Contacts of the helix formed by residues 24 - 36 (chain A) in PDB entry 1ZDR
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 LEU 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 TRP* 4.0 15.3 - - + -
23A HIS* 1.3 78.3 - - - +
25A PRO* 1.3 69.7 - - - +
26A ALA 3.1 1.8 - - - -
27A ASP* 2.8 27.8 + - + +
28A LEU* 3.1 16.0 + - - +
115A THR* 5.0 1.1 - - + -
117A ILE* 3.8 34.5 - - + -
149A ASN* 3.5 40.8 - - + +
150A PRO 4.2 1.6 - - - -
151A TYR* 4.6 14.4 - - + +
153A HIS* 4.0 30.1 - - + +
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Residues in contact with PRO 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 HIS* 3.7 24.9 - - + +
24A LEU* 1.3 87.2 - - - +
26A ALA* 1.3 62.2 + - - +
28A LEU* 3.1 13.7 + - + +
29A ALA* 2.8 25.9 + - - +
148A LYS* 3.0 39.9 - - + +
149A ASN* 3.1 9.4 - - - +
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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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24A LEU* 5.5 0.2 - - + -
25A PRO* 1.3 73.7 - - - +
27A ASP* 1.3 56.6 + - - +
29A ALA* 3.4 6.2 + - - +
30A TYR* 3.1 27.2 + - - +
33A ARG* 4.8 2.6 + - - -
144A GLY 5.3 2.2 - - - +
149A ASN* 2.7 34.7 + - - +
153A HIS* 4.1 19.3 - - + +
155A PHE* 4.1 8.5 - - + -
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Residues in contact with ASP 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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6A VAL 5.8 0.2 - - - -
7A ALA* 3.3 22.4 - - + +
20A LEU* 6.1 0.7 - - - +
22A TRP* 5.1 3.4 + - - +
24A LEU* 2.8 25.1 + - + +
26A ALA* 1.3 76.4 - - - +
28A LEU* 1.3 68.2 + - + +
30A TYR* 3.6 5.4 - - - +
31A PHE* 2.9 32.3 + - - +
115A THR* 2.7 41.5 + - + +
155A PHE* 3.9 11.2 - - + -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 5.0 16.6 - - + -
23A HIS* 3.8 31.4 - - + +
24A LEU 3.1 11.4 + - - +
25A PRO* 3.1 16.2 + - + +
27A ASP* 1.3 83.6 - - - +
29A ALA* 1.3 62.8 + - - +
31A PHE* 3.5 8.3 + - + +
32A LYS* 3.0 24.1 + - - +
3486A SO4 4.0 30.8 + - - +
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Residues in contact with ALA 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 PRO 2.8 16.5 + - - +
26A ALA* 3.7 6.7 - - - +
28A LEU* 1.3 78.7 - - - +
30A TYR* 1.3 56.3 + - - +
32A LYS* 3.4 7.5 + - - +
33A ARG* 2.9 49.4 + - - +
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Residues in contact with TYR 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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5A ILE* 4.4 12.8 - - + -
26A ALA 3.1 17.7 + - - +
27A ASP* 3.6 10.5 - - - +
29A ALA* 1.3 71.0 - - - +
31A PHE* 1.3 73.0 + - - +
33A ARG* 3.2 24.3 + - - +
34A VAL* 2.8 50.6 + - + +
113A TYR* 3.7 26.9 - - + +
114A VAL 6.1 0.7 - - - -
115A THR* 4.2 5.8 - - - -
155A PHE* 3.7 53.0 - + + +
156A ILE 4.9 1.4 + - - -
157A ILE* 4.3 12.6 - - - +
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Residues in contact with PHE 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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5A ILE* 3.8 37.2 - - + -
27A ASP* 2.9 23.2 + - - +
28A LEU* 3.6 7.6 - - + +
30A TYR* 1.3 77.9 - - - +
32A LYS* 1.3 61.6 - - + +
34A VAL* 3.4 0.3 + - - +
35A THR* 2.8 46.2 + - + +
40A ILE* 4.7 1.6 - - + -
54A LEU* 3.8 11.0 - - + -
57A ARG* 3.8 18.8 - - - -
96A ILE* 3.6 47.1 - - + -
3486A SO4 3.5 26.9 - - - +
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Residues in contact with LYS 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 LEU 3.0 18.6 + - - +
29A ALA* 3.7 7.6 - - - +
31A PHE* 1.3 83.7 - - + +
33A ARG* 1.3 58.3 + - - +
35A THR* 3.6 5.5 + - - -
36A MET* 2.9 57.1 + - + +
55A PRO* 6.2 0.8 - - - +
57A ARG* 4.1 4.0 - - - +
3484A SO4 3.2 41.3 + - - +
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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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26A ALA 4.8 2.0 + - - -
29A ALA* 2.9 37.7 + - - +
30A TYR* 3.6 33.9 - - - +
32A LYS* 1.3 79.2 - - - +
34A VAL* 1.3 66.1 + - + +
36A MET* 3.6 13.4 + - - +
155A PHE* 6.1 0.6 - - - -
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Residues in contact with VAL 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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5A ILE* 4.0 15.0 - - + -
30A TYR* 2.8 52.5 + - + +
31A PHE 3.8 2.7 - - - +
33A ARG* 1.3 81.7 - - + +
35A THR* 1.3 60.8 + - - +
38A HIS* 3.3 17.7 + - - -
94A PHE* 3.5 31.7 - - + -
113A TYR* 4.1 15.7 - - + -
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Residues in contact with THR 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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5A ILE* 4.4 8.5 - - + -
31A PHE* 2.8 44.5 + - + +
32A LYS 3.6 0.3 + - - -
34A VAL* 1.3 78.2 - - - +
36A MET* 1.3 67.9 + - - +
37A GLY 3.3 0.5 + - - -
38A HIS* 2.9 22.6 + - - +
40A ILE* 3.7 28.0 - - + -
57A ARG* 2.9 30.1 + - - +
94A PHE* 4.1 21.1 - - + -
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Residues in contact with MET 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 LYS* 2.9 53.0 + - + +
33A ARG* 3.9 11.4 - - - +
34A VAL 3.4 2.2 - - - +
35A THR* 1.3 74.3 + - - +
37A GLY* 1.3 60.2 + - - +
38A HIS* 3.1 20.8 + - - -
55A PRO 4.1 2.7 - - - +
56A GLY* 3.7 30.5 - - - +
57A ARG* 3.5 20.2 - - - +
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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