Contacts of the helix formed by residues 69 - 84 (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 TYR 69 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K PRO* 3.3 44.1 - - + +
65K LEU* 3.2 20.3 + - + -
66K ASP 2.8 20.8 - - - +
67K LYS 4.8 0.9 - - - -
68K LEU* 1.3 113.1 - - + +
70K GLU* 1.3 60.9 + - - +
71K ALA* 4.3 8.3 - - + +
72K CYS* 3.2 23.0 + - - +
73K ARG* 2.9 16.1 + - - -
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Residues in contact with GLU 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69K TYR* 1.3 73.4 - - - +
71K ALA* 1.3 58.0 + - - +
73K ARG* 3.3 34.9 + - - +
74K TYR* 2.9 29.8 + - - +
128K ILE* 3.2 27.5 - - + +
129K LYS* 3.3 42.1 + - - +
132K ILE* 4.4 11.6 - - + +
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Residues in contact with ALA 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K TYR* 3.8 20.4 + - + -
69K TYR* 3.2 5.0 - - + +
70K GLU* 1.3 78.9 - - - +
72K CYS* 1.3 65.4 + - - +
74K TYR* 3.3 6.1 + - - +
75K LEU* 3.1 21.7 + - - +
128K ILE* 3.9 24.5 - - + +
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Residues in contact with CYS 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K PRO 4.5 7.9 - - - -
41K TYR* 3.7 32.8 - - - -
60K LEU* 3.7 23.7 - - + +
65K LEU* 3.9 17.9 - - - +
66K ASP* 4.1 5.2 - - - -
69K TYR* 3.2 30.4 + - - +
71K ALA* 1.3 78.9 - - - +
73K ARG* 1.3 64.5 + - - +
75K LEU* 3.1 4.4 + - - +
76K ALA* 2.9 23.9 + - - +
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Residues in contact with ARG 73 (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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66K ASP* 3.1 33.3 + - + +
67K LYS* 5.0 9.6 + - - +
69K TYR 2.9 9.4 + - - +
70K GLU* 3.4 38.0 + - - +
72K CYS* 1.3 75.3 - - - +
74K TYR* 1.3 63.8 + - - +
76K ALA* 3.3 0.5 + - - +
77K ALA* 3.0 22.5 + - - +
92K VAL* 3.6 33.8 + - + +
93K LEU* 4.4 14.2 + - + +
132K ILE* 4.1 17.7 - - + +
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Residues in contact with TYR 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J GLN* 3.8 16.8 - - + -
17J GLN* 6.1 0.2 - - - -
18J GLN* 2.8 25.5 + - - -
41K TYR* 5.3 4.0 - - - -
70K GLU 2.9 13.4 + - - +
71K ALA 3.5 8.3 - - - +
73K ARG* 1.3 77.3 - - - +
75K LEU* 1.3 62.9 + - + +
77K ALA* 3.2 5.9 + - - +
78K ARG* 2.8 59.4 + - + +
128K ILE* 3.6 32.1 - - + -
131K SER* 4.2 5.6 + - - -
132K ILE* 3.9 36.5 - - + +
134K LEU* 6.0 0.5 - - - +
135K LEU* 3.7 33.0 - - + +
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Residues in contact with LEU 75 (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* 4.8 2.7 - - - +
41K TYR* 3.6 24.0 - - + +
44K ALA* 3.7 13.5 - - + -
45K GLN* 3.4 51.1 - - - +
48K TYR* 4.0 25.8 - - + -
60K LEU* 3.8 9.6 - - + -
71K ALA 3.1 8.6 + - - +
72K CYS 3.1 8.5 + - - +
74K TYR* 1.3 85.9 - - + +
76K ALA* 1.3 55.8 + - - +
78K ARG* 3.1 9.7 + - + +
79K CYS* 2.9 37.4 + - - -
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Residues in contact with ALA 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57K ALA* 5.0 6.3 - - - +
60K LEU* 3.7 24.3 - - + +
61K ARG* 5.0 8.5 - - + -
66K ASP* 4.4 12.6 - - + -
72K CYS 2.9 15.0 + - - +
73K ARG 3.7 4.0 - - - +
75K LEU* 1.3 75.1 - - - +
77K ALA* 1.3 62.6 + - - +
79K CYS* 3.1 8.6 + - - +
80K HIS* 3.1 32.9 + - - +
92K VAL* 4.6 10.1 - - + -
