Contacts of the helix formed by residues 26 - 35 (chain D) in PDB entry 2ISZ
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 26 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D THR* 3.0 31.5 + - + +
25D PRO* 1.3 82.4 - - - +
27D ARG* 1.3 66.0 + - - +
28D ALA* 3.9 3.8 - - + +
29D ARG* 3.0 39.6 + - + +
30D ILE* 3.3 9.9 + - - +
59D ASP 4.8 0.9 - - - +
60D ARG* 3.8 24.0 - - + +
61D HIS* 3.8 11.9 - - + -
62D LEU* 3.9 6.7 - - - -
4E T 4.1 25.6 - - - +
5E G 3.7 13.5 - - - +
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Residues in contact with ARG 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 1.3 73.2 - - - +
28D ALA* 1.3 57.6 + - - +
30D ILE* 3.1 3.0 + - - +
31D ALA* 2.9 27.4 + - - +
38D GLY 5.8 0.7 - - - +
41D VAL* 3.5 29.1 - - + +
42D SER* 3.8 27.5 + - - +
45D VAL* 3.8 23.2 - - + +
56D VAL* 3.5 35.5 - - - +
60D ARG* 3.8 29.5 + - - +
62D LEU* 3.9 14.9 - - + +
5E G 3.3 25.7 + - - +
6E T 2.9 29.8 + - - -
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Residues in contact with ALA 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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26D LEU* 4.6 1.6 - - + -
27D ARG* 1.3 75.8 - - - +
29D ARG* 1.3 70.0 + - - +
31D ALA* 3.4 8.3 + - - +
32D GLU* 3.0 29.6 + - - +
4E T 3.7 40.6 - - + +
5E G 2.8 16.7 + - - +
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Residues in contact with ARG 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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18D LEU* 3.5 40.4 - - + -
23D VAL* 3.9 11.8 - - + +
24D THR 4.2 7.3 + - - +
26D LEU* 3.0 32.4 + - - +
28D ALA* 1.3 87.8 - - - +
30D ILE* 1.3 60.6 + - - +
32D GLU* 2.6 49.1 + - - +
33D ARG* 3.1 30.4 + - - +
4E T 2.4 33.3 + - - -
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Residues in contact with ILE 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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11D TYR* 3.8 41.5 - - + +
14D THR* 4.3 21.5 - - + -
15D ILE* 4.2 15.5 - - + -
18D LEU* 5.0 4.3 - - + -
26D LEU 3.3 7.2 + - - +
27D ARG 3.1 6.8 + - - +
29D ARG* 1.3 74.7 - - - +
31D ALA* 1.3 66.0 + - - +
33D ARG 3.3 0.3 + - - -
34D LEU* 3.0 48.5 + - + +
36D GLN* 5.6 0.4 - - - +
41D VAL* 4.2 5.2 - - + -
45D VAL* 4.4 5.4 - - + -
62D LEU* 3.4 30.5 - - + -
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Residues in contact with ALA 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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27D ARG 2.9 12.8 + - - +
28D ALA* 3.5 12.3 - - - +
30D ILE* 1.3 74.9 - - - +
32D GLU* 1.3 53.9 + - - +
35D ASP* 2.8 29.6 + - - -
36D GLN* 2.9 31.4 + - - +
37D SER 4.6 3.8 - - - -
38D GLY* 4.7 4.5 - - - +
41D VAL* 3.7 18.5 - - + +
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Residues in contact with GLU 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 ALA 3.0 10.1 + - - +
29D ARG* 2.6 51.8 + - - +
31D ALA* 1.3 79.4 - - - +
33D ARG* 1.3 67.4 + - + +
35D ASP* 3.4 10.7 + - - +
4E T 4.7 5.0 + - - -
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Residues in contact with ARG 33 (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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14D THR* 4.5 17.3 - - + -
17D ASP* 4.0 15.0 + - - +
18D LEU* 3.5 25.5 - - - +
21D GLU* 2.4 46.6 + - - -
23D VAL* 4.8 4.0 - - - +
29D ARG* 3.1 20.9 + - + +
30D ILE 4.2 2.0 - - - +
32D GLU* 1.3 87.2 + - + +
34D LEU* 1.3 67.4 + - + +
35D ASP* 3.3 1.8 - - - +
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Residues in contact with LEU 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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4D LEU* 4.2 26.6 - - + +
10D MET* 3.8 25.4 - - + +
11D TYR* 3.7 25.4 - - + -
14D THR* 3.5 24.0 - - - +
30D ILE* 3.0 35.9 + - + +
33D ARG* 1.3 84.3 - - + +
35D ASP* 1.3 72.2 + - - +
36D GLN* 3.4 16.2 + - + +
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Residues in contact with ASP 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 ALA 2.8 13.6 + - - -
32D GLU 3.4 7.5 + - - +
33D ARG 3.3 3.3 - - - +
34D LEU* 1.3 83.0 - - - +
36D GLN* 1.3 60.7 + - - +
2001D NA 4.2 3.0 - - - -
24F C 3.8 6.9 + - - -
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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