Contacts of the helix formed by residues 34 - 43 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE 3.4 3.2 + - - -
33A ALA* 1.3 72.2 - - - +
35A SER* 1.3 63.0 + - - +
37A VAL* 3.0 6.9 + - + +
38A LYS* 2.9 40.8 + - - +
278A PRO* 5.0 1.3 - - + -
289A GLN* 2.9 40.4 + - + +
291A TYR* 3.9 27.4 - - + -
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 4.0 9.4 - - - +
34A ALA* 1.3 77.4 - - - +
36A TYR* 1.3 60.1 + - - +
38A LYS* 4.4 3.3 - - - +
39A TYR* 3.0 29.6 + - - +
222A GLU* 3.7 33.0 + - - +
223A LYS* 5.4 0.7 + - - +
226A TYR* 3.8 20.8 - - - -
227A GLU* 2.7 34.2 + - - +
287A PHE* 4.7 1.4 - - - -
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Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.8 21.2 - - + +
17A GLN* 5.6 1.3 - - - -
32A ILE* 4.7 1.8 - - + -
33A ALA* 3.1 36.1 + - + +
35A SER* 1.3 77.5 - - - +
37A VAL* 1.3 65.4 + - - +
39A TYR* 3.4 8.6 - + - +
40A LEU* 3.2 28.8 + - - +
70A LEU* 4.0 16.2 - - + -
72A PRO* 3.7 28.5 - - + -
73A GLY* 2.9 28.6 + - - -
109A THR* 4.2 10.2 - - + +
220A HIS* 3.2 14.9 + - - -
222A GLU* 3.1 40.4 + - + -
223A LYS* 5.4 0.7 + - - -
287A PHE* 5.1 7.8 - + - -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 4.0 18.6 - - + -
32A ILE* 4.2 16.2 - - + -
33A ALA 4.4 0.7 - - - +
34A ALA 3.0 9.1 + - - +
36A TYR* 1.3 74.4 - - - +
38A LYS* 1.3 67.8 + - + +
40A LEU* 3.3 4.3 + - - +
41A GLU* 3.0 44.7 + - - +
47A VAL* 4.0 9.1 - - + +
273A ILE* 4.1 27.6 - - + -
291A TYR* 3.9 30.1 - - + +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 2.9 30.8 + - + +
35A SER* 3.9 1.5 - - - +
37A VAL* 1.3 78.8 - - + +
39A TYR* 1.3 63.0 + - - +
41A GLU* 3.3 7.1 + - - +
42A SER* 2.9 21.1 + - - -
226A TYR* 3.4 50.0 + - + +
288A GLN* 5.6 1.8 - - - +
289A GLN* 2.9 28.9 + - - +
38B LYS* 6.2 3.6 - - + -
41B GLU* 2.9 31.9 + - - +
226B TYR* 5.2 1.6 - - - -
274B TYR* 3.9 11.9 + - - -
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER 3.0 19.6 + - - +
36A TYR* 3.4 8.5 - + - +
38A LYS* 1.3 76.2 - - - +
40A LEU* 1.3 78.6 + - + +
42A SER* 2.7 24.9 + - - -
70A LEU* 4.4 14.4 - - + -
107A TRP* 4.1 13.7 - + - -
109A THR* 5.7 0.9 - - - -
221A PRO* 3.5 30.1 - - + +
222A GLU* 3.8 25.1 - - + -
226A TYR* 3.6 11.3 - + + -
244A ALA* 3.3 31.4 - - + -
247A LEU* 3.3 27.4 + - - +
248A ALA* 3.4 26.5 + - + +
251A PHE* 5.7 2.7 - + + -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.8 33.4 - - + +
14A ILE* 3.8 30.1 - - + -
36A TYR 3.2 11.9 + - - +
39A TYR* 1.3 91.4 - - + +
41A GLU* 1.3 64.6 + - - +
43A ALA* 3.1 14.7 + - - +
45A ALA* 3.5 24.4 + - + +
47A VAL* 3.9 15.3 - - + -
70A LEU* 4.1 10.1 - - + -
248A ALA* 4.9 3.4 - - + -
251A PHE* 3.7 30.3 - - + -
252A VAL* 4.8 4.5 - - + -
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.0 27.9 + - - +
38A LYS* 3.9 6.6 - - - +
40A LEU* 1.3 76.7 - - - +
42A SER* 1.3 63.1 + - - +
44A GLY 3.0 12.0 + - - -
45A ALA 3.3 19.1 - - - +
46A ARG* 4.9 0.8 - - - -
47A VAL* 4.1 11.1 + - + +
273A ILE* 3.6 26.7 - - - +
274A TYR* 3.7 18.1 + - - -
38B LYS* 2.9 35.3 + - - +
225B PRO* 3.3 15.7 - - - +
226B TYR* 3.4 15.1 - - + -
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS 2.9 6.7 + - - -
39A TYR* 2.7 20.3 + - - -
41A GLU* 1.3 75.8 - - - +
43A ALA* 1.3 56.5 + - - +
44A GLY 3.3 0.7 - - - -
226A TYR* 3.4 24.6 + - - -
245A PHE* 3.4 24.9 - - - -
248A ALA* 4.2 4.5 - - - +
42B SER* 4.1 7.4 - - - -
225B PRO* 3.7 6.8 - - - +
226B TYR* 3.3 21.8 + - - -
241B VAL* 3.3 17.2 - - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU 3.1 3.9 + - - +
41A GLU 3.0 1.4 - - - -
42A SER* 1.3 78.3 + - - +
44A GLY* 1.3 60.3 + - - +
45A ALA 3.6 1.1 - - - -
245A PHE* 4.3 4.5 - - + -
248A ALA* 3.5 30.5 - - + -
249A GLU* 3.6 12.2 - - + +
252A VAL* 3.4 36.3 - - + +
256A ARG* 3.9 9.4 + - - -
241B VAL* 3.7 14.3 - - - +
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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