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Residues in contact with ALA 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K ARG 3.0 12.6 + - - +
74K TYR* 3.4 10.5 - - - +
76K ALA* 1.3 75.9 - - - +
78K ARG* 1.3 62.7 + - - +
80K HIS 3.3 1.7 + - - -
81K TYR* 3.0 23.2 + - - +
89K ALA* 3.6 13.7 - - + +
92K VAL* 3.9 10.5 - - + +
93K LEU* 3.1 35.9 - - + -
135K LEU* 3.8 12.2 - - + +
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Residues in contact with ARG 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J GLN 3.5 1.4 + - - -
17J GLN* 2.7 54.2 + - - +
18J GLN* 4.0 11.3 + - - +
19J TYR* 5.1 2.2 - - - +
48K TYR* 3.8 32.5 + - + +
74K TYR* 2.8 48.4 + - + +
75K LEU* 3.1 15.9 + - + +
77K ALA* 1.3 78.5 - - - +
79K CYS* 1.3 56.2 + - - +
81K TYR* 3.3 9.6 + - + +
82K ALA* 2.9 29.6 + - - +
134K LEU* 5.9 2.4 - - - +
135K LEU* 3.7 25.8 - - + +
138K LYS* 5.8 7.5 - - - +
165K GLU* 4.8 5.1 + - - -
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Residues in contact with CYS 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K TYR* 3.5 29.8 - - + -
53K TYR* 3.7 23.6 - - + +
56K ALA* 3.5 29.8 - - - -
57K ALA* 4.2 10.3 - - + +
60K LEU* 5.3 0.2 - - - -
75K LEU* 2.9 31.3 + - - -
76K ALA* 3.1 8.5 + - - +
78K ARG* 1.3 75.2 - - - +
80K HIS* 1.3 65.7 + - - +
82K ALA* 3.3 0.7 + - - +
83K ALA* 3.0 23.6 + - - +
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Residues in contact with HIS 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K HIS* 5.9 4.3 + - - -
57K ALA* 3.6 26.3 - - + +
61K ARG* 4.5 27.9 + - + -
76K ALA* 3.1 25.2 + - + +
77K ALA 3.3 2.0 + - - +
79K CYS* 1.3 76.0 - - - +
81K TYR* 1.3 57.2 + - - +
83K ALA* 3.1 7.2 + - + +
84K LYS 3.0 6.8 + - - -
85K GLU* 3.0 55.1 + - + +
86K HIS 4.9 0.2 - - - -
88K GLN* 3.9 21.8 + - + -
89K ALA* 3.7 27.8 - - + +
92K VAL* 4.7 7.3 - - + +
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Residues in contact with TYR 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K TYR* 5.8 1.8 - - - -
77K ALA 3.0 13.3 + - - +
78K ARG* 3.5 13.9 - - + +
80K HIS* 1.3 75.1 - - - +
82K ALA* 1.3 65.9 + - + +
84K LYS* 2.9 38.5 + - - +
86K HIS* 3.4 36.5 - + - -
89K ALA* 4.1 3.3 - - + +
135K LEU* 4.0 19.3 - - + -
138K LYS* 3.7 57.3 + - + +
139K ILE* 3.8 16.4 - - + -
142K ALA* 4.5 3.5 - - + +
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Residues in contact with ALA 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48K TYR* 3.7 15.0 - - + +
53K TYR* 3.6 43.0 - - + +
78K ARG 2.9 16.9 + - - +
79K CYS 3.3 2.7 + - - +
81K TYR* 1.3 81.3 - - + +
83K ALA* 1.3 59.0 - - - +
84K LYS* 3.4 13.2 + - - +
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Residues in contact with ALA 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K TYR* 4.3 14.1 - - + -
54K HIS* 3.9 31.6 + - + +
79K CYS 3.0 14.8 + - - +
80K HIS* 3.3 13.0 - - + +
81K TYR 3.1 0.2 - - - -
82K ALA* 1.3 74.9 - - - +
84K LYS* 1.3 66.1 + - - +
85K GLU* 3.1 12.4 + - + +
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Residues in contact with LYS 84 (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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80K HIS 3.0 0.2 + - - -
81K TYR* 2.9 35.8 + - - -
82K ALA* 3.9 11.0 - - - +
83K ALA* 1.3 83.2 - - - +
85K GLU* 1.3 68.1 + - - +
86K HIS* 3.4 28.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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