Contacts of the helix formed by residues 31 - 38 (chain B) in PDB entry 2ZTC
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 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ALA* 1.3 75.3 - - - +
32B PRO* 1.3 64.9 - - - +
33B ALA* 3.5 9.2 - - - +
34B THR* 2.8 29.8 + - - +
35B LEU* 2.7 33.4 + - - +
61B GLY 5.1 0.4 + - - -
62B PHE* 5.6 3.4 - - + -
86B MET* 3.6 17.4 - - + +
89B LEU* 3.6 21.5 + - + +
90B ALA* 3.5 31.4 - - + +
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Residues in contact with PRO 32 (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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158A LEU* 4.9 6.3 - - + -
182A SER* 5.3 3.4 - - - +
185A LEU* 3.6 29.6 - - + -
186A ARG* 4.3 18.4 + - + +
189A LEU* 3.6 23.8 - - + -
14B LEU 4.0 7.6 - - - +
30B ALA 3.8 2.7 - - - +
31B THR* 1.3 89.1 - - - +
33B ALA* 1.3 53.0 + - - +
35B LEU* 3.6 14.2 - - + +
36B ALA* 2.6 39.2 + - - +
90B ALA* 4.0 15.9 - - + +
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Residues in contact with ALA 33 (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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186A ARG* 4.6 8.6 - - + +
31B THR* 3.5 11.9 - - - +
32B PRO* 1.3 79.5 - - - +
34B THR* 1.3 61.2 + - - +
36B ALA* 3.1 19.9 - - - +
37B THR* 3.7 7.3 - - - +
89B LEU 5.2 1.3 - - - +
90B ALA 5.2 5.1 + - - +
93B ASP* 4.1 27.1 - - - +
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Residues in contact with THR 34 (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 ALA* 4.1 16.8 - - + -
31B THR* 2.8 29.4 + - - +
33B ALA* 1.3 67.1 - - - +
35B LEU* 1.3 64.7 + - - +
36B ALA 2.8 6.3 + - - -
37B THR* 2.9 24.5 + - + +
38B LEU* 4.0 6.8 - - + +
46B LEU* 4.4 22.0 - - + -
61B GLY 4.6 1.2 + - - -
62B PHE* 4.4 6.5 - - - -
63B PRO* 3.6 38.0 - - + +
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Residues in contact with LEU 35 (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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182A SER* 6.6 0.7 - - - -
12B VAL* 3.9 12.3 - - + +
13B ALA 3.1 20.0 - - - +
14B LEU* 3.0 33.2 - - - +
15B ASP 3.6 0.7 - - - +
16B HIS* 2.9 40.4 - - - +
17B VAL* 4.0 10.1 - - + +
30B ALA* 4.1 14.6 - - + +
31B THR 2.7 16.6 + - - +
32B PRO* 3.6 17.9 - - + +
34B THR* 1.3 73.0 - - - +
36B ALA* 1.3 55.3 + - - +
38B LEU* 2.8 40.5 + - + +
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Residues in contact with ALA 36 (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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182A SER* 5.6 2.2 - - - -
186A ARG* 3.6 43.6 + - - +
32B PRO 2.6 17.1 + - - +
33B ALA* 3.1 17.3 - - - +
34B THR 2.8 0.4 + - - -
35B LEU* 1.3 73.8 - - - +
37B THR* 1.3 62.3 + - + +
38B LEU 3.2 6.1 + - - +
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Residues in contact with THR 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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33B ALA 3.7 11.4 - - - +
34B THR* 2.9 21.1 + - + +
36B ALA* 1.3 74.8 - - + +
38B LEU* 1.3 71.0 + - - +
39B ARG* 3.9 4.3 + - - +
63B PRO* 6.0 5.4 - - + -
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Residues in contact with LEU 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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9B VAL* 4.6 4.3 - - + -
12B VAL* 4.3 19.5 - - + +
17B VAL* 3.9 32.5 - - + -
19B ILE* 6.2 0.4 - - + -
34B THR* 4.0 8.5 - - + +
35B LEU* 2.8 35.4 + - + +
36B ALA 3.8 4.9 - - - +
37B THR* 1.3 87.2 - - - +
39B ARG* 1.3 63.1 + - - +
40B GLN 4.3 0.4 - - - -
44B ALA* 3.8 28.9 - - + -
46B LEU* 4.2 27.4 - - + -
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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