Contacts of the helix formed by residues 63 - 77 (chain F) in PDB entry 4JCQ
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 HIS 63 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F GLU* 3.6 23.5 + - - -
30F ILE* 2.7 24.9 + - - +
31F ASN* 4.0 11.3 - - + +
32F GLN* 5.6 0.7 - - + -
62F GLY* 1.3 72.8 - - - -
64F VAL* 1.3 64.8 + - - +
65F GLU* 3.3 26.5 - - - +
66F ALA* 3.2 9.8 + - + +
67F GLY* 3.1 18.9 + - - -
92F ALA* 4.3 2.4 - - - +
121F GLY 3.8 3.1 - - - -
122F VAL 3.2 25.1 + - - -
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Residues in contact with VAL 64 (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 GLY 3.8 1.2 + - - -
63F HIS* 1.3 71.1 - - - +
65F GLU* 1.3 68.6 - - + +
67F GLY* 3.1 1.9 + - - -
68F ASP* 2.8 47.9 + - - +
92F ALA* 4.9 8.1 - - - -
118F PRO* 6.3 0.4 - - + -
120F GLY 5.0 0.7 - - - +
121F GLY* 3.2 27.2 + - - +
139F MET* 3.9 26.2 - - + -
142F ARG* 3.8 13.5 - - - +
143F ILE* 3.9 20.6 - - + -
112G ARG* 4.7 6.5 - - - +
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Residues in contact with GLU 65 (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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32F GLN* 4.4 14.7 - - + +
63F HIS* 3.4 27.0 - - - +
64F VAL* 1.3 90.0 + - + +
66F ALA* 1.3 59.8 + - - +
68F ASP* 3.5 9.1 + - - -
69F THR* 3.1 21.3 + - - -
121F GLY 5.0 0.7 - - - +
58G ASN* 3.3 16.6 + - - +
87G GLY* 3.5 13.1 - - - +
88G TRP* 3.5 65.0 - - + +
112G ARG* 5.8 1.6 - - - +
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Residues in contact with ALA 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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30F ILE* 3.8 7.6 - - + +
31F ASN* 3.4 41.5 - - - +
32F GLN* 3.8 6.5 - - + +
35F ALA* 3.9 8.6 - - + +
63F HIS* 3.2 13.5 + - + +
65F GLU* 1.3 78.1 - - - +
67F GLY* 1.3 64.9 + - - +
69F THR* 3.4 2.8 + - - -
70F ILE* 3.2 28.6 + - - +
58G ASN* 4.4 5.6 - - - +
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Residues in contact with GLY 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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30F ILE* 3.5 14.9 - - - +
63F HIS 3.1 12.0 + - - -
64F VAL 3.1 4.5 + - - -
66F ALA* 1.3 74.5 - - - +
68F ASP* 1.3 59.5 + - - +
70F ILE 3.5 0.3 + - - -
71F HIS* 2.9 31.1 + - - +
92F ALA* 4.6 10.1 - - - -
95F THR* 4.7 5.6 - - - +
96F ILE* 3.7 16.1 - - - +
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Residues in contact with ASP 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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64F VAL* 2.8 26.8 + - - +
65F GLU* 3.6 10.5 - - - +
66F ALA 3.3 0.2 - - - -
67F GLY* 1.3 77.3 - - - +
69F THR* 1.3 56.7 + - - +
71F HIS* 3.5 5.3 + - - +
72F ASP* 3.0 35.4 + - - +
95F THR* 4.4 12.6 - - - +
142F ARG* 2.8 44.8 + - - -
143F ILE* 5.2 1.9 - - - +
146F LEU* 5.3 0.2 - - - +
87G GLY* 4.2 5.5 - - - +
110G ASN* 3.5 26.3 - - + +
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Residues in contact with THR 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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35F ALA* 4.5 3.8 - - + -
39F SER* 3.9 7.2 - - - +
65F GLU 3.1 5.2 + - - -
66F ALA* 3.7 8.5 - - - -
67F GLY 3.3 0.4 - - - -
68F ASP* 1.3 72.4 - - - +
70F ILE* 1.3 60.6 + - - +
72F ASP* 3.3 1.8 + - - +
73F MET* 2.8 37.8 + - + +
27G TYR* 3.4 39.5 - - + +
58G ASN* 2.6 30.2 + - - -
86G THR* 2.8 30.2 + - + +
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Residues in contact with ILE 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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26F ILE* 3.9 11.9 - - + -
30F ILE* 4.2 5.2 - - + -
34F LEU* 3.7 30.7 - - + -
35F ALA* 3.8 24.9 - - + +
38F VAL* 4.0 18.4 - - + -
39F SER* 5.5 0.9 - - - +
42F LEU* 5.3 0.2 - - + -
66F ALA 3.2 16.6 + - - +
