
34A GLU 2.9 16.0 + - - +
35A ILE 3.7 4.0 - - - +
37A ALA* 1.3 78.4 - - - +
39A ALA* 1.3 63.7 + - - +
40A GLY* 3.3 1.4 + - - -
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Residues in contact with ALA 39 (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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13A THR* 3.9 31.4 - - + +
14A ILE* 4.4 9.4 - - + -
17A ALA* 3.8 17.5 - - + -
35A ILE 2.9 18.3 + - - +
36A VAL 4.1 2.5 - - - +
38A HIS* 1.3 77.1 - - - +
40A GLY* 1.3 61.4 + - - +
41A VAL* 3.4 18.8 + - + +
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Residues in contact with GLY 40 (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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36A VAL 3.0 7.6 + - - -
37A ALA* 3.3 8.4 + - - -
38A HIS 3.2 5.5 + - - -
39A ALA* 1.3 79.1 - - - +
41A VAL* 1.3 62.8 + - - +
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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