Contacts of the helix formed by residues 26 - 35 (chain A) in PDB entry 3F6W
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* 3.7 5.8 - - - +
25A ILE* 1.3 80.6 - - - +
27A GLN* 1.3 65.0 + - - +
28A LYS* 3.7 8.6 + - - +
29A GLU* 3.0 25.5 + - - +
30A LEU* 2.9 20.1 + - - +
2C LYS* 3.4 34.1 - - + +
49D ARG* 5.9 3.4 - - - +
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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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20A ARG* 3.6 24.8 - - - +
26A THR* 1.3 72.7 - - - +
28A LYS* 1.3 57.6 + - - +
30A LEU* 3.1 3.7 + - - +
31A ALA* 2.8 31.0 + - - +
38A GLN* 3.3 29.8 + - + +
41A VAL* 3.8 19.8 - - + +
42A SER* 3.5 30.2 + - - +
45A GLU* 2.8 27.1 + - - +
46A ASN* 5.2 3.2 + - - -
43D LYS* 5.0 12.7 + - - +
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Residues in contact with LYS 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* 3.3 8.4 - - - +
27A GLN* 1.3 77.9 - - - +
29A GLU* 1.3 57.1 + - - +
31A ALA* 3.4 2.6 + - - +
32A ALA* 3.0 27.0 + - + +
38A GLN* 3.7 31.8 - - + +
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Residues in contact with GLU 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 ILE* 3.5 20.6 - - + -
26A THR* 3.0 24.9 + - - +
28A LYS* 1.3 75.3 - - - +
30A LEU* 1.3 64.3 + - - +
32A ALA* 3.3 10.7 + - - +
33A ARG* 3.1 52.0 + - - +
-1C ASN* 4.6 15.8 - - - +
2C LYS* 6.4 0.4 - - + -
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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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20A ARG* 3.9 13.2 - - - -
25A ILE* 3.7 9.3 - - + +
26A THR 2.9 14.4 + - - +
27A GLN 3.6 7.4 - - - +
29A GLU* 1.3 75.4 - - - +
31A ALA* 1.3 63.8 + - - +
33A ARG* 3.1 6.0 + - + +
34A LEU* 3.0 37.0 + - + +
41A VAL* 4.0 11.0 - - + -
59A PHE* 3.5 46.7 - - + +
62A GLY* 3.8 37.2 - - - +
63A ILE* 3.8 14.1 - - + -
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Residues in contact with ALA 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 GLN 2.8 16.1 + - - +
28A LYS 3.7 4.5 - - - +
30A LEU* 1.3 77.7 - - - +
32A ALA* 1.3 57.4 + - - +
34A LEU* 3.0 6.8 + - - -
35A GLY 2.8 24.8 + - - -
36A ARG* 3.0 29.2 + - - +
37A PRO 3.6 13.7 - - - +
38A GLN* 3.6 15.5 - - + +
41A VAL* 3.8 12.1 - - + +
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Residues in contact with ALA 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 LYS* 3.0 14.2 + - + +
29A GLU* 3.6 16.4 - - - +
30A LEU 3.3 0.2 - - - -
31A ALA* 1.3 74.3 - - - +
33A ARG* 1.3 64.9 + - + +
35A GLY* 3.0 14.1 + - - +
36A ARG 4.9 0.9 - - - -
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Residues in contact with ARG 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 ILE* 3.3 30.1 - - - +
29A GLU* 3.1 42.8 + - - +
30A LEU* 3.1 10.3 + - - +
32A ALA* 1.3 77.4 - - + +
34A LEU* 1.3 61.9 + - - +
35A GLY 3.4 0.3 + - - -
61A ARG 5.4 0.6 + - - -
62A GLY* 2.9 39.7 + - - +
63A ILE* 4.7 2.4 - - - +
64A GLY* 5.9 0.2 - - - -
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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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30A LEU* 3.0 38.9 + - + +
31A ALA* 3.0 7.4 + - - +
33A ARG* 1.3 78.3 - - - +
35A GLY* 1.3 63.2 + - - +
36A ARG* 3.9 21.5 + - + +
40A PHE* 3.7 33.7 - - + -
41A VAL* 4.2 6.1 - - + -
58A ASP* 3.4 39.7 - - + +
59A PHE* 4.2 12.1 - - + +
62A GLY* 4.6 4.0 - - - -
1B THR* 4.0 12.5 - - - +
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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 ALA 2.8 5.0 + - - -
32A ALA* 3.0 13.0 + - - -
33A ARG 3.2 1.0 + - - -
34A LEU* 1.3 80.3 - - - +
36A ARG* 1.3 61.5 + - - +
-1B ASN* 4.9 6.4 + - - +
1B THR* 3.8 21.0 + - - +
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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