Contacts of the helix formed by residues 53 - 76 (chain F) in PDB entry 3PJA
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 ASP 53 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F ILE* 1.3 67.8 + - - +
55F PRO* 3.6 17.1 - - + +
56F LYS* 3.4 26.9 + - - +
57F ARG* 3.3 35.4 + - - +
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Residues in contact with ILE 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F VAL* 5.5 12.3 - - + -
53F ASP* 1.3 71.4 - - - +
55F PRO* 1.3 75.2 - - + +
57F ARG* 2.8 42.6 - - + +
58F CYS* 3.0 11.0 + - - +
108F LEU* 3.9 49.4 - - + +
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Residues in contact with PRO 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ASP* 3.6 13.9 - - + +
54F ILE* 1.3 94.4 - - + +
56F LYS* 1.3 63.0 + - - +
58F CYS* 3.2 11.1 + - + +
59F LEU* 3.0 21.2 + - - +
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Residues in contact with LYS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ASP* 3.4 27.1 + - - +
54F ILE 3.2 0.8 - - - -
55F PRO* 1.3 78.9 - - - +
57F ARG* 1.3 63.2 + - - +
59F LEU* 3.0 40.4 + - + +
60F LYS* 3.0 47.9 + - + +
63F GLU* 5.4 2.8 + - - -
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU* 3.2 31.4 + - + +
42F LEU* 4.1 19.7 - - + +
44F GLY* 3.1 34.6 - - - +
45F VAL* 4.5 6.6 - - - +
53F ASP* 3.3 34.3 + - - +
54F ILE* 2.8 50.9 - - + +
56F LYS* 1.3 78.0 - - - +
58F CYS* 1.3 63.9 + - - +
60F LYS* 3.4 12.8 + - + +
61F ALA* 3.0 24.8 + - - +
108F LEU* 5.4 2.2 - - - -
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Residues in contact with CYS 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 4.3 8.7 - - - +
54F ILE* 3.0 18.3 + - - +
55F PRO* 3.5 12.6 - - + +
57F ARG* 1.3 75.2 - - - +
59F LEU* 1.3 62.8 + - - +
61F ALA* 3.4 2.6 + - - +
62F ARG* 3.0 31.2 + - - +
105F VAL* 3.8 19.0 - - + +
108F LEU* 3.7 37.7 - - - -
109F GLU* 3.8 24.5 - - + +
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Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F PRO 3.0 11.3 + - - +
56F LYS* 3.0 38.7 + - + +
58F CYS* 1.3 74.4 - - - +
60F LYS* 1.3 67.7 + - + +
62F ARG* 3.1 15.1 + - + +
63F GLU* 3.0 39.1 + - + +
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Residues in contact with LYS 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU* 3.7 33.0 - - + -
56F LYS* 3.0 48.8 + - + +
57F ARG* 3.8 11.0 - - + +
59F LEU* 1.3 78.7 - - - +
61F ALA* 1.3 64.2 + - - +
63F GLU* 3.0 32.3 + - - +
64F HIS* 3.1 11.8 + - - -
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ILE* 4.1 12.2 - - + +
41F LEU* 3.9 12.7 - - + +
42F LEU* 3.8 25.8 - - + -
57F ARG 3.0 18.4 + - - +
58F CYS 3.5 5.2 - - - +
60F LYS* 1.3 77.4 - - - +
62F ARG* 1.3 62.7 + - - +
64F HIS* 3.0 16.7 + - - +
65F PHE* 3.0 17.9 + - + -
105F VAL* 3.9 10.3 - - + -
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Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F CYS 3.0 19.3 + - - +
59F LEU* 3.1 11.0 + - + +
61F ALA* 1.3 75.1 - - - +
63F GLU* 1.3 62.5 + - - +
65F PHE* 3.3 25.6 + - + +
66F GLY 3.7 2.8 + - - -
69F LYS* 5.0 2.9 + - - -
105F VAL* 3.8 20.9 - - + +
106F VAL* 4.6 7.3 - - - +
109F GLU* 2.7 43.3 + - - -
122F ILE* 3.9 34.0 - - + +
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F LYS* 5.4 2.6 + - - -
59F LEU* 3.0 39.1 + - + +
60F LYS* 3.0 22.7 + - - +
62F ARG* 1.3 78.4 - - - +
64F HIS* 1.3 61.5 + - - +
66F GLY* 3.1 14.9 + - - -
67F THR* 4.0 2.9 + - - -
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Residues in contact with HIS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F THR* 4.0 13.1 - - + +
37F GLU* 3.4 36.0 + - + +
38F ILE* 3.5 21.5 - - + -
41F LEU* 3.8 24.9 - - + +
60F LYS* 3.1 8.1 + - - +
61F ALA 3.0 9.9 + - - +
63F GLU* 1.3 70.8 - - - +
65F PHE* 1.3 57.1 + - - +
66F GLY 2.9 5.6 - - - -
67F THR* 2.9 36.2 + - + -
68F VAL* 3.1 10.6 + - - +
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Residues in contact with PHE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ILE* 3.7 24.2 - - + -
61F ALA 3.0 26.7 + - - -
62F ARG* 3.4 17.5 - - + +
63F GLU 3.2 0.6 - - - -
64F HIS* 1.3 76.1 - - - +
66F GLY* 1.3 56.4 + - - +
67F THR 3.4 0.2 - - - -
68F VAL* 3.3 14.6 - - + +
69F LYS* 3.0 34.9 + - - +
98F LEU* 4.3 11.9 - - + -
101F LEU* 3.8 11.7 - - + -
102F ALA* 3.6 32.5 - - + -
