Contacts of the helix formed by residues 32 - 42 (chain D) in PDB entry 1THF
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 PRO 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D GLY 3.6 24.0 - - - +
16D ARG* 4.4 6.5 - - - +
17D VAL* 4.0 13.0 - - + +
30D GLY 3.3 9.6 - - - +
31D ASP* 1.3 91.1 - - - +
33D VAL* 1.3 57.1 + - + +
35D LEU* 4.9 0.4 - - + -
36D GLY* 2.9 26.8 + - - +
49D PHE* 3.7 28.0 - - + -
65D LEU* 3.8 17.5 - - + -
68D LYS* 4.6 13.5 - - - +
69D VAL* 3.8 14.6 - - + +
73D ILE* 5.2 0.3 - - - +
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Residues in contact with VAL 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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31D ASP* 3.0 13.4 + - - +
32D PRO* 1.3 75.7 - - + +
34D GLU* 1.3 61.8 + - - +
36D GLY* 3.9 0.2 - - - -
37D LYS* 2.9 36.9 + - + +
68D LYS* 3.7 43.5 - - + +
69D VAL* 4.0 9.2 - - + +
72D GLN* 3.6 31.4 - - + -
73D ILE* 4.4 3.6 - - - +
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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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26D LEU* 3.7 19.7 - - + +
27D ARG* 2.8 33.8 + - - +
28D ASP* 2.8 32.7 + - - +
31D ASP* 3.4 21.2 + - + +
33D VAL* 1.3 81.6 - - - +
35D LEU* 1.3 57.7 + - - +
37D LYS* 3.9 4.8 - - - +
38D PHE* 3.0 28.5 + - + +
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Residues in contact with LEU 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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10D LEU* 3.9 19.5 - - + -
17D VAL* 3.7 25.1 - - + -
23D PHE* 4.0 19.5 - - + -
26D LEU* 3.7 24.2 - - + -
28D ASP 4.9 0.2 + - - -
29D SER* 3.5 26.9 - - - +
31D ASP 3.0 17.7 + - - +
32D PRO* 4.5 1.8 - - + +
34D GLU* 1.3 73.7 - - - +
36D GLY* 1.3 66.5 + - - +
38D PHE* 3.3 7.0 + - + +
39D TYR* 3.0 53.4 + - + +
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Residues in contact with GLY 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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10D LEU* 4.6 6.2 - - - +
32D PRO 2.9 19.7 + - - -
35D LEU* 1.3 77.4 - - - +
37D LYS* 1.3 60.1 + - - +
39D TYR* 3.3 3.6 + - - +
40D SER* 3.1 22.0 + - - -
47D LEU* 3.6 29.2 - - - +
49D PHE* 4.9 0.2 - - - -
73D ILE* 3.9 10.7 - - - +
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Residues in contact with LYS 37 (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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33D VAL* 2.9 22.3 + - + +
34D GLU* 3.9 4.7 - - - +
36D GLY* 1.3 72.8 - - - +
38D PHE* 1.3 64.6 + - - +
40D SER* 3.1 11.0 - - - -
41D GLU* 2.7 57.6 + - + +
72D GLN* 4.1 22.9 + - + +
73D ILE* 3.8 11.7 - - + +
74D ASP* 5.1 7.3 + - - -
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Residues in contact with PHE 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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23D PHE* 4.0 19.7 - + - -
25D ASN* 3.7 22.9 - - - -
26D LEU* 3.8 31.0 - - + -
34D GLU 3.0 15.1 + - - +
35D LEU* 3.4 14.1 - - + +
37D LYS* 1.3 74.4 - - - +
39D TYR* 1.3 77.5 + + - +
41D GLU* 2.9 24.8 + - + +
42D ILE* 3.1 54.1 + - + +
230D ARG* 4.7 8.1 - - - -
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Residues in contact with TYR 39 (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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8D ALA* 4.5 2.7 - - + -
10D LEU* 3.6 27.7 - - + +
23D PHE* 3.4 25.1 - + - -
35D LEU* 3.0 47.0 + - + +
36D GLY 3.3 6.5 + - - +
38D PHE* 1.3 87.5 - + - +
40D SER* 1.3 61.0 + - - +
42D ILE* 3.2 23.2 + - + +
43D GLY 3.4 0.2 + - - -
44D ILE* 3.0 54.2 + - + -
47D LEU* 3.9 15.3 - - + -
227D PHE* 3.4 36.4 + + + +
228D HIS* 4.5 1.0 + - - -
234D VAL* 5.1 1.3 - - + -
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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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36D GLY 3.1 12.9 + - - -
37D LYS* 3.1 16.2 - - - -
39D TYR* 1.3 75.4 - - - +
41D GLU* 1.3 62.2 + - - +
42D ILE 3.6 0.2 + - - -
43D GLY* 3.8 7.1 + - - -
44D ILE 4.4 4.2 - - - +
73D ILE* 5.2 1.1 - - - -
74D ASP* 4.1 13.2 + - - +
75D ILE* 3.6 45.1 + - - +
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Residues in contact with GLU 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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37D LYS* 2.7 53.2 + - - +
38D PHE* 2.9 16.5 + - + +
40D SER* 1.3 80.0 - - - +
42D ILE* 1.3 60.9 + - + +
43D GLY 3.4 0.6 + - - -
252D GLY 4.5 11.6 - - - +
253D LEU* 5.8 0.3 - - - -
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Residues in contact with ILE 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 PHE* 3.1 56.2 + - + +
39D TYR* 3.2 28.2 + - + +
41D GLU* 1.3 80.7 - - + +
43D GLY* 1.3 57.0 + - - +
233D ASP* 6.2 0.4 - - - +
234D VAL* 3.8 28.6 - - + +
235D ARG* 4.3 4.0 + - - +
253D LEU* 3.3 18.6 - - - +
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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