Contacts of the helix formed by residues 34 - 46 (chain N) in PDB entry 6L49
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 TYR 34 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25M PHE* 3.7 30.7 - + + -
26M PRO* 3.9 23.3 - - + -
29M ARG* 4.8 5.2 - - + +
30M VAL* 3.4 26.5 + - + +
33M LEU* 4.5 16.4 - - + +
55M LEU* 5.3 4.3 - - + +
33N SER* 1.3 79.3 - - - +
35N SER* 1.3 61.9 + - - +
36N ILE 3.7 1.1 - - - -
37N TYR* 3.7 16.4 - + + -
38N VAL* 3.3 31.3 + - + +
56N MET* 3.3 6.8 - - - +
60N ASN* 3.1 22.2 + - + +
63N VAL* 4.0 26.2 - - + -
64N ASN* 4.3 14.1 - - - -
67N PHE* 6.0 2.8 - + + -
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Residues in contact with SER 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J C 4.0 7.8 + - - -
33N SER* 3.3 17.2 + - - -
34N TYR* 1.3 77.7 - - - +
36N ILE* 1.3 76.4 + - - +
39N TYR* 2.9 28.6 + - - +
56N MET* 3.7 32.7 - - - +
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Residues in contact with ILE 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J G 3.3 50.9 - - + +
219J C 3.5 32.5 - - + +
35N SER* 1.3 85.1 + - - +
37N TYR* 1.3 70.5 + - + +
39N TYR* 3.6 12.9 - - + +
40N LYS* 2.8 45.3 + - - +
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Residues in contact with TYR 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J G 3.1 54.2 + - - -
219J C 4.2 9.8 + - - -
18M SER* 6.0 0.2 - - - -
24M GLN* 3.3 22.2 - - - +
25M PHE* 3.6 23.3 - - + -
26M PRO* 3.7 33.6 - - + +
29M ARG* 4.1 10.8 + - + -
33N SER 3.5 16.6 - - - -
34N TYR* 3.7 27.1 - + + +
35N SER 3.2 0.4 - - - -
36N ILE* 1.3 79.0 - - + +
38N VAL* 1.3 60.5 + - - +
40N LYS* 3.2 11.4 + - + +
41N VAL* 2.9 31.9 + - - +
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Residues in contact with VAL 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M PHE* 3.8 21.3 - - + -
59M THR* 3.9 16.2 - - - +
63M LEU* 3.4 28.6 - - + +
34N TYR* 3.3 25.1 + - + +
37N TYR* 1.3 75.1 - - - +
39N TYR* 1.3 58.7 + - - +
41N VAL* 3.3 6.2 + - - -
42N LEU* 2.9 25.8 + - - +
51N ILE* 4.5 2.9 - - + -
56N MET* 3.7 23.1 - - + -
59N MET* 4.2 13.0 - - + +
63N VAL* 4.4 8.7 - - + -
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Residues in contact with TYR 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-223I G 3.2 41.0 + - + -
-222I G 2.7 42.5 + - - -
35N SER 2.9 19.0 + - - +
36N ILE* 3.6 15.3 - - + +
38N VAL* 1.3 78.6 - - - +
40N LYS* 1.3 63.7 + - + +
42N LEU* 3.4 10.3 + - + +
43N LYS* 2.9 66.6 + - + +
50N GLY* 4.9 1.3 - - - -
51N ILE* 4.7 15.7 - - + -
56N MET* 5.2 0.4 - - - -
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Residues in contact with LYS 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217J A 5.3 1.8 - - - -
218J G 3.4 33.5 + - - -
24M GLN* 4.5 20.9 - - + +
36N ILE* 2.8 32.6 + - - +
37N TYR* 3.2 10.0 + - + +
39N TYR* 1.3 80.2 - - + +
41N VAL* 1.3 61.3 + - - +
43N LYS* 3.4 6.4 + - - +
44N GLN* 2.9 35.4 + - + +
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Residues in contact with VAL 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M GLN* 3.8 24.7 - - + -
25M PHE* 4.9 4.0 - - + -
56M GLU* 4.4 12.8 - - + +
59M THR* 3.8 28.9 - - + -
60M ALA* 4.0 21.8 - - + -
63M LEU* 3.8 11.0 - - + -
37N TYR 2.9 21.4 + - - +
38N VAL* 3.7 6.1 - - - +
40N LYS* 1.3 77.5 - - - +
42N LEU* 1.3 55.7 + - - +
44N GLN* 3.2 9.7 + - - +
45N VAL* 2.9 31.0 + - + +
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Residues in contact with LEU 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M LEU* 3.8 30.7 - - + +
78M ILE* 3.8 25.6 - - + -
38N VAL 2.9 17.6 + - - +
39N TYR* 3.6 10.1 - - + +
41N VAL* 1.3 78.1 - - - +
43N LYS* 1.3 52.5 + - + +
45N VAL* 3.3 6.6 + - + +
46N HIS* 2.6 43.5 + - + +
49N THR* 3.5 22.9 - - + +
50N GLY* 3.6 33.0 - - - +
51N ILE* 3.8 14.6 - - + +
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Residues in contact with LYS 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-223I G 4.2 5.4 + - - -
-222I G 5.3 0.2 - - - -
39N TYR* 2.9 63.6 + - + +
40N LYS* 3.4 6.5 + - - +
42N LEU* 1.3 74.7 - - - +
44N GLN* 1.3 61.1 + - - +
46N HIS 3.3 13.8 - - - +
47N PRO* 2.9 38.2 + - + +
48N ASP* 4.6 0.4 - - - +
49N THR 3.1 27.8 + - - +
50N GLY* 4.0 3.4 - - - +
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Residues in contact with GLN 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M GLN* 3.1 49.5 + - - +
56M GLU* 4.7 2.9 - - - +
40N LYS* 2.9 18.7 + - + +
41N VAL* 3.2 8.7 + - - +
43N LYS* 1.3 79.7 - - - +
45N VAL* 1.3 62.9 + - + +
47N PRO* 5.7 0.9 - - - +
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Residues in contact with VAL 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M ALA* 4.3 25.1 - - + +
63M LEU* 4.2 16.6 - - + -
64M GLU* 3.5 24.1 - - - +
41N VAL* 2.9 20.7 + - + +
42N LEU* 3.4 12.8 - - + +
44N GLN* 1.3 80.9 - - + +
46N HIS* 1.3 87.3 + - - +
47N PRO* 4.5 3.4 - - - +
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Residues in contact with HIS 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M LEU 4.1 3.3 + - - -
64M GLU* 3.4 50.7 + - - -
67M GLY* 4.0 10.4 - - - -
68M ASN* 3.2 15.7 + - - -
71M ARG* 3.5 39.6 + - - +
42N LEU* 2.6 30.2 + - + +
43N LYS* 3.3 13.7 - - - +
44N GLN 3.5 0.8 - - - -
45N VAL* 1.3 93.6 + - - +
47N PRO* 1.3 71.6 - - - +
48N ASP 3.6 0.4 - - - +
49N THR* 3.7 29.2 - - - +
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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