69F THR* 1.3 72.3 - - + +
71F HIS* 1.3 66.3 + - - +
73F MET* 3.3 5.7 + - - +
74F ILE* 3.0 31.7 + - + +
96F ILE* 3.7 43.5 - - + -
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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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67F GLY 2.9 18.8 + - - +
68F ASP* 3.6 7.0 - - - +
70F ILE* 1.3 78.2 - - - +
72F ASP* 1.3 85.5 + - - +
74F ILE* 3.4 2.3 + - - -
75F LYS* 3.3 44.2 + - + +
95F THR* 3.1 33.7 - - + +
96F ILE* 4.3 3.3 - - - +
98F LEU 4.6 1.2 + - - -
99F ALA* 3.5 36.3 - - + +
146F LEU* 3.7 28.1 - - + +
110G ASN* 3.7 14.6 + - - -
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Residues in contact with ASP 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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68F ASP 3.0 18.2 + - - +
69F THR* 3.9 2.7 - - - +
71F HIS* 1.3 96.8 + - - +
73F MET* 1.3 62.1 + - - +
75F LYS* 3.3 6.8 + - - +
76F PHE* 2.8 31.5 + - - +
86G THR* 4.8 0.9 + - - +
108G LEU* 3.5 27.4 - - + +
109G PRO* 3.4 15.7 - - + +
110G ASN* 2.8 45.8 + - - +
184G GLU 4.7 1.2 - - - +
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Residues in contact with MET 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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38F VAL* 6.3 0.2 - - + -
39F SER* 3.7 27.1 - - - +
42F LEU* 4.2 15.5 - - + -
43F LEU* 3.9 39.0 - - + -
69F THR* 2.8 29.7 + - + +
70F ILE* 3.8 5.6 - - - +
72F ASP* 1.3 72.1 - - - +
74F ILE* 1.3 65.1 + - - +
76F PHE* 4.0 15.3 - - + -
77F ILE* 3.2 34.6 + - + +
25G LEU* 6.3 0.2 - - + -
27G TYR* 4.7 3.1 - - - -
56G PHE* 3.8 28.7 - - + -
86G THR* 5.7 0.2 - - - -
108G LEU* 4.1 11.4 - - + -
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Residues in contact with ILE 74 (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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42F LEU* 4.1 12.3 - - + -
55F ILE* 3.9 28.0 - - + -
70F ILE* 3.0 22.8 + - + +
71F HIS 3.5 6.5 - - - +
73F MET* 1.3 77.8 - - - +
75F LYS* 1.3 60.6 + - - +
77F ILE* 3.5 18.1 - - - +
79F PRO 4.8 1.4 - - - +
81F VAL* 3.8 30.7 - - + +
83F VAL* 5.2 3.8 - - + -
96F ILE* 3.9 36.3 - - + +
99F ALA* 3.7 24.5 - - + +
100F ALA* 4.4 1.8 - - - +
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Residues in contact with LYS 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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71F HIS* 3.3 37.4 + - + +
72F ASP* 3.3 10.1 + - - +
73F MET 3.3 0.4 - - - -
74F ILE* 1.3 75.3 - - - +
76F PHE* 1.3 62.1 + - - +
77F ILE 3.8 4.9 - - - +
98F LEU 4.9 3.2 + - - -
99F ALA* 3.3 28.5 - - - +
101F GLU* 4.8 12.2 + - - +
149F GLU* 5.3 6.7 + - - -
184G GLU* 3.6 33.6 + - + +
185G ASN* 3.0 25.2 + - - +
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Residues in contact with PHE 76 (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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72F ASP 2.8 18.9 + - - +
73F MET* 3.3 25.7 + - + +
75F LYS* 1.3 76.2 - - - +
77F ILE* 1.3 69.2 + - + +
56G PHE* 3.9 20.2 - + - -
108G LEU* 3.8 20.9 - - + -
183G ILE* 3.6 19.7 - - + -
184G GLU 3.2 13.7 - - - +
185G ASN* 3.4 27.1 + - - +
186G ARG* 3.2 63.1 + - - +
189G LEU* 3.9 25.1 - - + -
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Residues in contact with ILE 77 (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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42F LEU* 3.9 33.9 - - + +
43F LEU* 4.6 1.3 - - + -
46F GLU* 3.4 27.1 - - + +
53F ILE* 3.8 29.2 - - + -
73F MET* 3.2 32.7 + - + +
74F ILE 3.5 10.4 - - - +
75F LYS 3.8 6.9 - - - +
76F PHE* 1.3 83.0 - - + +
78F LYS* 1.3 63.8 + - - +
79F PRO* 3.8 12.9 - - + +
81F VAL* 3.9 17.0 - - + -
185G ASN* 5.3 1.2 + - - -
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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