Contacts of the helix formed by residues 26 - 38 (chain D) in PDB entry 3QOQ
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 GLY 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D PRO* 3.3 1.0 + - - +
25D GLU* 1.3 79.5 - - - +
27D MSE 1.3 63.0 + - - +
28D ARG 3.4 2.0 + - - -
29D GLU* 3.7 9.8 + - - +
30D GLN* 3.2 35.0 + - - +
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Residues in contact with MSE 27 (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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47C ILE* 3.8 33.9 - - + -
50C LEU* 4.1 21.5 - - + -
51C GLU* 4.6 8.5 - - - -
54C LEU* 4.5 12.8 - - + -
23D LEU* 3.5 34.3 - - + -
24D PRO* 3.3 45.4 + - + +
26D GLY* 1.3 74.7 - - - +
28D ARG* 1.3 60.4 + - - +
30D GLN* 3.3 11.3 - - - +
31D ILE* 2.8 45.4 + - - +
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Residues in contact with ARG 28 (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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17C ASP* 3.9 34.1 - - + +
18C LYS 4.9 7.7 + - - -
19C PHE* 4.2 16.4 - - - +
23D LEU* 4.6 16.0 - - + +
24D PRO 4.5 2.0 + - - -
25D GLU 4.6 0.6 + - - +
26D GLY 3.4 0.8 - - - -
27D MSE 1.3 79.3 - - - +
29D GLU* 1.3 71.5 + - - +
31D ILE* 3.7 4.7 - - - +
32D ALA* 2.8 29.1 + - - +
42D MSE 4.6 21.8 - - + +
2E C 2.7 46.8 + - - -
3E T 5.8 1.4 + - - -
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Residues in contact with GLU 29 (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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17C ASP* 4.9 2.9 - - - +
25D GLU 5.1 5.8 - - - +
26D GLY* 3.7 8.8 + - - +
27D MSE 3.4 0.2 - - - -
28D ARG* 1.3 90.6 + - - +
30D GLN* 1.3 62.3 + - - +
32D ALA* 3.5 8.7 - - + +
33D GLU* 3.0 36.7 + - + +
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Residues in contact with GLN 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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54C LEU* 3.7 33.7 - - + +
26D GLY* 3.2 28.9 + - - +
27D MSE 3.2 11.9 + - - +
29D GLU* 1.3 78.5 - - - +
31D ILE* 1.3 61.9 - - - +
33D GLU* 3.5 7.9 + - - +
34D VAL* 3.3 28.6 + - + +
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Residues in contact with ILE 31 (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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50C LEU* 4.1 23.6 - - + -
54C LEU* 4.3 19.1 - - + -
23D LEU* 3.6 30.5 - - + -
27D MSE 2.8 23.5 + - - +
28D ARG 3.7 3.1 - - - +
30D GLN* 1.3 72.9 - - - +
32D ALA* 1.3 67.3 + - - +
34D VAL* 3.3 6.7 + - - +
35D ALA* 2.9 22.7 + - - +
42D MSE 3.8 31.0 - - + +
45D GLU* 4.4 10.7 - - + +
46D ILE* 4.1 18.6 - - + -
49D ARG* 6.2 1.8 - - - -
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Residues in contact with ALA 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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28D ARG* 2.8 20.9 + - - +
29D GLU* 3.5 11.4 - - + +
31D ILE* 1.3 77.8 - - - +
33D GLU* 1.3 62.4 + - + +
35D ALA* 3.4 2.1 + - - +
36D ARG* 3.0 33.3 + - + +
42D MSE 4.3 19.3 - - + +
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.0 27.5 + - + +
30D GLN* 3.7 8.2 - - - +
31D ILE 3.2 0.2 - - - -
32D ALA* 1.3 76.5 - - + +
34D VAL* 1.3 60.2 + - + +
36D ARG* 3.1 33.7 + - - +
37D SER* 2.9 27.4 + - - -
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Residues in contact with VAL 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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54C LEU* 3.7 20.0 - - + -
57C GLU* 3.4 22.4 - - + +
30D GLN* 3.3 16.2 - - + +
31D ILE* 3.3 6.8 + - - +
33D GLU* 1.3 75.8 - - + +
35D ALA* 1.3 58.2 + - - +
37D SER* 3.0 10.3 + - - -
38D HIS* 2.9 35.7 + - + -
45D GLU* 3.2 23.3 - - + +
49D ARG* 3.3 17.9 - - - +
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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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31D ILE 2.9 18.5 + - - +
32D ALA 3.6 5.2 - - - +
34D VAL* 1.3 76.6 - - - +
36D ARG* 1.3 62.8 + - + +
38D HIS 3.0 3.5 + - - -
39D HIS 2.9 18.7 + - - -
40D ARG 3.1 26.8 + - - +
41D SER 4.1 3.1 - - - +
42D MSE 4.1 12.6 - - + +
45D GLU* 3.6 28.4 - - + +
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Residues in contact with ARG 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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32D ALA* 3.0 22.1 + - + +
33D GLU* 3.1 37.7 + - - +
35D ALA* 1.3 75.3 - - + +
37D SER* 1.3 62.1 + - - +
39D HIS* 3.3 21.4 + - - +
40D ARG 5.0 1.1 - - - -
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Residues in contact with SER 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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57C GLU* 5.4 2.2 + - - -
33D GLU 2.9 13.2 + - - -
34D VAL* 3.0 17.2 + - - -
36D ARG* 1.3 78.7 - - - +
38D HIS* 1.3 65.1 + - - +
39D HIS* 3.3 11.5 + - - -
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Residues in contact with HIS 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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57C GLU* 3.4 30.6 + - - -
34D VAL* 2.9 27.6 + - + -
35D ALA 3.0 1.3 + - - +
37D SER* 1.3 80.6 + - - +
39D HIS* 1.3 71.1 + - - +
40D ARG* 3.3 27.8 + - - +
45D GLU* 3.4 31.2 - - - +
49D ARG* 3.9 2.6 + - - -
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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