Contacts of the helix formed by residues 25 - 36 (chain A) in PDB entry 5UFL
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 ASN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A THR* 5.1 5.3 - - - +
16A GLN* 3.7 24.2 + - - +
17A TYR* 4.1 29.7 + - + +
24A ALA* 1.3 79.8 - - - +
26A ALA* 1.3 62.8 + - - +
28A GLN* 4.6 1.9 - - - +
29A LEU* 3.3 23.9 + - - +
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Residues in contact with ALA 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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17A TYR* 4.5 7.7 - - + -
24A ALA 4.4 1.9 - - - +
25A ASN* 1.3 79.2 - - - +
27A THR* 1.3 58.9 + - - +
29A LEU* 3.6 2.3 + - - +
30A LEU* 3.0 39.8 + - + +
72A LEU* 4.3 26.2 - - + +
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Residues in contact with THR 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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24A ALA* 3.6 19.9 + - - -
25A ASN 3.4 0.6 - - - -
26A ALA* 1.3 76.0 - - - +
28A GLN* 1.3 60.8 + - - +
30A LEU* 3.1 12.6 + - + +
31A ARG* 2.9 65.8 + - + +
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Residues in contact with GLN 28 (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* 4.5 17.6 - - + +
16A GLN* 5.8 0.3 - - - +
24A ALA* 3.1 34.9 + - - +
25A ASN* 4.6 2.5 - - - +
27A THR* 1.3 78.9 - - - +
29A LEU* 1.3 57.7 + - - +
31A ARG* 3.5 22.7 + - - +
32A HIS* 2.7 41.6 + - + +
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Residues in contact with LEU 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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10A LEU* 4.5 3.6 - - + +
13A THR* 3.6 20.9 - - - +
14A VAL* 3.5 29.8 - - + +
17A TYR* 4.4 20.4 - - + -
25A ASN 3.3 16.5 + - - +
26A ALA 3.7 2.9 - - - +
27A THR 3.2 0.4 - - - -
28A GLN* 1.3 78.5 - - - +
30A LEU* 1.3 62.7 + - - +
32A HIS* 3.4 2.9 + - - +
33A LEU* 3.1 47.9 + - + +
59A LEU* 5.5 1.6 - - + -
62A LEU* 4.3 22.0 - - + -
72A LEU* 3.7 22.7 - - + -
76A ILE* 6.3 1.1 - - + -
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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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26A ALA* 3.0 33.7 + - + +
27A THR* 3.5 9.9 - - + +
29A LEU* 1.3 75.0 - - - +
31A ARG* 1.3 52.1 + - + +
33A LEU* 3.4 6.9 + - + +
34A GLU* 2.8 38.1 + - - +
71A SER* 3.7 33.4 - - - +
72A LEU* 4.4 11.9 - - + -
75A SER* 3.5 33.0 - - - +
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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 THR* 2.9 48.0 + - + +
28A GLN* 3.8 22.7 - - - +
29A LEU 3.3 0.2 - - - -
30A LEU* 1.3 76.4 - - + +
32A HIS* 1.3 64.7 + - + +
34A GLU* 3.4 13.2 + - - +
35A VAL* 3.1 26.7 + - - +
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Residues in contact with HIS 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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6A CYS* 4.9 5.4 - - + +
9A SER* 3.1 35.9 + - - +
10A LEU* 4.0 24.2 - - + +
13A THR* 3.9 22.2 - - + +
28A GLN* 2.7 32.6 + - + +
29A LEU* 3.4 5.4 + - - +
31A ARG* 1.3 78.9 - - + +
33A LEU* 1.3 59.7 + - - +
35A VAL* 3.6 17.2 - - + +
36A ILE* 3.1 20.6 - - - +
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Residues in contact with LEU 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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10A LEU* 5.1 13.9 - - + -
29A LEU* 3.1 42.8 + - + +
30A LEU* 3.7 8.5 - - + +
32A HIS* 1.3 77.5 - - + +
34A GLU* 1.3 64.1 + - - +
36A ILE* 3.6 14.6 - - + +
37A SER* 4.0 0.7 - - - -
59A LEU* 4.4 22.0 - - + -
72A LEU* 5.4 1.6 - - + -
75A SER* 3.9 24.2 - - - +
76A ILE* 3.9 17.9 - - + +
79A LEU* 3.4 45.0 - - + +
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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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30A LEU* 2.8 21.9 + - - +
31A ARG* 3.4 13.6 + - - +
33A LEU* 1.3 74.5 - - - +
35A VAL* 1.3 61.8 + - - +
37A SER* 3.5 17.5 - - - -
79A LEU* 5.6 0.9 - - - -
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Residues in contact with VAL 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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6A CYS* 5.0 13.2 - - + -
31A ARG 3.1 16.0 + - - +
32A HIS* 3.6 20.4 - - + +
34A GLU* 1.3 76.4 - - - +
36A ILE* 1.3 62.4 + - + +
37A SER 2.9 11.9 + - - +
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Residues in contact with ILE 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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6A CYS* 3.7 28.7 - - - -
7A LEU 4.6 2.5 - - - +
10A LEU* 4.5 17.9 - - + -
32A HIS 3.1 22.9 - - - +
33A LEU* 3.6 11.2 - - - +
34A GLU 3.4 0.2 - - - -
35A VAL* 1.3 76.8 - - + +
37A SER* 1.3 61.3 + - - +
43A ARG 4.6 5.3 + - - -
44A LEU* 3.7 35.2 - - + +
45A PHE* 3.8 32.0 - - + -
79A LEU* 3.7 21.6 - - + +
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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