105F VAL* 4.4 14.1 - - + -
122F ILE* 4.0 25.8 - - + +
123F LEU* 3.5 34.1 - - + -
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Residues in contact with GLY 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F ARG 3.7 3.4 + - - -
63F GLU 3.1 10.4 + - - -
64F HIS 2.9 1.6 + - - -
65F PHE* 1.3 75.7 - - - +
67F THR* 1.3 65.2 + - - +
68F VAL 3.1 1.1 - - - -
69F LYS* 3.0 23.7 + - - +
70F THR* 3.0 21.8 + - - +
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Residues in contact with THR 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F THR* 3.8 23.3 - - + +
63F GLU 4.0 2.7 + - - -
64F HIS* 3.1 24.3 + - + -
66F GLY* 1.3 74.3 - - - +
68F VAL* 1.3 64.5 + - - +
70F THR* 3.2 9.8 + - - +
71F HIS* 3.0 40.7 + - + +
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Residues in contact with VAL 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 4.2 11.9 - - + -
34F THR* 3.5 27.4 - - + -
38F ILE* 4.4 2.5 - - + -
64F HIS 3.1 5.1 + - - +
65F PHE* 3.3 24.0 - - + +
66F GLY 3.1 0.2 - - - -
67F THR* 1.3 78.7 - - - +
69F LYS* 1.3 62.7 + - - +
71F HIS* 3.1 4.0 + - - +
72F LEU* 3.0 36.6 + - + +
98F LEU* 4.1 24.0 - - + -
123F LEU* 3.8 29.4 - - + +
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Residues in contact with LYS 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F ARG 5.0 3.0 + - - -
65F PHE* 3.0 28.8 + - - +
66F GLY* 3.0 12.4 + - - +
68F VAL* 1.3 75.2 - - - +
70F THR* 1.3 66.1 + - + +
72F LEU* 3.2 3.8 + - - +
73F THR* 3.0 27.4 + - - +
121F GLU 3.5 19.3 - - - -
122F ILE* 2.8 27.8 + - - +
123F LEU 3.3 24.7 - - - +
124F GLY* 3.8 9.9 - - - +
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Residues in contact with THR 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F GLY 3.0 15.0 + - - +
67F THR* 3.2 12.8 + - - +
69F LYS* 1.3 77.7 - - + +
71F HIS* 1.3 66.8 + - - +
73F THR* 3.3 8.5 + - - -
74F SER* 3.0 26.7 + - - -
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Residues in contact with HIS 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 3.6 16.0 - - + +
30F SER* 2.6 34.1 + - - -
31F LEU* 3.7 21.1 - - + -
34F THR* 4.4 7.6 + - - -
67F THR* 3.0 34.9 + - + +
68F VAL 3.1 4.5 + - - +
70F THR* 1.3 86.7 + - - +
72F LEU* 1.3 57.6 + - - +
74F SER* 3.2 12.6 + - - -
75F LEU 3.0 20.3 + - - -
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 3.5 28.7 - - + -
68F VAL* 3.0 23.3 + - + +
69F LYS 3.9 3.6 - - - +
71F HIS* 1.3 73.2 - - - +
73F THR* 1.3 61.3 + - - +
74F SER 3.1 0.4 - - - -
75F LEU* 3.4 20.0 - - + +
76F LYS* 3.0 34.5 + - - +
95F LEU* 5.0 5.8 - - + -
98F LEU* 4.8 7.6 - - + -
123F LEU* 3.3 41.5 - - + +
124F GLY 4.5 6.1 - - - +
125F ILE* 3.9 17.3 - - + -
133F PHE* 5.0 12.6 - - + -
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Residues in contact with THR 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F LYS* 3.0 14.6 + - - +
70F THR* 3.7 10.7 - - - -
72F LEU* 1.3 76.6 - - - +
74F SER* 1.3 61.3 + - - +
76F LYS* 3.5 32.7 + - + +
77F THR* 3.4 19.7 - - + +
124F GLY* 4.6 4.2 + - - -
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Residues in contact with SER 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F VAL* 4.1 9.5 - - - +
70F THR 3.0 12.9 + - - -
71F HIS* 3.2 19.7 + - - -
73F THR* 1.3 76.8 - - - +
75F LEU* 1.3 62.4 + - - +
77F THR* 2.6 27.0 + - - -
78F LYS* 3.4 22.4 + - - +
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Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 3.8 36.6 - - + +
27F VAL* 3.7 28.5 - - + -
28F VAL* 5.0 2.2 - - + -
31F LEU* 4.8 4.3 - - + -
71F HIS 3.0 13.4 + - - +
72F LEU* 3.2 28.9 + - + +
74F SER* 1.3 73.3 + - - +
76F LYS* 1.3 62.8 + - - +
77F THR 3.0 4.5 - - - -
78F LYS* 2.8 24.8 + - + +
79F PHE* 3.6 14.5 - - + -
91F TRP* 4.3 21.3 - - + -
133F PHE* 4.3 18.4 - - + -
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Residues in contact with LYS 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F LEU* 3.0 22.2 + - - +
73F THR* 3.5 29.3 + - + +
74F SER 3.3 0.2 - - - -
75F LEU* 1.3 75.3 - - - +
77F THR* 1.3 58.8 + - + +
79F PHE* 3.2 31.1 - - - +
81F ALA* 5.2 4.7 + - - +
124F GLY 3.3 23.2 + - - -
125F ILE* 4.9 1.8 - - - +
126F GLU* 2.7 38.6 + - - +
133F PHE* 4.0 28.0 - - + +
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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