Contacts of the helix formed by residues 29 - 33 (chain D) in PDB entry 5L1Z
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 LYS 29 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B TRP* 5.6 13.5 - - - +
259B ARG 6.0 2.2 - - - +
261B CYS* 6.2 2.2 - - - -
65C PHE* 3.2 58.7 - - + +
27D CYS* 2.9 14.2 + - + -
28D LYS* 1.3 83.9 - - + +
30D CYS* 1.3 64.7 + - - +
31D CYS 3.3 0.7 - - - -
32D PHE 3.7 5.8 + - - -
33D HIS* 3.8 5.5 + - - -
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Residues in contact with CYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D THR* 2.9 33.0 - - - +
25D CYS* 2.9 26.7 - - - +
27D CYS* 3.2 8.5 + - - -
29D LYS* 1.3 77.4 - - - +
31D CYS* 1.3 61.6 + - - +
32D PHE 3.0 7.0 + - - -
33D HIS* 3.1 22.4 + - - +
37D CYS* 3.4 10.6 - - - +
41D LYS* 3.7 4.6 + - - +
102D ZN 2.7 34.5 - - - -
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Residues in contact with CYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ARG* 4.4 3.4 - - - -
255B ILE* 3.6 25.4 - - + -
26D TYR* 3.2 21.1 - - - -
27D CYS 3.0 27.2 + - - +
28D LYS 4.5 3.1 - - - +
29D LYS 3.3 0.6 - - - -
30D CYS* 1.3 76.8 - - - +
32D PHE* 1.3 78.0 + - + +
33D HIS 3.6 0.2 - - - -
38D PHE* 3.1 32.3 + - - +
41D LYS* 4.3 17.3 - - - -
42D ALA* 4.5 11.4 - - + +
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Residues in contact with PHE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B PHE* 4.4 6.5 - + - -
207B TRP* 4.4 9.0 - + - -
252B LEU* 5.7 0.4 - - + -
255B ILE* 4.2 6.5 - - + -
56C LEU* 4.7 5.6 - - + -
62C MET* 3.3 48.5 - - + -
65C PHE* 2.6 47.1 - - + +
66C ILE* 3.3 36.1 - - + -
1D MET* 3.1 13.6 - - + +
28D LYS 4.1 9.9 - - - -
29D LYS 3.7 3.9 + - - +
30D CYS 3.0 0.4 - - - -
31D CYS* 1.3 99.3 - - + +
33D HIS* 1.3 58.9 + - - +
34D CYS 3.2 3.6 - - - -
38D PHE* 3.8 31.2 - + - -
42D ALA* 4.9 0.4 - - + -
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C PHE* 4.1 7.4 - - - +
67C GLY* 5.3 1.7 + - - -
1D MET* 4.7 2.8 - - - +
18D PRO* 3.5 23.6 - - + +
20D THR* 2.9 45.0 + - - -
21D ALA 3.6 7.0 + - - -
22D CYS* 3.6 2.9 - - - -
23D THR* 4.0 26.5 - - + +
29D LYS 3.8 4.6 + - - +
30D CYS* 3.1 24.2 + - - +
31D CYS 3.6 0.2 - - - -
32D PHE* 1.3 79.8 - - - +
34D CYS* 1.3 59.5 + - - +
37D CYS* 3.8 2.2 - - - -
101D ZN 2.8 29.2 - - - -
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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