Contacts of the helix formed by residues 36 - 45 (chain D) in PDB entry 1GZ0
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 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ILE* 4.0 20.4 - - + -
27D ILE* 4.4 10.5 - - + -
28D LEU* 5.6 1.6 - - + +
31D ARG 5.7 1.3 - - - +
33D ASP* 2.9 41.2 + - + +
35D ARG* 1.3 77.5 - - - +
37D LEU* 1.3 66.0 + - - +
38D PRO* 3.3 4.0 - - - -
39D LEU* 3.3 6.7 + - + +
40D ILE* 2.9 38.2 + - + +
68D GLN 4.2 7.2 - - - +
69D GLY* 3.5 23.8 - - - +
70D ILE* 3.7 36.6 - - + -
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Residues in contact with LEU 37 (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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32D GLU* 5.5 7.4 - - + -
33D ASP 3.0 18.0 + - - +
34D LYS* 3.7 19.1 - - + +
36D LEU* 1.3 76.9 - - - +
38D PRO* 1.3 63.4 - - + +
40D ILE* 3.5 11.5 + - + +
41D HIS* 2.9 56.9 + - + +
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Residues in contact with PRO 38 (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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34D LYS 3.4 13.0 - - - +
35D ARG* 3.8 13.7 - - - +
36D LEU 3.3 2.2 - - - -
37D LEU* 1.3 92.4 - - + +
39D LEU* 1.3 78.5 + - + +
41D HIS* 3.1 9.6 + - + +
42D ALA* 2.8 23.9 + - - +
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Residues in contact with LEU 39 (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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8D ILE* 3.7 44.6 - - + +
11D VAL* 3.9 9.4 - - + -
12D GLN* 3.6 34.8 - - + +
15D LEU* 4.4 8.7 - - + -
35D ARG 4.7 5.2 - - - +
36D LEU* 3.3 8.7 + - + +
38D PRO* 1.3 82.6 - - + +
40D ILE* 1.3 53.7 + - - +
42D ALA* 3.0 7.7 + - + +
43D LEU* 2.6 44.1 + - + +
70D ILE* 3.8 29.2 - - + -
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Residues in contact with ILE 40 (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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27D ILE* 3.3 48.2 - - + -
36D LEU* 2.9 33.7 + - + +
37D LEU* 3.8 13.0 - - + +
39D LEU* 1.3 78.4 - - + +
41D HIS* 1.3 54.9 + - + +
43D LEU* 3.1 12.2 + - + +
44D GLU* 2.7 50.6 + - + +
50D ILE* 3.6 17.4 - - + +
70D ILE* 5.3 1.8 - - + -
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Residues in contact with HIS 41 (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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37D LEU* 2.9 44.8 + - + +
38D PRO* 3.1 7.8 + - + +
40D ILE* 1.3 75.8 - - + +
42D ALA* 1.3 66.5 + - - +
44D GLU* 3.4 20.2 + - + +
45D SER* 3.1 26.7 + - - -
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Residues in contact with ALA 42 (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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15D LEU* 3.7 22.2 - - + -
38D PRO 2.8 12.2 + - - +
39D LEU* 3.4 8.7 - - + +
41D HIS* 1.3 76.9 - - - +
43D LEU* 1.3 62.4 + - - +
45D SER* 3.3 10.0 + - - -
46D GLN* 3.3 27.9 - - - +
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Residues in contact with LEU 43 (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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11D VAL* 4.2 14.1 - - + -
15D LEU* 3.7 28.0 - - + -
22D PHE* 4.2 24.0 - - + -
25D VAL* 3.6 37.7 - - + -
39D LEU 2.6 30.2 + - - +
40D ILE* 3.4 9.4 - - + +
42D ALA* 1.3 71.7 - - - +
44D GLU* 1.3 63.9 + - - +
46D GLN* 3.2 14.4 + - - +
48D VAL* 3.3 26.4 + - + +
50D ILE* 3.6 15.5 - - + -
70D ILE* 4.3 4.9 - - + -
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Residues in contact with GLU 44 (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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40D ILE* 2.7 34.6 + - + +
41D HIS* 3.8 19.5 - - + +
43D LEU* 1.3 72.8 - - - +
45D SER* 1.3 58.0 + - - +
47D GLY* 2.8 23.4 + - - -
48D VAL 4.9 2.9 - - - -
50D ILE* 3.8 16.6 - - + +
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Residues in contact with SER 45 (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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41D HIS 3.1 16.1 + - - -
42D ALA* 3.3 11.3 + - - -
43D LEU 3.4 0.2 - - - -
44D GLU* 1.3 78.0 - - - +
46D GLN* 1.3 59.4 + - - +
47D GLY 3.4 1.1 - - - -
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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