Contacts of the helix formed by residues 26 - 38 (chain A) in PDB entry 1HF0
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 4.2 3.4 - - - +
25A PHE* 1.3 78.0 - - - +
27A GLN* 1.3 64.4 + - - +
28A GLY* 2.8 6.0 + - - -
29A ASP* 2.8 48.2 + - - +
30A VAL* 3.0 11.8 + - - +
104B LYS* 3.9 19.7 - - - -
105B ARG 5.7 0.7 - - - +
107B SER* 6.1 1.8 - - - -
9M A 3.9 31.0 - - - +
10M A 3.2 14.1 - - - -
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Residues in contact with GLN 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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17A LYS* 5.7 0.8 - - - +
20A ARG* 2.9 26.5 - - - +
26A THR* 1.3 70.3 - - - +
28A GLY* 1.3 60.6 + - - +
30A VAL* 3.8 1.0 - - - +
31A GLY* 3.2 18.2 + - - -
44A GLN* 4.0 18.9 - - + +
47A ILE* 3.7 32.0 - - + +
48A SER* 3.1 26.1 - - - +
51A GLU* 3.0 21.6 + - - +
10M A 2.9 45.1 + - - +
11M A 2.8 23.0 + - - -
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Residues in contact with GLY 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 THR* 2.8 8.1 + - - -
27A GLN* 1.3 77.5 - - - +
29A ASP* 1.3 64.1 + - - -
30A VAL 3.0 1.0 + - - -
31A GLY* 3.1 4.0 + - - -
32A LEU* 3.0 23.4 + - - +
44A GLN* 4.1 21.1 - - - +
10M A 4.5 0.4 + - - -
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Residues in contact with ASP 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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25A PHE* 3.9 23.3 - - + -
26A THR* 2.8 39.9 + - - +
28A GLY* 1.3 69.5 - - - -
30A VAL* 1.3 64.7 + - - +
32A LEU* 3.5 5.5 + - - +
33A ALA* 3.1 22.7 + - - +
104B LYS* 3.0 28.8 + - - -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 4.4 4.5 - - + -
20A ARG* 3.9 20.2 - - + -
25A PHE* 4.1 3.8 - - + -
26A THR 3.0 14.5 + - - +
27A GLN* 3.8 8.7 - - - +
29A ASP* 1.3 72.3 - - - +
31A GLY* 1.3 53.9 + - - +
32A LEU 2.6 16.6 + - - -
33A ALA* 2.9 3.2 + - - +
34A MET* 2.7 45.6 + - + +
47A ILE* 4.2 14.8 - - + -
67A LEU* 4.3 6.1 - - + -
70A TRP* 3.4 47.8 - - + -
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN 3.2 8.8 + - - -
28A GLY 3.1 7.0 + - - -
30A VAL* 1.3 78.9 - - - +
32A LEU* 1.3 58.9 + - - +
34A MET* 3.6 13.4 - - - +
35A GLY 3.7 2.6 + - - -
41A ASP* 4.3 3.1 - - - +
42A PHE* 3.0 41.9 + - - +
43A SER 5.1 1.3 - - - -
44A GLN 5.4 0.2 - - - -
47A ILE* 4.0 12.8 - - - +
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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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28A GLY 3.0 14.8 + - - +
29A ASP* 3.8 6.3 - - - +
30A VAL 2.6 6.5 + - - -
31A GLY* 1.3 72.1 - - - +
33A ALA* 1.3 67.4 + - + +
34A MET 3.0 1.1 - - - -
35A GLY* 3.1 11.4 + - - -
36A LYS* 3.3 45.4 + - + +
41A ASP* 5.6 1.8 - - - -
32B LEU* 4.3 30.7 - - + -
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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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25A PHE* 5.3 8.1 - - + -
29A ASP 3.1 16.3 + - - +
30A VAL 2.9 2.9 + - - +
32A LEU* 1.3 78.2 - - + +
34A MET* 1.3 55.9 + - - +
36A LYS* 3.7 8.3 - - - +
37A LEU* 2.7 41.2 + - + +
70A TRP* 4.2 17.5 - - + +
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Residues in contact with MET 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 VAL* 2.7 36.9 + - + +
31A GLY* 3.6 13.0 - - - +
33A ALA* 1.3 79.2 - - - +
35A GLY* 1.3 56.6 + - - +
37A LEU* 4.8 1.6 - - - -
38A TYR* 3.1 40.6 + - + +
40A ASN* 4.3 3.9 + - + +
41A ASP 5.1 0.4 - - - -
42A PHE* 3.8 29.6 - - + -
47A ILE* 4.9 2.2 - - + -
63A LEU* 4.7 4.5 - - + -
66A LEU* 3.8 27.4 - - + +
67A LEU* 3.6 21.8 - - + -
70A TRP* 3.8 30.7 - - + -
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Residues in contact with GLY 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 GLY 3.7 2.8 + - - -
32A LEU 3.1 10.4 + - - -
34A MET* 1.3 79.9 - - - +
36A LYS* 1.3 60.1 + - - +
39A GLY* 2.9 29.3 + - - +
40A ASN 3.3 24.1 - - - +
41A ASP* 4.0 9.6 - - - +
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Residues in contact with LYS 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 LEU* 3.3 38.8 - - + +
33A ALA* 3.2 8.2 + - - +
35A GLY* 1.3 76.0 - - - +
37A LEU* 1.3 58.8 + - - +
38A TYR 3.0 9.0 + - - -
39A GLY* 3.5 6.9 + - - -
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Residues in contact with LEU 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* 2.7 24.9 + - + +
34A MET* 4.6 1.6 - - - +
36A LYS* 1.3 72.8 - - - +
38A TYR* 1.3 58.5 + - + +
70A TRP* 4.6 16.8 - - + -
73A ASP* 6.2 5.4 - - + -
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Residues in contact with TYR 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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34A MET* 3.1 25.6 + - + +
36A LYS 3.0 0.4 - - - -
37A LEU* 1.3 78.7 - - + +
39A GLY* 1.3 54.6 + - - +
40A ASN* 2.7 23.4 + - + +
66A LEU* 5.7 8.7 - - + +
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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