Contacts of the helix formed by residues 27 - 41 (chain A) in PDB entry 6U81
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 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL 4.6 4.5 - - - +
26A TRP* 1.3 75.0 - - - +
28A PRO* 1.3 74.6 - - + +
29A SER* 3.5 8.6 + - - -
30A GLN* 2.9 47.0 + - - +
31A SER* 2.9 24.8 + - - -
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Residues in contact with PRO 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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26A TRP 4.4 1.8 - - - +
27A THR* 1.3 88.7 - - + +
29A SER* 1.3 61.2 + - - +
31A SER* 3.3 6.9 + - - +
32A GLU* 3.1 29.8 + - - +
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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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27A THR* 3.2 10.0 + - - -
28A PRO* 1.3 76.6 - - - +
30A GLN* 1.3 68.2 + - - +
32A GLU* 3.4 12.4 + - - +
33A ALA* 3.2 22.0 + - - +
56A ILE* 5.3 0.4 - - - +
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Residues in contact with GLN 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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24A LEU* 5.9 0.5 - - - +
25A VAL 4.2 2.8 - - - +
26A TRP* 3.7 19.7 - - + -
27A THR* 2.9 53.4 + - - +
29A SER* 1.3 84.4 + - - +
31A SER* 1.3 62.2 + - - +
33A ALA* 3.2 7.3 + - - +
34A LEU* 3.0 28.0 + - - +
56A ILE* 3.1 41.5 + - + +
57A GLY 4.3 1.0 + - - -
58A ILE* 3.2 31.4 - - - +
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Residues in contact with SER 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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26A TRP* 3.2 20.7 + - - +
27A THR 2.9 16.6 + - - -
28A PRO* 3.7 7.6 - - - +
30A GLN* 1.3 77.1 - - - +
32A GLU* 1.3 57.9 + - - +
34A LEU* 3.7 11.8 - - - +
35A ARG* 3.0 49.9 + - - +
66A TRP* 6.2 0.2 - - - -
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Residues in contact with GLU 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 PRO* 3.1 18.3 + - - +
29A SER* 3.7 12.7 - - - +
30A GLN 3.2 0.2 - - - -
31A SER* 1.3 77.3 - - - +
33A ALA* 1.3 56.6 + - - +
35A ARG* 3.4 28.9 + - - +
36A ALA* 2.8 32.5 + - - +
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Residues in contact with ALA 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 3.2 12.4 + - - +
30A GLN 3.2 4.5 + - - +
32A GLU* 1.3 76.7 - - - +
34A LEU* 1.3 62.5 + - - +
36A ALA* 3.8 4.7 - - - +
37A CYS* 3.0 26.2 + - - +
52A LEU* 4.0 11.2 - - + +
56A ILE* 3.6 31.0 - - + -
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Residues in contact with LEU 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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26A TRP* 3.8 41.1 - - + -
30A GLN 3.0 19.7 + - - +
31A SER* 3.7 9.6 - - - +
33A ALA* 1.3 73.6 - - - +
35A ARG* 1.3 65.9 + - - +
37A CYS* 3.8 1.6 - - - +
38A PHE* 2.9 24.6 + - - +
52A LEU* 3.8 24.2 - - + -
56A ILE* 4.0 13.5 - - + -
63A VAL* 4.6 13.0 - - + -
66A TRP* 3.4 48.9 - - + +
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Residues in contact with ARG 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 SER* 3.0 41.6 + - - +
32A GLU* 3.4 31.2 + - - +
34A LEU* 1.3 75.4 - - - +
36A ALA* 1.3 64.1 + - - +
38A PHE* 3.1 4.7 + - - +
39A GLU* 2.9 37.1 + - - +
66A TRP* 4.1 15.9 - - + -
70A GLU* 6.0 2.2 - - - +
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Residues in contact with ALA 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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32A GLU 2.8 21.5 + - - +
33A ALA* 3.8 7.0 - - - +
35A ARG* 1.3 73.2 - - - +
37A CYS* 1.3 63.1 + - - +
39A GLU* 3.0 13.2 + - - +
40A ARG* 3.0 22.2 + - - +
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Residues in contact with CYS 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 ALA 3.0 18.3 + - - +
34A LEU 3.9 2.5 - - - +
36A ALA* 1.3 76.2 - - - +
38A PHE* 1.3 57.5 + - - +
40A ARG* 3.5 17.5 - - - +
41A ASN* 3.0 32.8 + - - +
44A PRO* 5.1 0.2 - - - -
48A THR* 4.0 26.7 - - - -
52A LEU* 4.0 25.1 - - + -
67A PHE* 3.9 16.8 - - + -
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Residues in contact with PHE 38 (chain A).
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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34A LEU 2.9 18.3 + - - +
35A ARG* 3.1 6.7 + - - +
37A CYS* 1.3 75.4 - - - +
39A GLU* 1.3 68.5 + - + +
42A PRO* 3.2 45.7 - - + +
66A TRP* 3.8 10.3 - + + -
67A PHE* 3.6 27.8 - + - -
70A GLU* 3.5 25.6 - - + -
71A ARG* 3.7 25.4 - - + -
74A GLN* 3.8 38.6 - - + -
85A TRP* 4.2 9.4 - + - -
89A ARG* 4.0 1.2 + - - -
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Residues in contact with GLU 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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35A ARG* 2.9 28.6 + - - +
36A ALA* 3.6 9.2 - - - +
38A PHE* 1.3 80.2 - - + +
40A ARG* 1.3 59.9 + - - +
89A ARG* 2.7 27.2 + - - +
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Residues in contact with ARG 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 ALA 3.0 12.3 + - - +
37A CYS* 3.5 18.7 - - - +
38A PHE 3.3 0.2 - - - -
39A GLU* 1.3 80.9 - - - +
41A ASN* 1.3 66.7 + - - +
48A THR* 4.4 13.6 + - - +
51A ARG* 4.2 22.4 - - - +
89A ARG* 3.7 12.3 + - - +
93A GLU* 5.4 4.4 + - - -
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Residues in contact with ASN 41 (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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37A CYS* 3.0 17.9 + - - +
38A PHE 3.4 2.9 - - - -
40A ARG* 1.3 84.6 - - + +
42A PRO* 1.3 72.2 - - - +
43A TYR* 2.8 42.9 + - - +
44A PRO* 3.3 15.9 - - + +
48A THR* 6.3 1.8 - - + -
67A PHE* 3.7 3.3 - - - -
88A ARG* 5.2 2.2 - - - +
89A ARG* 3.5 25.0 + - - +
93A GLU* 3.4 25.3 + - - +
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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