Contacts of the helix formed by residues 24 - 33 (chain A) in PDB entry 3HW2
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 GLU 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR 5.6 1.3 - - - +
23A LYS* 1.3 78.2 - - - +
25A ALA* 1.3 69.9 + - - +
26A TRP 3.4 1.3 - - - +
27A TRP* 3.0 12.2 + - + +
28A LYS* 2.8 23.1 + - - +
55A PHE* 3.4 46.1 - - + +
128A TYR* 4.7 2.5 - - - +
833B ALA 5.2 0.2 - - - -
834B ASN* 3.6 8.0 - - - +
835B THR* 2.2 56.7 + - - +
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Residues in contact with ALA 25 (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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23A LYS 3.9 0.6 + - - -
24A GLU* 1.3 78.0 + - - +
26A TRP* 1.3 74.9 + - + +
28A LYS* 3.5 8.0 + - - +
29A VAL* 3.4 22.4 + - - +
859B GLU* 6.1 0.7 - - - +
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Residues in contact with TRP 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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24A GLU 3.4 0.2 - - - -
25A ALA* 1.3 86.6 - - + +
27A TRP* 1.3 59.7 + - - +
29A VAL* 3.6 20.6 - - + +
30A LEU* 2.8 31.7 + - - +
55A PHE* 4.8 0.9 - - - -
123A VAL* 4.6 8.6 - - + +
124A MET* 3.6 29.2 - - + -
126A ASN* 3.3 39.2 + - - +
128A TYR* 3.7 34.0 + + + +
832B ARG* 4.8 2.0 - - - -
859B GLU* 3.7 29.9 + - + +
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Residues in contact with TRP 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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22A THR 5.5 0.7 - - - -
23A LYS* 3.6 29.1 - - + +
24A GLU* 3.0 30.6 + - + +
26A TRP* 1.3 75.5 - - - +
28A LYS* 1.3 54.8 - - - +
30A LEU* 3.1 7.7 + - + +
31A TRP* 2.8 39.1 + - + +
47A ASP* 3.2 48.0 + - - -
48A ARG* 3.6 11.2 - - - -
50A LEU* 4.1 20.3 - - + +
51A HIS* 3.5 35.2 - + + -
55A PHE* 3.5 47.4 - + + -
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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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21A ASN* 3.2 35.6 + - + -
23A LYS* 3.7 27.3 + - + -
24A GLU 2.8 16.5 + - - +
25A ALA* 3.6 11.0 - - - +
27A TRP* 1.3 71.3 - - - +
29A VAL* 1.3 63.5 + - + +
31A TRP* 3.4 6.1 - - - +
32A GLU* 3.0 32.8 + - - +
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Residues in contact with VAL 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 ALA 3.4 14.5 + - - +
26A TRP* 3.6 32.1 - - + +
27A TRP 3.2 0.4 - - - -
28A LYS* 1.3 73.4 - - + +
30A LEU* 1.3 69.1 + - - +
32A GLU* 2.8 22.7 + - - +
33A LYS* 3.4 25.0 + - - +
124A MET* 4.6 10.8 - - + -
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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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26A TRP 2.8 22.4 + - - +
27A TRP* 3.6 6.3 - - + +
29A VAL* 1.3 72.4 - - - +
31A TRP* 1.3 66.3 + - - +
33A LYS* 3.0 13.5 + - - +
34A ILE* 3.4 26.2 + - + +
50A LEU* 4.1 29.2 - - + -
54A LEU* 4.5 13.2 - - + -
55A PHE* 6.2 0.4 - - + -
100A ILE* 6.2 0.2 - - + -
109A LEU* 3.7 37.5 - - + +
110A LEU* 4.7 9.2 - - + +
123A VAL* 4.3 19.7 - - + -
124A MET* 4.0 14.8 - - - -
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Residues in contact with TRP 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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23A LYS* 3.5 24.6 - - + +
27A TRP* 2.8 23.2 + - + +
28A LYS* 3.4 11.7 - - - +
30A LEU* 1.3 71.7 - - - +
32A GLU* 1.3 67.1 + - - +
34A ILE* 2.8 11.6 + - + -
35A LYS* 2.5 52.6 + - + +
38A PHE* 4.3 25.6 - + - -
43A LYS* 3.1 47.5 - - + +
46A ALA* 4.3 0.9 - - + -
47A ASP* 4.0 24.0 - - + -
50A LEU* 3.5 28.9 - - + -
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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 LYS* 3.0 21.2 + - - +
29A VAL* 2.8 14.1 + - - +
31A TRP* 1.3 86.4 - - - +
33A LYS* 1.3 60.7 + - + +
34A ILE 3.4 0.4 - - - -
35A LYS* 2.9 55.9 + - - +
36A ASP* 4.9 0.5 - - - +
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Residues in contact with LYS 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 VAL* 3.7 24.2 - - + +
30A LEU* 3.0 8.2 + - - +
32A GLU* 1.3 81.2 - - + +
34A ILE* 1.3 62.6 + - - +
35A LYS* 5.2 0.4 - - - -
36A ASP* 5.2 1.8 - - - -
37A PHE* 3.8 14.2 - - - -
102A ASP* 4.5 18.3 + - - +
109A LEU* 3.8 34.9 - - + +
124A MET* 4.4 14.2 - - + +
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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