Contacts of the helix formed by residues 36 - 50 (chain K) in PDB entry 5G04
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 GLU 36 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7K ARG* 4.1 12.2 + - - -
33K SER* 4.0 12.6 + - - +
34K ARG 3.1 9.7 + - - +
35K GLU* 1.3 74.2 - - - +
37K PRO* 1.3 82.8 - - + +
38K GLN* 4.1 17.5 + - - +
39K ASP* 3.7 29.0 + - + +
40K ILE* 3.0 28.8 + - - +
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Residues in contact with PRO 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K GLU 4.9 0.4 - - - +
36K GLU* 1.3 94.0 - - + +
38K GLN* 1.3 70.7 + - + +
40K ILE* 4.2 2.1 - - + +
41K TYR* 3.3 19.4 + - - +
65K LEU* 4.5 8.5 - - + +
69K TYR* 3.3 47.6 - - + +
72K CYS* 4.5 8.7 - - - -
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Residues in contact with GLN 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K GLU* 3.3 18.9 + - - +
37K PRO* 1.3 88.0 - - + +
39K ASP* 1.3 67.1 + - - +
41K TYR* 3.4 19.2 - - - +
42K TRP* 3.6 17.3 + - - +
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Residues in contact with ASP 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ARG* 3.3 31.5 + - - +
26K ALA 4.9 3.1 - - - +
29K VAL* 3.5 20.0 - - + +
30K ALA* 4.4 18.3 - - - +
33K SER* 2.7 35.9 + - - -
36K GLU* 3.2 24.1 + - + +
38K GLN* 1.3 78.5 - - - +
40K ILE* 1.3 63.5 + - - +
42K TRP* 3.3 18.5 + - - +
43K LEU* 3.4 10.6 + - - +
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Residues in contact with ILE 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ALA* 5.0 6.7 - - + -
35K GLU* 3.7 15.5 - - + -
36K GLU 3.0 38.0 + - - +
37K PRO* 4.9 0.2 - - + -
39K ASP* 1.3 72.8 - - - +
41K TYR* 1.3 65.8 + - - +
43K LEU* 3.1 11.4 + - + +
44K ALA* 2.9 22.1 + - - +
59K ALA* 4.2 16.6 - - + +
60K LEU* 4.4 6.7 - - + -
63K ARG* 3.3 33.9 - - + +
65K LEU* 3.4 39.7 - - + -
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Residues in contact with TYR 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ASP* 5.5 2.0 + - - -
37K PRO 3.3 14.7 + - - +
38K GLN* 3.4 13.9 - - - +
39K ASP 3.2 0.4 - - - -
40K ILE* 1.3 78.1 - - - +
42K TRP* 1.3 95.6 + + - +
44K ALA* 3.2 5.2 + - - +
45K GLN* 2.9 39.6 + - - +
60K LEU* 4.9 1.5 - - + +
71K ALA* 3.8 33.3 + - + +
72K CYS* 3.7 23.8 - - - -
74K TYR* 5.3 3.6 - - - -
75K LEU* 3.6 26.3 - - + +
128K ILE* 5.2 6.2 - - - +
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Residues in contact with TRP 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ASP* 4.2 17.7 - - - -
7K ARG* 5.5 6.5 - - + -
10K VAL* 4.9 16.8 - - + -
11K ARG* 3.4 62.2 - - + +
14K LEU* 4.5 15.3 - - + +
26K ALA* 4.5 7.4 - - + -
38K GLN* 3.6 15.1 + - + +
39K ASP* 3.3 14.1 + - - +
40K ILE 3.3 0.4 - - - -
41K TYR* 1.3 110.0 - + - +
43K LEU* 1.3 58.6 + - - +
45K GLN* 3.2 25.7 + - + +
46K CYS* 2.9 32.2 + - - +
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Residues in contact with LEU 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K LEU* 3.8 25.1 - - + +
26K ALA* 4.1 17.1 - - - +
27K ASP* 3.9 38.4 - - - +
30K ALA* 4.4 13.9 - - + -
39K ASP 3.4 9.7 + - - +
40K ILE* 3.1 15.7 + - + +
42K TRP* 1.3 77.0 - - - +
