Contacts of the helix formed by residues 37 - 49 (chain N) in PDB entry 5GSE
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 37 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M PHE* 4.2 15.9 - + + -
26M PRO* 4.5 16.4 - - + -
29M ARG* 5.1 6.9 - - + +
30M VAL* 5.3 6.7 - - + +
33M LEU* 3.2 30.4 - - + +
55M LEU* 5.1 4.9 - - + +
36N SER* 1.3 76.8 - - - +
38N SER* 1.3 62.5 + - - +
39N ILE 3.4 2.2 - - - -
40N TYR* 3.3 20.4 + + + -
41N VAL* 3.1 31.9 + - + +
63N ASN* 2.4 36.4 + - - +
66N VAL* 3.6 36.1 - - + -
67N ASN* 3.3 24.7 + - - -
70N PHE* 4.7 12.3 - - - -
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Residues in contact with SER 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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36N SER* 2.6 28.2 + - - -
37N TYR* 1.3 78.3 - - - +
39N ILE* 1.3 62.0 + - - +
41N VAL* 3.3 5.0 - - - +
42N TYR* 2.9 29.3 + - - +
59N MET* 3.5 37.9 - - - +
63N ASN* 3.9 3.3 + - - +
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Residues in contact with ILE 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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225I G 3.5 53.2 - - + +
226I C 3.9 17.9 - - + +
36N SER 5.8 0.4 - - - +
38N SER* 1.3 78.9 - - - +
40N TYR* 1.3 83.8 + - + +
42N TYR* 3.4 8.3 + - - +
43N LYS* 2.9 39.0 + - - +
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Residues in contact with TYR 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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225I G 2.7 39.1 + - - -
24M GLN 2.9 24.9 - - - +
25M PHE* 3.9 23.6 - - + -
26M PRO* 3.5 35.9 - - + +
29M ARG* 3.0 34.9 + - - -
36N SER 4.1 2.5 - - - -
37N TYR* 3.3 20.4 + + - +
38N SER 3.2 0.8 - - - -
39N ILE* 1.3 87.2 - - + +
41N VAL* 1.3 61.2 + - - +
42N TYR 3.1 1.3 - - - -
43N LYS* 3.1 19.1 + - - +
44N VAL* 2.9 32.7 + - - +
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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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25M PHE* 4.0 11.0 - - + -
59M THR* 3.9 28.3 - - + -
63M LEU* 3.2 9.7 - - + +
37N TYR* 3.1 21.0 + - + +
38N SER* 3.3 11.2 - - - +
40N TYR* 1.3 76.3 - - - +
42N TYR* 1.3 60.4 + - - +
44N VAL 4.5 0.4 - - - +
45N LEU* 2.9 29.6 + - - +
54N ILE* 5.4 1.6 - - + -
59N MET* 3.3 29.2 - - + -
62N MET* 4.3 23.8 - - + +
63N ASN* 5.7 0.4 - - - +
66N VAL* 4.5 6.1 - - + -
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Residues in contact with TYR 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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21J G 3.3 41.2 + - + -
22J G 3.2 30.0 + - - -
38N SER 2.9 17.8 + - - +
39N ILE* 3.5 9.0 - - - +
41N VAL* 1.3 76.7 - - - +
43N LYS* 1.3 62.1 + - + +
45N LEU* 3.5 4.6 - - + +
46N LYS* 2.9 72.1 + - + +
54N ILE* 4.0 20.4 - - + -
59N MET* 4.8 5.4 - - + -
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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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225I G 3.3 24.8 + - - -
24M GLN* 4.0 37.2 + - + +
39N ILE* 2.9 31.6 + - - +
40N TYR* 3.1 29.2 + - - +
42N TYR* 1.3 80.3 - - + +
44N VAL* 1.3 56.9 + - - +
46N LYS* 3.4 4.7 + - - +
47N GLN* 2.9 28.2 + - - +
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Residues in contact with VAL 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* 3.8 20.4 - - + -
25M PHE* 3.7 20.6 - - + -
56M GLU* 3.8 13.9 - - + +
59M THR* 4.4 7.9 - - + -
60M ALA* 3.6 41.5 - - + +
63M LEU* 4.5 2.2 - - + -
40N TYR 2.9 19.7 + - - +
41N VAL 4.1 3.1 - - - +
43N LYS* 1.3 75.0 - - - +
45N LEU* 1.3 63.1 + - - +
47N GLN* 3.0 12.2 + - + +
48N VAL* 2.9 27.7 + - + +
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Residues in contact with LEU 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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63M LEU* 3.8 21.9 - - + +
78M ILE* 3.6 26.7 - - + -
41N VAL 2.9 21.4 + - - +
42N TYR* 3.5 7.4 - - + +
43N LYS 3.2 0.2 - - - -
44N VAL* 1.3 77.1 - - - +
46N LYS* 1.3 61.2 + - - +
48N VAL* 3.3 5.4 - - + +
49N HIS* 2.6 42.5 + - + +
52N THR* 3.9 25.6 - - - +
53N GLY* 3.9 16.6 - - - +
54N ILE* 3.7 32.1 - - + -
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Residues in contact with LYS 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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21J G 4.6 0.6 + - - -
22J G 5.1 2.2 - - - -
42N TYR* 2.9 68.9 + - + +
43N LYS* 4.0 4.5 - - - +
45N LEU* 1.3 77.0 - - - +
47N GLN* 1.3 60.2 + - - +
49N HIS 3.8 4.0 - - - +
50N PRO* 3.2 49.4 - - + +
51N ASP 5.0 1.6 - - - -
52N THR 2.7 24.7 + - - -
53N GLY* 3.8 4.6 - - - -
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Residues in contact with GLN 47 (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* 3.3 40.4 + - - +
56M GLU* 4.1 5.2 + - - +
43N LYS 2.9 13.3 + - - +
44N VAL* 3.0 14.1 + - + +
46N LYS* 1.3 79.0 - - - +
48N VAL* 1.3 59.3 + - + +
50N PRO* 4.7 3.3 - - - +
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Residues in contact with VAL 48 (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* 4.7 8.3 - - + +
63M LEU* 4.4 15.7 - - + -
64M GLU* 3.7 34.5 - - + +
44N VAL* 2.9 24.3 + - + +
45N LEU* 3.3 10.8 - - + +
47N GLN* 1.3 77.8 - - + +
49N HIS* 1.3 79.2 + - + +
50N PRO* 3.8 6.5 - - - +
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Residues in contact with HIS 49 (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 3.5 21.8 - - - -
64M GLU* 3.1 18.6 + - + +
67M GLY* 3.6 11.3 - - - -
68M ASN* 2.9 35.6 + - - -
71M ARG* 3.4 25.2 + - - -
45N LEU* 2.6 24.6 + - + +
46N LYS* 3.8 1.9 - - - -
48N VAL* 1.3 82.8 + - + +
50N PRO* 1.3 68.5 - - - +
51N ASP* 3.1 12.0 + - - +
52N THR* 3.0 34.8 + - + +
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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