Contacts of the helix formed by residues 34 - 43 (chain D) in PDB entry 1L9X
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 ALA 34 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ILE 3.3 2.6 + - - -
33D ALA* 1.3 72.5 - - - +
35D SER* 1.3 62.8 + - - +
37D VAL* 2.9 6.3 + - - +
38D LYS* 2.9 40.3 + - + +
278D PRO* 5.0 0.9 - - + -
289D GLN* 2.9 42.6 + - + +
291D TYR* 3.9 26.9 - - + -
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Residues in contact with SER 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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33D ALA* 3.9 10.4 - - - +
34D ALA* 1.3 76.7 - - - +
36D TYR* 1.3 59.9 + - - +
38D LYS* 3.5 2.6 + - - +
39D TYR* 3.0 29.5 + - - +
222D GLU* 3.7 32.7 + - - +
223D LYS* 5.4 0.7 + - - -
226D TYR* 3.8 17.7 - - - -
227D GLU* 2.7 37.2 + - - +
287D PHE* 4.6 1.6 - - - -
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Residues in contact with TYR 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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14D ILE* 3.8 19.7 - - + +
17D GLN* 5.4 1.6 - - - -
32D ILE* 4.7 2.0 - - + -
33D ALA* 3.2 35.7 + - + +
34D ALA 3.1 0.8 - - - -
35D SER* 1.3 76.3 - - - +
37D VAL* 1.3 66.6 + - - +
39D TYR* 3.4 9.1 - + - +
40D LEU* 3.3 26.9 + - - +
70D LEU* 4.0 15.7 - - + -
72D PRO* 3.7 29.4 - - + -
73D GLY* 3.0 27.6 + - - -
109D THR* 4.1 10.9 - - + +
220D HIS* 3.3 15.9 + - - -
222D GLU* 3.2 40.9 + - + -
223D LYS* 5.5 0.7 + - - -
287D PHE* 5.0 8.0 - + - -
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Residues in contact with VAL 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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14D ILE* 4.0 18.2 - - + -
32D ILE* 4.2 13.0 - - + -
33D ALA 4.3 0.9 - - - +
34D ALA 2.9 8.6 + - - +
36D TYR* 1.3 75.4 - - - +
38D LYS* 1.3 62.9 + - + +
40D LEU* 3.3 3.5 + - - +
41D GLU* 2.9 51.1 + - - +
47D VAL* 4.0 9.1 - - + +
273D ILE* 4.1 27.1 - - + -
291D TYR* 3.9 32.5 - - + +
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Residues in contact with LYS 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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38C LYS* 6.1 5.2 - - + -
41C GLU* 2.9 33.0 + - - +
226C TYR* 5.1 1.4 - - - -
274C TYR* 3.9 9.9 + - - -
34D ALA* 2.9 28.6 + - + +
35D SER* 3.9 2.4 - - - +
37D VAL* 1.3 78.1 - - + +
39D TYR* 1.3 57.8 + - - +
41D GLU* 3.8 7.8 - - - +
42D SER* 2.9 25.8 + - - -
226D TYR* 3.4 50.1 + - + +
288D GLN* 5.6 1.8 - - - +
289D GLN* 2.8 34.6 - - - +
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Residues in contact with TYR 39 (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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35D SER 3.0 20.2 + - - +
36D TYR* 3.4 8.3 - + - +
38D LYS* 1.3 75.4 - - - +
40D LEU* 1.3 79.2 + - + +
42D SER* 2.7 23.1 + - - -
70D LEU* 4.4 14.4 - - + -
107D TRP* 4.2 13.6 - + - -
109D THR* 5.7 1.1 - - - -
221D PRO* 3.5 29.0 - - + +
222D GLU* 3.8 24.2 - - + -
226D TYR* 3.7 11.8 - + + -
244D ALA* 3.2 32.5 - - + -
247D LEU* 3.3 26.4 + - - +
248D ALA* 3.4 28.3 + - + +
251D PHE* 5.6 2.4 - + + +
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Residues in contact with LEU 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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12D ILE* 3.7 33.0 - - + -
14D ILE* 3.7 29.6 - - + -
36D TYR 3.3 11.2 + - - +
37D VAL 3.9 2.9 - - - +
39D TYR* 1.3 94.5 - - + +
41D GLU* 1.3 65.5 + - - +
43D ALA* 3.1 13.9 + - - +
45D ALA* 3.4 24.6 + - + +
47D VAL* 3.9 12.8 - - + -
70D LEU* 4.0 11.4 - - + -
248D ALA* 4.9 3.4 - - + -
251D PHE* 3.7 30.3 - - + -
252D VAL* 4.8 4.7 - - + -
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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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38C LYS* 2.9 37.8 + - - +
225C PRO* 3.3 15.2 - - - +
226C TYR* 3.5 15.0 - - + -
228C TRP* 6.3 0.2 - - - +
37D VAL* 2.9 29.7 + - - +
38D LYS* 3.9 7.3 - - - +
40D LEU* 1.3 76.5 - - - +
42D SER* 1.3 57.7 + - - +
43D ALA 3.0 0.2 - - - -
44D GLY 2.9 17.3 + - - -
45D ALA 3.3 18.8 - - - +
46D ARG* 5.0 1.3 - - - -
47D VAL* 4.1 9.6 + - + +
273D ILE* 3.6 26.9 - - - +
274D TYR* 3.8 16.9 + - - +
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Residues in contact with SER 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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42C SER* 4.0 7.6 - - - -
225C PRO* 3.7 6.7 - - - +
226C TYR* 3.3 23.2 + - - -
241C VAL* 3.3 17.5 - - - +
245C PHE* 5.6 0.3 - - - +
38D LYS 2.9 15.6 + - - -
39D TYR* 2.7 20.4 + - - -
40D LEU 3.2 0.2 - - - -
41D GLU* 1.3 75.4 - - - +
43D ALA* 1.3 55.8 + - - +
44D GLY 3.3 1.1 - - - -
226D TYR* 3.4 16.1 + - - -
245D PHE* 3.4 24.2 - - - -
248D ALA* 4.3 3.8 - - - +
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Residues in contact with ALA 43 (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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241C VAL* 3.6 12.3 - - - +
40D LEU 3.1 3.5 + - - +
41D GLU 3.0 1.6 - - - -
42D SER* 1.3 77.6 + - - +
44D GLY* 1.3 59.9 + - - +
45D ALA 3.6 0.9 - - - -
245D PHE* 4.3 5.2 - - + -
248D ALA* 3.5 29.8 - - + +
249D GLU* 3.6 11.0 - - - +
252D VAL* 3.4 29.1 - - + +
256D ARG* 3.3 19.6 + - - -
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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