Contacts of the helix formed by residues 22 - 35 (chain D) in PDB entry 3PHW
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 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D SER 4.3 3.4 - - - +
21D ASP* 1.3 77.6 - - - +
23D ILE* 1.3 65.7 + - - +
24D GLU* 3.7 7.3 + - - +
25D ASN* 3.0 42.5 + - - +
26D VAL* 3.0 13.4 + - - +
52D ASP 3.8 8.3 - - - -
53D GLY* 4.5 9.6 - - - +
54D ARG 3.1 13.7 - - - +
55D THR* 4.0 13.5 - - + +
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Residues in contact with ILE 23 (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 THR* 1.3 72.1 - - - +
24D GLU* 1.3 57.2 + - - +
26D VAL* 3.2 6.2 + - + +
27D LYS* 3.0 50.7 + - - +
43D LEU* 4.0 11.7 - - + -
50D LEU* 3.6 47.8 - - + +
51D GLU 2.9 28.3 - - - +
52D ASP* 3.3 8.9 + - - +
54D ARG 2.9 13.2 + - - +
55D THR 4.3 9.9 - - - +
56D LEU* 4.2 18.8 - - + -
59D TYR* 4.4 3.4 - - + -
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Residues in contact with GLU 24 (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 THR* 3.1 8.0 - - - +
23D ILE* 1.3 75.1 - - - +
25D ASN* 1.3 65.3 + - - +
27D LYS* 3.6 6.3 + - - +
28D ALA* 3.2 21.7 + - - +
38D PRO* 5.7 0.7 - - - +
52D ASP* 3.2 51.6 - - + +
53D GLY* 4.1 6.9 + - - -
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Residues in contact with ASN 25 (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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20D SER 4.9 1.0 + - - -
21D ASP* 2.9 32.0 + - - +
22D THR* 3.0 34.5 + - - +
24D GLU* 1.3 76.9 - - - +
26D VAL* 1.3 57.6 + - - +
28D ALA* 3.2 9.4 - - - +
29D LYS* 3.0 33.4 + - - +
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Residues in contact with VAL 26 (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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3D ILE* 4.9 2.7 - - + -
15D LEU* 3.8 21.3 - - + -
17D VAL* 4.7 4.7 - - + -
21D ASP* 4.3 9.0 - - + -
22D THR 3.0 16.3 + - - +
23D ILE* 3.2 9.2 + - + +
25D ASN* 1.3 74.7 - - - +
27D LYS* 1.3 66.1 + - - +
29D LYS* 3.0 10.3 + - - +
30D ILE* 3.0 24.2 + - + +
43D LEU* 4.0 17.7 - - + -
56D LEU* 4.2 33.2 - - + -
67D LEU* 4.5 14.4 - - + -
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 5.3 9.1 - - - +
23D ILE* 3.0 29.8 + - - +
24D GLU* 4.0 4.9 - - - +
26D VAL* 1.3 75.2 - - - +
28D ALA* 1.3 64.2 + - - +
30D ILE* 3.1 2.4 + - - -
31D GLN* 3.0 19.4 + - - +
38D PRO* 3.9 27.9 + - + +
41D GLN* 3.0 62.5 + - + +
42D ARG* 5.2 0.8 - - - +
43D LEU* 3.5 17.3 - - + +
50D LEU 4.8 5.0 + - - -
52D ASP* 2.6 34.8 + - - +
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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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24D GLU 3.2 12.4 + - - +
25D ASN* 3.2 13.5 - - - +
27D LYS* 1.3 80.2 - - - +
29D LYS* 1.3 62.3 + - + +
31D GLN* 3.1 13.0 + - - +
32D ASP* 3.1 28.3 + - - +
38D PRO* 4.6 8.6 - - + +
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Residues in contact with LYS 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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15D LEU* 4.3 15.0 - - + +
16D GLU 3.5 26.0 + - - +
17D VAL* 4.1 13.2 - - + +
21D ASP* 3.3 29.8 - - - +
25D ASN* 3.0 20.0 + - - +
26D VAL* 3.0 11.6 + - - +
28D ALA* 1.3 76.3 - - + +
30D ILE* 1.3 61.9 + - - +
32D ASP* 3.4 13.4 + - - +
33D LYS* 3.2 22.2 + - - +
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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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5D VAL* 4.1 21.3 - - + -
7D THR* 5.8 0.2 - - + -
13D ILE* 4.8 7.2 - - + -
15D LEU* 3.9 23.1 - - + -
26D VAL* 3.0 16.6 + - + +
27D LYS 3.1 8.0 + - - +
29D LYS* 1.3 75.6 - - - +
31D GLN* 1.3 56.8 + - - +
33D LYS* 4.4 1.8 - - - +
34D GLU* 2.7 40.1 + - + -
35D GLY 3.5 0.3 + - - -
36D ILE* 4.2 8.5 + - + -
41D GLN* 3.6 28.7 - - - +
43D LEU* 3.7 26.7 - - + -
69D LEU* 4.2 15.7 - - + -
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Residues in contact with GLN 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 LYS 3.0 10.2 + - - +
28D ALA* 3.1 11.5 + - - +
30D ILE* 1.3 77.3 - - - +
32D ASP* 1.3 60.1 + - - +
35D GLY* 2.7 33.0 + - - +
36D ILE 3.2 26.4 + - - +
37D PRO* 4.2 4.2 - - - +
38D PRO* 3.6 30.7 - - + +
33E ARG* 3.1 52.8 + - - +
34E GLN 5.3 2.1 - - - +
147E SER* 4.5 3.6 + - - -
151E HIS* 3.8 11.4 + - - -
153E ASP* 3.4 12.2 + - - +
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Residues in contact with ASP 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* 3.1 18.2 + - - +
29D LYS* 3.4 17.0 - - - +
30D ILE 3.2 0.2 - - - -
31D GLN* 1.3 79.4 - - - +
33D LYS* 1.3 58.9 + - + +
35D GLY 4.9 0.2 + - - -
33E ARG* 3.9 29.7 + - - +
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Residues in contact with LYS 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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13D ILE* 4.0 19.1 - - + -
14D THR* 2.9 43.4 + - - +
15D LEU* 4.7 7.4 - - + -
29D LYS 3.2 14.3 + - - +
30D ILE* 4.0 4.0 - - - +
31D GLN 3.1 0.4 - - - -
32D ASP* 1.3 82.2 - - + +
34D GLU* 1.3 79.8 + - + +
35D GLY 3.6 0.2 - - - -
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Residues in contact with GLU 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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7D THR* 4.4 10.3 - - + -
11D LYS* 2.9 36.1 + - - +
13D ILE* 3.2 43.8 - - + +
30D ILE* 2.7 18.2 + - + +
33D LYS* 1.3 90.2 - - - +
35D GLY* 1.3 57.6 + - - +
36D ILE* 3.2 25.1 + - + +
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Residues in contact with GLY 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 GLN* 2.7 25.5 + - - +
33D LYS 3.6 1.2 - - - -
34D GLU* 1.3 77.8 - - - +
36D ILE* 1.3 62.7 + - - +
37D PRO* 3.3 9.0 - - - +
33E ARG* 5.5 2.7 - - - -
147E SER* 4.7 11.1 + - - -
148E GLY* 5.1 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