Contacts of the helix formed by residues 36 - 45 (chain B) in PDB entry 1Z6T
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 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ILE* 4.2 6.5 - - - +
35B LEU* 1.3 86.5 - - - +
37B ILE* 1.3 60.2 + - - +
38B SER* 2.7 25.9 + - - +
39B GLU* 3.2 24.6 + - - +
40B GLU* 3.2 24.8 + - - +
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 4.2 19.3 - - + -
36B THR* 1.3 72.4 - - - +
38B SER* 1.3 61.2 + - - +
40B GLU* 3.7 21.3 - - - +
41B GLU* 2.9 41.5 + - + +
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B THR* 2.7 25.3 + - - +
37B ILE* 1.3 81.6 - - - +
39B GLU* 1.3 56.8 + - - +
41B GLU* 3.5 9.7 - - - +
42B LYS* 2.9 28.1 + - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MET* 5.3 0.2 - - - -
35B LEU* 3.3 23.0 - - + +
36B THR* 3.2 30.5 + - - +
37B ILE 3.2 0.2 - - - -
38B SER* 1.3 76.7 + - - +
40B GLU* 1.3 54.8 + - - +
42B LYS* 3.0 9.9 + - - +
43B VAL* 2.7 39.8 + - - +
59B MET* 3.2 44.9 - - + +
63B LYS* 3.1 24.0 + - - -
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B SER* 4.6 7.1 - - - +
26B MET* 3.8 35.4 - - + +
27B ASP* 4.3 13.4 - - - +
30B ILE* 4.1 14.3 - - + +
35B LEU* 5.0 1.2 - - + +
36B THR 3.2 12.3 + - - +
37B ILE* 3.4 27.5 + - - +
39B GLU* 1.3 76.5 - - - +
41B GLU* 1.3 58.5 + - - +
43B VAL* 3.9 0.2 - - - +
44B ARG* 2.9 49.1 + - + +
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ILE* 2.9 31.5 + - + +
38B SER* 3.5 8.9 - - - +
40B GLU* 1.3 75.8 + - - +
42B LYS* 1.3 57.4 + - - +
44B ARG* 4.0 5.9 - - - +
45B ASN* 3.1 26.0 + - - +
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER 2.9 15.4 + - - +
39B GLU* 3.0 11.2 + - - +
41B GLU* 1.3 77.3 - - - +
43B VAL* 1.3 59.5 + - - +
45B ASN* 3.0 28.0 + - - +
46B GLU* 4.1 9.0 - - - +
55B MET* 4.1 19.6 - - - +
59B MET* 3.8 21.8 - - + +
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR* 4.1 1.8 - - - +
26B MET* 3.7 31.9 - - + -
35B LEU* 6.3 0.2 - - + -
39B GLU 2.7 22.9 + - - +
40B GLU 3.2 0.2 + - - -
42B LYS* 1.3 70.3 - - - +
44B ARG* 1.3 66.5 + - - +
45B ASN 3.2 0.2 - - - -
46B GLU* 3.3 10.0 + - - +
52B ARG* 3.1 48.6 - - + +
55B MET* 3.7 15.0 - - + -
56B LEU* 3.8 14.8 - - + -
59B MET* 3.5 26.2 - - - -
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MET* 4.7 7.1 - - + +
40B GLU* 2.9 30.0 + - + +
41B GLU* 4.0 5.2 - - - +
43B VAL* 1.3 74.1 - - - +
45B ASN* 1.3 67.6 + - - +
46B GLU 2.9 4.9 + - - +
52B ARG* 3.1 42.1 + - - +
376B ARG* 5.4 4.4 - - - +
413B ASP* 3.7 42.5 + - - +
416B GLN* 5.9 5.5 - - - +
417B GLU* 4.8 15.8 + - - +
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Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLU 3.1 16.6 + - - +
42B LYS* 3.0 28.9 + - - +
44B ARG* 1.3 74.0 - - - +
46B GLU* 1.3 64.7 + - - +
47B PRO* 3.7 4.0 - - - +
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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