Contacts of the helix formed by residues 34 - 43 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE 3.4 3.0 + - - -
33B ALA* 1.3 72.1 - - - +
35B SER* 1.3 62.8 + - - +
37B VAL* 2.9 6.4 + - - +
38B LYS* 2.9 41.1 + - + +
278B PRO* 5.0 0.9 - - + -
289B GLN* 3.0 41.7 + - + +
291B TYR* 3.9 28.5 - - + -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 3.9 10.2 - - - +
34B ALA* 1.3 76.4 - - - +
36B TYR* 1.3 59.8 + - - +
38B LYS* 3.6 3.2 + - - +
39B TYR* 3.0 29.5 + - - +
222B GLU* 3.7 32.3 - - - +
223B LYS* 5.3 0.9 + - - -
226B TYR* 3.8 17.8 - - - -
227B GLU* 2.6 37.8 + - - +
287B PHE* 4.6 1.6 - - - -
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 3.8 20.8 - - + +
32B ILE* 4.7 1.1 - - + -
33B ALA* 3.1 36.7 + - + +
34B ALA 3.1 1.0 - - - -
35B SER* 1.3 77.6 - - - +
37B VAL* 1.3 64.7 + - - +
39B TYR* 3.5 8.2 - + - +
40B LEU* 3.3 28.6 + - - +
70B LEU* 4.1 15.3 - - + -
72B PRO* 3.8 26.5 - - + -
73B GLY* 2.9 30.5 + - - -
109B THR* 4.0 11.0 - - + -
220B HIS* 3.2 15.1 + - - -
222B GLU* 3.1 39.7 + - + -
223B LYS* 5.3 1.0 + - - -
287B PHE* 5.0 7.1 - + - -
1002B BME 4.7 0.2 + - - -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.0 18.4 - - + -
32B ILE* 4.3 11.9 - - + -
34B ALA* 2.9 9.1 + - - +
36B TYR* 1.3 76.4 - - - +
38B LYS* 1.3 67.6 + - + +
40B LEU* 3.3 3.8 + - - +
41B GLU* 3.0 47.7 + - + +
47B VAL* 4.0 8.9 - - + +
273B ILE* 4.2 25.8 - - + -
291B TYR* 3.9 33.7 - - + +
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 6.2 3.8 - - + -
41A GLU* 2.9 29.5 + - - +
226A TYR* 5.2 1.4 - - - -
274A TYR* 3.8 15.6 + - - -
34B ALA* 2.9 28.5 + - + +
35B SER 3.8 1.8 - - - +
37B VAL* 1.3 79.2 - - + +
39B TYR* 1.3 57.8 + - - +
41B GLU* 3.9 7.1 - - - +
42B SER* 2.9 32.1 + - - -
226B TYR* 3.4 44.2 + - + +
288B GLN* 5.5 1.8 - - - +
289B GLN* 2.8 29.2 + - - +
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER 3.0 18.9 + - - +
36B TYR* 3.5 9.0 - + - +
37B VAL 3.2 0.2 - - - -
38B LYS* 1.3 76.7 - - - +
40B LEU* 1.3 79.2 + - + +
42B SER* 2.7 23.6 + - - -
43B ALA 3.8 0.2 + - - -
70B LEU* 4.5 15.0 - - + -
107B TRP* 4.1 13.2 - + - -
109B THR* 5.6 1.1 - - - -
221B PRO* 3.4 29.4 - - + +
222B GLU* 3.8 24.2 - - + -
226B TYR* 3.6 10.9 - + + -
244B ALA* 3.2 33.0 - - + -
247B LEU* 3.2 27.0 + - - +
248B ALA* 3.4 26.3 + - + +
251B PHE* 5.6 2.9 - + + +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 3.7 31.2 - - + -
14B ILE* 3.8 31.6 - - + -
36B TYR 3.3 11.0 + - - +
37B VAL 3.9 2.7 - - - +
39B TYR* 1.3 91.7 - - + +
41B GLU* 1.3 65.6 + - - +
43B ALA* 3.1 14.2 + - - +
45B ALA* 3.5 24.5 + - + +
47B VAL* 3.9 11.2 - - + -
70B LEU* 4.0 11.0 - - + -
248B ALA* 4.9 3.8 - - + -
251B PHE* 3.6 30.1 - - + -
252B VAL* 4.9 4.7 - - + -
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Residues in contact with GLU 41 (chain B).
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 36.1 + - - +
225A PRO* 3.3 15.4 - - - +
226A TYR* 3.4 14.9 - - + -
37B VAL* 3.0 29.0 + - - +
38B LYS* 3.9 6.8 - - - +
39B TYR 3.4 0.2 - - - -
40B LEU* 1.3 76.3 - - - +
42B SER* 1.3 63.7 + - - +
44B GLY 3.0 11.8 + - - -
45B ALA 3.3 18.4 - - - +
46B ARG* 4.9 1.1 - - - -
47B VAL* 4.1 10.5 + - + +
273B ILE* 3.7 25.5 - - - +
274B TYR* 3.8 17.2 + - - -
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Residues in contact with SER 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER* 4.1 7.9 - - - -
225A PRO* 3.7 7.3 - - - +
226A TYR* 3.4 21.5 + - - -
241A VAL* 3.4 17.0 - - - +
245A PHE* 5.8 0.2 - - - +
38B LYS 2.9 7.8 + - - -
39B TYR* 2.7 20.8 + - - -
40B LEU 3.2 0.2 - - - -
41B GLU* 1.3 76.5 - - - +
43B ALA* 1.3 55.8 + - - +
44B GLY 3.3 0.4 - - - -
226B TYR* 3.4 24.9 + - - -
245B PHE* 3.5 21.8 - - - +
248B ALA* 4.2 6.2 - - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A VAL* 3.7 14.4 - - - +
40B LEU 3.1 3.0 + - - +
41B GLU 3.0 1.4 - - - -
42B SER* 1.3 77.7 + - - +
44B GLY* 1.3 60.3 + - - +
45B ALA 3.7 0.7 - - - -
245B PHE* 4.3 4.5 - - + -
248B ALA* 3.4 32.3 - - + -
249B GLU* 3.6 11.2 - - + +
252B VAL* 3.4 34.6 - - + +
256B ARG* 3.7 9.5 + - - -
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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