Contacts of the helix formed by residues 26 - 35 (chain A) in PDB entry 1U1L
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLU 3.5 5.3 + - - +
25A THR* 1.3 74.7 - - - +
27A ASP* 1.3 73.9 + - - +
28A GLU* 3.5 13.8 + - + +
29A SER* 2.6 35.0 + - - +
30A LEU* 2.8 23.2 + - - +
45A VAL* 3.4 8.7 - - - -
47A ARG* 3.4 19.3 + - - +
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Residues in contact with ASP 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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26A THR* 1.3 80.1 + - - +
28A GLU* 1.3 62.4 + - + +
30A LEU* 3.5 2.2 + - - -
31A ARG* 2.9 31.8 + - - +
43A CYS* 3.6 17.0 - - + +
44A VAL* 3.9 14.9 - - - +
45A VAL* 2.8 36.9 + - - +
47A ARG* 3.9 11.0 + - - -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.1 12.2 - - + +
27A ASP* 1.3 79.2 - - + +
29A SER* 1.3 61.3 + - - +
31A ARG* 3.5 21.2 + - - +
32A SER* 2.9 30.2 + - - -
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Residues in contact with SER 29 (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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24A GLU 4.2 1.4 + - - -
25A THR* 3.4 0.7 - - - -
26A THR* 2.6 40.1 + - - +
28A GLU* 1.3 75.2 - - - +
30A LEU* 1.3 65.3 + - - +
32A SER* 3.5 8.4 + - - -
33A HIS* 3.3 19.6 + - - +
79A VAL* 4.4 3.7 - - - +
80A ASP* 2.9 32.8 + - - -
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Residues in contact with LEU 30 (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 ILE* 4.4 3.6 - - + -
21A LEU* 4.0 30.3 - - + -
25A THR* 4.1 10.3 - - + -
26A THR 2.8 16.2 + - - +
27A ASP 3.7 3.6 - - - +
29A SER* 1.3 77.8 + - - +
31A ARG* 1.3 63.3 + - - +
33A HIS* 3.1 11.3 + - - +
34A PHE* 3.2 45.1 + - + -
43A CYS* 3.8 17.0 - - - -
44A VAL 3.9 21.1 - - - +
45A VAL* 4.2 11.0 - - + -
58A GLY* 4.6 0.9 - - - -
59A PHE 4.4 6.1 - - - +
60A VAL* 3.8 13.5 - - + -
79A VAL* 4.4 7.6 - - + -
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Residues in contact with ARG 31 (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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27A ASP 2.9 19.0 + - - +
28A GLU* 3.7 19.2 + - - +
30A LEU* 1.3 77.1 - - - +
32A SER* 1.3 64.5 + - - +
35A GLU* 2.8 73.1 + - + +
40A LEU* 3.2 45.1 + - + +
41A THR 4.8 1.0 - - - -
42A ASP* 4.3 5.1 - - - +
43A CYS* 3.3 36.0 + - - +
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Residues in contact with SER 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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28A GLU 2.9 19.4 + - - -
29A SER* 3.7 10.3 - - - -
30A LEU 3.3 0.2 - - - -
31A ARG* 1.3 76.4 - - - +
33A HIS* 1.3 59.4 + - - +
35A GLU* 4.4 11.3 + - - +
36A GLN* 4.1 11.8 - - - +
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Residues in contact with HIS 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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29A SER 3.3 9.4 + - - +
30A LEU 3.1 7.9 + - - +
31A ARG 3.1 0.8 - - - -
32A SER* 1.3 78.3 - - - +
34A PHE* 1.3 77.9 + + - +
35A GLU 3.3 0.2 - - - -
36A GLN* 2.9 37.6 + - - +
37A TRP* 3.1 29.1 - + - -
77A HIS* 2.9 28.0 + - - +
78A LYS 3.5 27.6 + - - -
79A VAL* 3.7 26.6 - - + +
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Residues in contact with PHE 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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16A LEU* 5.5 1.6 - - + -
18A ILE* 3.7 34.3 - - + -
30A LEU* 3.2 40.6 + - + +
33A HIS* 1.3 91.0 - + - +
35A GLU* 1.3 58.1 + - - +
36A GLN 2.9 10.0 + - - -
37A TRP* 3.1 16.1 + + - -
40A LEU* 4.3 5.6 - - + -
60A VAL* 3.6 26.7 - - + -
62A TYR* 2.7 44.2 + + + +
71A ALA* 4.8 4.5 - - + -
77A HIS* 3.7 36.1 - + + -
79A VAL* 4.2 7.0 - - + -
84A VAL* 4.5 1.3 - - + -
86A PRO* 4.6 2.7 - - + -
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Residues in contact with GLU 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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31A ARG* 2.8 69.7 + - + +
32A SER* 4.6 8.5 - - - +
33A HIS 3.3 0.6 - - - -
34A PHE* 1.3 72.7 - - - +
36A GLN* 1.3 59.8 + - - +
37A TRP 3.0 6.3 + - - -
38A GLY 3.2 23.8 + - - +
39A THR* 5.9 0.4 - - - -
40A LEU* 3.7 15.5 + - + +
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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