44K ALA* 1.3 63.8 + - - +
46K CYS* 3.3 2.3 - - - +
47K LEU* 3.1 34.2 + - + +
55K ARG* 5.6 0.2 - - - +
59K ALA* 5.1 10.5 - - + -
63K ARG* 5.3 8.5 - - - +
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Residues in contact with ALA 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K ILE* 2.9 12.1 + - - +
41K TYR 3.5 7.4 - - - +
43K LEU* 1.3 78.1 - - - +
45K GLN* 1.4 62.6 + - - +
47K LEU* 3.3 7.0 + - - -
48K TYR* 2.9 21.5 + - - +
56K ALA* 3.5 18.3 - - + +
59K ALA* 4.8 5.4 - - + -
60K LEU* 3.5 40.8 - - + -
75K LEU* 3.7 5.8 - - + +
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Residues in contact with GLN 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ASP 3.9 12.5 - - - +
17J GLN* 2.6 36.1 + - - +
14K LEU* 4.5 7.4 - - + -
41K TYR* 2.9 28.2 + - + +
42K TRP* 3.3 35.7 - - + +
44K ALA* 1.4 75.8 - - - +
46K CYS* 1.3 63.0 + - - +
48K TYR* 3.2 5.3 + - - +
49K LEU* 3.1 33.8 + - + +
75K LEU* 3.4 30.4 - - + +
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Residues in contact with CYS 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K VAL* 4.8 1.1 - - - -
14K LEU* 4.1 11.9 - - - +
19K TYR 4.4 1.8 - - - -
22K ALA* 3.5 20.0 - - - -
23K LEU* 3.2 45.8 - - + -
26K ALA* 3.7 9.2 - - - -
42K TRP 2.9 10.5 + - - +
43K LEU* 3.3 12.1 - - - +
45K GLN* 1.3 74.7 - - - +
47K LEU* 1.3 52.2 + - - +
49K LEU* 3.1 12.5 - - - +
50K THR* 2.2 37.8 + - - -
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Residues in contact with LEU 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261J ASP* 5.6 2.2 - - - +
23K LEU* 4.0 13.2 - - + -
43K LEU* 3.1 29.6 + - + +
44K ALA* 3.5 3.8 - - - +
46K CYS* 1.3 79.8 - - - +
48K TYR* 1.3 61.1 + - - +
50K THR* 3.1 8.4 + - - -
52K GLN* 2.9 51.1 + - + +
55K ARG* 3.4 67.1 - - + +
56K ALA* 3.5 17.0 - - + +
59K ALA* 4.7 4.9 - - + -
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Residues in contact with TYR 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J GLN* 3.2 34.8 - - + -
19J TYR* 5.9 4.7 - + - -
44K ALA 2.9 14.2 + - - +
45K GLN 3.2 8.0 + - - +
47K LEU* 1.3 77.6 - - - +
49K LEU* 1.3 65.7 + - + +
51K ALA* 3.1 11.1 + - - -
53K TYR* 3.2 40.5 + + - -
56K ALA* 3.8 4.6 - - - +
75K LEU* 4.0 16.6 - - + -
78K ARG* 3.8 37.9 + - + +
79K CYS* 3.5 21.5 - - - -
81K TYR* 5.8 2.1 - - - -
82K ALA* 3.7 19.5 - - + +
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Residues in contact with LEU 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J GLN* 3.8 24.5 - - - +
19J TYR* 5.3 6.5 - - - +
14K LEU* 3.9 17.7 - - + -
19K TYR* 3.2 65.7 - - + +
45K GLN* 3.1 19.7 - - + +
46K CYS* 3.1 27.8 - - - +
48K TYR* 1.3 84.0 - - + +
50K THR* 1.3 58.0 + - - +
51K ALA* 3.2 1.7 + - - +
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Residues in contact with THR 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TYR* 4.7 11.9 + - + +
20K GLN* 4.1 24.2 - - + +
23K LEU* 3.8 17.7 - - + +
46K CYS 2.2 29.2 + - - -
47K LEU* 3.5 8.9 - - - -
48K TYR 3.1 0.8 - - - -
49K LEU* 1.3 80.4 - - - +
51K ALA* 1.3 66.9 + - - +
52K GLN* 3.4 26.5 + - - +
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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