Contacts of the helix formed by residues 27 - 37 (chain D) in PDB entry 1JW9
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 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D PHE* 4.2 1.6 - - - +
26D PRO* 1.3 89.1 - - + +
28D VAL* 1.3 66.2 + - - +
29D GLU* 3.4 10.6 + - - +
30D ALA* 3.1 28.1 + - - +
31D LEU* 3.3 11.8 + - - +
62D PHE 3.8 6.1 - - - -
63D ASP* 3.7 18.6 - - - +
64D HIS 3.2 10.8 - - - +
65D PRO* 4.4 4.0 - - + -
66D LEU* 3.9 10.2 - - - +
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D THR* 1.3 73.6 - - - +
29D GLU* 1.3 64.4 + - - +
31D LEU* 3.2 4.2 + - - +
32D ARG* 2.9 21.4 + - + +
53D ALA* 3.8 16.4 - - + -
55D VAL* 3.7 29.4 - - + -
60D VAL* 4.3 3.4 - - + -
61D SER 4.9 0.2 - - - +
62D PHE* 3.5 36.1 + - + +
64D HIS* 3.0 20.1 + - + +
66D LEU* 4.0 17.0 - - + -
72D VAL* 4.8 3.1 - - + -
74D PHE* 3.8 15.7 - - + -
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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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27D THR* 3.2 6.9 - - - +
28D VAL* 1.3 73.5 - - - +
30D ALA* 1.3 56.7 + - - +
32D ARG* 3.2 23.7 + - - -
33D GLN* 2.7 65.1 + - + +
48D ASP* 4.6 6.2 - - - +
62D PHE* 2.7 41.3 + - + +
63D ASP* 5.0 4.9 - - - +
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Residues in contact with ALA 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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25D PHE* 3.9 7.2 - - + -
26D PRO* 3.5 37.5 - - + -
27D THR* 3.1 13.2 + - - +
29D GLU* 1.3 72.9 - - - +
31D LEU* 1.3 66.6 + - - +
33D GLN* 4.0 4.1 - - - +
34D HIS* 3.0 26.9 + - - +
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Residues in contact with LEU 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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2D ILE* 4.9 2.2 - - + -
4D VAL* 4.0 15.7 - - + -
21D VAL* 4.4 12.3 - - + -
25D PHE* 3.6 40.5 - - + -
27D THR 3.3 7.7 + - - +
28D VAL* 3.2 7.6 + - - +
30D ALA* 1.3 80.4 - - - +
32D ARG* 1.3 62.1 + - - +
34D HIS* 3.4 1.2 + - - +
35D MET* 3.0 52.0 + - + +
66D LEU* 3.7 21.1 - - + -
72D VAL* 4.2 8.3 - - + -
74D PHE* 4.0 20.0 - - + -
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Residues in contact with ARG 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 VAL* 2.9 18.6 + - + +
29D GLU* 3.2 21.9 + - - +
31D LEU* 1.3 75.3 - - - +
33D GLN* 1.3 97.5 + - - +
35D MET* 3.2 4.9 + - - +
36D ALA* 2.8 47.6 + - - +
43D ALA 5.6 0.2 + - - -
46D LEU* 2.7 48.3 + - + +
47D GLU* 4.3 1.0 - - - +
48D ASP* 3.8 26.0 + - - +
51D LEU* 3.7 23.3 - - + -
62D PHE* 3.9 16.4 - - + -
74D PHE* 4.3 14.1 - - + -
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Residues in contact with GLN 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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29D GLU* 2.7 49.6 + - + +
30D ALA* 4.0 4.7 - - - +
32D ARG* 1.3 90.8 - - - +
34D HIS* 1.3 63.9 + - - +
36D ALA* 3.4 6.2 + - - +
37D ALA* 3.3 23.0 + - - +
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Residues in contact with HIS 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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25D PHE* 3.7 32.5 - + + -
30D ALA 3.0 19.3 + - - +
31D LEU 3.7 2.0 - - - +
33D GLN* 1.3 78.4 - - - +
35D MET* 1.3 73.8 + - + +
37D ALA* 3.5 11.4 + - - +
38D GLN* 4.1 15.2 - - + +
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Residues in contact with MET 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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4D VAL* 4.2 7.2 - - + -
6D PHE* 4.0 24.9 - - - -
19D THR* 5.3 5.6 - - - -
21D VAL* 5.4 4.9 - - + -
31D LEU* 3.0 55.4 + - + +
34D HIS* 1.3 84.1 - - + +
36D ALA* 1.3 63.0 + - - +
38D GLN* 3.2 37.5 + - - +
42D TRP* 3.5 19.7 - - + +
46D LEU* 3.6 15.3 - - + -
74D PHE* 3.4 24.5 - - + -
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Residues in contact with ALA 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 ARG* 2.8 42.6 + - - +
33D GLN* 3.8 6.5 - - - +
34D HIS 3.3 0.4 - - - -
35D MET* 1.3 71.4 - - - +
37D ALA* 1.3 57.1 + - - +
38D GLN 3.3 0.2 - - - -
39D SER 3.4 5.9 - - - +
42D TRP* 4.0 10.5 - - - -
43D ALA* 3.2 41.4 + - + +
46D LEU* 4.0 7.5 - - + +
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Residues in contact with ALA 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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33D GLN 3.3 13.4 + - - +
34D HIS* 4.1 6.7 - - - +
35D MET 3.2 1.6 + - - -
36D ALA* 1.3 76.7 - - - +
38D GLN* 1.3 63.2 + - - +
39D SER* 3.3 2.8 - - - -
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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