Contacts of the helix formed by residues 33 - 42 (chain D) in PDB entry 4GCK
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 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ARG* 3.6 16.5 + - + +
32D ILE* 1.3 76.2 - - - +
34D THR* 1.3 59.2 + - - +
35D ALA* 3.7 7.7 + - - +
36D LYS* 3.0 42.0 + - - +
37D LEU* 3.0 24.5 + - - +
32Z C 3.6 38.6 - - - +
33Z A 3.0 13.9 - - - +
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Residues in contact with THR 34 (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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33D THR* 1.3 68.8 - - - +
35D ALA* 1.3 64.1 + - - +
37D LEU* 4.2 7.9 - - - -
38D ALA* 2.9 26.0 + - - +
45D GLU* 2.7 34.9 + - - +
48D LEU* 3.6 7.5 - - - +
49D TYR* 3.3 30.7 - - + +
55D LYS* 4.0 23.8 - - + -
58D MET* 4.8 4.0 - - + -
33Z A 2.7 36.4 + - + +
34Z C 4.0 0.3 - - - -
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Residues in contact with ALA 35 (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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33D THR* 3.2 8.8 - - - +
34D THR* 1.3 83.0 + - - +
36D LYS* 1.3 58.1 + - - +
38D ALA* 3.2 4.6 + - - +
39D ALA* 2.9 27.3 + - - +
45D GLU* 3.2 22.4 - - - +
32Z C 5.9 2.2 - - - +
33Z A 4.5 0.4 + - - -
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Residues in contact with LYS 36 (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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22D MET* 3.7 20.5 - - + +
27D ASP* 4.9 16.7 + - - +
30D GLN* 4.6 13.9 - - - +
31D ARG 4.2 13.1 + - - -
32D ILE* 4.9 0.7 - - - +
33D THR* 3.0 35.2 + - - +
35D ALA* 1.3 80.5 - - - +
37D LEU* 1.3 56.2 + - - +
39D ALA* 3.3 9.4 - - + +
40D SER* 3.0 27.9 + - - -
32Z C 5.5 1.2 + - - -
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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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15D ILE* 4.0 15.5 - - + +
18D SER* 4.2 4.9 - - - -
19D LEU* 3.7 38.1 - - + +
22D MET* 3.6 24.0 - - - +
32D ILE* 4.3 6.3 - - + -
33D THR 3.0 17.0 + - - +
34D THR* 3.8 8.5 - - - +
36D LYS* 1.3 73.8 - - - +
38D ALA* 1.3 68.1 + - - +
40D SER* 3.2 3.8 + - - -
41D VAL* 3.1 28.6 + - + +
48D LEU* 4.3 9.2 - - + -
55D LYS* 5.3 3.8 - - + -
58D MET* 3.4 37.9 - - + -
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Residues in contact with ALA 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 THR 2.9 19.3 + - - +
35D ALA* 3.4 5.2 - - - +
37D LEU* 1.3 76.0 - - - +
39D ALA* 1.3 63.1 + - - +
41D VAL* 3.3 1.6 + - - +
42D GLY 2.9 21.7 + - - -
43D VAL 3.0 23.3 - - - +
44D SER* 3.6 16.2 - - - +
45D GLU* 3.7 6.1 - - + +
48D LEU* 3.4 25.0 - - + +
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Residues in contact with ALA 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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35D ALA 2.9 12.6 + - - +
36D LYS* 3.3 15.5 - - + +
37D LEU 3.2 0.2 - - - -
38D ALA* 1.3 80.4 - - - +
40D SER* 1.3 67.1 + - - +
41D VAL 3.8 0.2 - - - -
42D GLY* 3.5 9.5 + - - -
43D VAL 4.9 0.7 - - - -
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Residues in contact with SER 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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18D SER* 4.3 14.3 + - - -
22D MET* 3.6 28.6 - - - +
36D LYS 3.0 13.3 + - - -
37D LEU 3.4 8.7 - - - -
39D ALA* 1.3 77.3 - - - +
41D VAL* 1.3 65.4 + - - +
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Residues in contact with VAL 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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11D ARG* 5.6 1.3 - - + -
14D GLU* 4.7 20.4 - - + +
15D ILE* 4.0 35.4 - - + -
18D SER* 4.0 21.5 + - - +
37D LEU* 3.1 19.0 + - + +
38D ALA* 3.6 5.8 - - - +
40D SER* 1.3 80.9 - - - +
42D GLY* 1.3 61.1 + - - +
43D VAL* 4.0 22.2 - - + +
48D LEU* 4.3 7.2 - - + -
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Residues in contact with GLY 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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38D ALA 2.9 7.5 + - - -
39D ALA* 3.5 6.7 + - - -
41D VAL* 1.3 77.6 - - - +
43D VAL* 1.3 68.0 + - - +
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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