Contacts of the helix formed by residues 60 - 81 (chain C) in PDB entry 4HFX
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 TRP 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP* 5.1 21.9 - - + +
59C SER* 1.3 75.3 - - - +
61C ARG* 1.3 61.3 + - - +
63C MSE 3.8 27.2 - - - +
64C TYR* 3.1 28.4 + - - +
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 6.1 2.9 - - + +
24C TYR* 3.1 38.6 + - - +
27C GLU* 2.6 53.0 + - - +
37C THR* 6.0 4.3 - - - +
38C ASP* 5.5 8.7 - - + +
59C SER* 3.3 8.8 + - - +
60C TRP* 1.3 78.4 - - - +
62C GLU* 1.3 59.3 + - + +
64C TYR* 3.9 3.3 - - - +
65C LEU* 3.2 45.0 + - + +
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C SER* 2.7 44.4 + - - +
60C TRP 3.3 0.4 - - - -
61C ARG* 1.3 79.0 - - + +
63C MSE 1.3 64.1 + - - +
65C LEU* 4.3 6.9 - - + +
66C ARG* 3.1 27.0 + - - +
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Residues in contact with MSE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C SER 3.0 17.6 + - - +
60C TRP* 3.8 31.6 - - + +
62C GLU* 1.3 76.3 - - - +
64C TYR* 1.3 57.9 + - - +
66C ARG* 3.5 28.2 - - - +
67C LEU* 2.9 57.5 + - + +
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Residues in contact with TYR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR* 3.5 27.5 - - - +
22B GLN* 4.6 2.4 + - - -
20C PRO* 3.6 29.9 - - + +
60C TRP 3.1 17.9 + - - +
61C ARG* 3.9 6.7 - - - +
63C MSE 1.3 78.0 - - - +
65C LEU* 1.3 65.4 + - + +
67C LEU* 3.5 4.7 + - - +
68C GLN* 2.7 67.6 + - + +
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PRO* 6.0 2.9 - - + +
24C TYR* 3.6 41.7 - - + +
61C ARG* 3.2 39.1 + - + +
62C GLU* 4.3 6.1 - - + +
64C TYR* 1.3 93.7 - - + +
66C ARG* 1.3 57.4 + - - +
68C GLN* 4.0 12.2 - - - +
69C ASP* 3.0 30.5 + - - +
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU 3.1 19.8 + - - +
63C MSE 3.5 37.5 - - - +
65C LEU* 1.3 78.1 - - - +
67C LEU* 1.3 78.6 + - - +
69C ASP* 3.8 4.1 - - - +
70C ALA* 3.0 29.9 + - + +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C MSE 2.9 53.6 + - + +
64C TYR* 4.1 4.0 - - - +
66C ARG* 1.3 95.7 - - + +
68C GLN* 1.3 60.5 + - - +
70C ALA* 3.6 9.0 - - + +
71C ARG* 2.9 27.7 + - - +
74C ARG* 5.0 1.6 + - - -
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Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 4.6 0.2 + - - -
21B ASP* 3.5 23.4 + - - -
22B GLN* 3.1 30.6 - - + +
25B ARG* 3.5 15.8 + - - +
20C PRO* 4.9 4.0 - - - +
21C ASP* 5.6 1.4 - - - +
64C TYR* 2.7 50.8 + - + +
65C LEU* 4.0 12.2 - - - +
67C LEU* 1.3 69.3 - - - +
69C ASP* 1.3 56.6 + - - +
71C ARG* 3.0 3.8 + - - +
72C GLU* 2.8 49.2 + - - +
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Residues in contact with ASP 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C LEU 3.0 20.1 + - - +
66C ARG* 3.8 4.9 - - - +
68C GLN* 1.3 76.9 + - - +
70C ALA* 1.3 63.6 + - - +
72C GLU* 3.0 18.5 + - - +
73C GLN* 2.8 50.3 + - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 3.0 20.3 + - + +
67C LEU* 3.6 13.9 - - + +
69C ASP* 1.3 78.1 + - - +
71C ARG* 1.3 60.7 + - - +
73C GLN* 3.5 12.4 + - - +
74C ARG* 3.4 37.0 + - - +
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 3.3 37.7 + - - +
18B CYS* 4.1 4.6 - - - +
19B THR* 4.7 1.8 - - - +
22B GLN* 3.3 35.1 + - - +
67C LEU 2.9 18.4 + - - +
68C GLN* 3.0 5.1 + - - +
70C ALA* 1.3 71.9 - - - +
72C GLU* 1.3 66.5 + - - +
74C ARG* 3.2 24.9 + - - +
75C LEU* 3.1 42.9 + - + +
101C SO4 3.1 40.7 + - - +
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 4.5 12.1 - - + +
25B ARG* 2.7 45.8 + - - +
26B ILE* 5.2 8.1 - - + +
68C GLN* 2.8 35.2 + - + +
69C ASP* 3.4 19.2 - - - +
71C ARG* 1.3 73.0 - - + +
73C GLN* 1.3 62.3 + - + +
75C LEU* 3.2 10.6 + - + +
76C ARG* 3.1 42.7 + - + +
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Residues in contact with GLN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASP* 2.8 48.7 + - - +
70C ALA* 3.8 12.4 - - - +
71C ARG 3.3 0.4 - - - -
72C GLU* 1.3 75.8 - - + +
74C ARG* 1.3 61.9 + - + +
76C ARG* 3.8 11.9 + - - +
77C VAL* 3.4 23.9 + - - +
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Residues in contact with ARG 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU 5.0 1.4 + - - -
70C ALA* 3.4 36.4 + - - +
71C ARG* 3.2 22.6 + - - +
72C GLU 3.2 0.2 - - - -
73C GLN* 1.3 76.5 - - + +
75C LEU* 1.3 67.1 + - + +
77C VAL* 3.2 9.4 + - - +
78C LEU* 3.0 36.6 + - + +
101C SO4 2.9 47.0 + - - -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.5 29.6 - - + -
15B LEU* 4.4 11.7 - - + -
18B CYS* 3.5 29.8 - - - -
22B GLN* 5.3 3.8 - - + -
26B ILE* 3.3 31.0 - - + -
71C ARG* 3.1 37.4 + - + +
72C GLU* 3.2 6.7 + - + +
74C ARG* 1.3 83.6 - - + +
76C ARG* 1.3 52.8 + - - +
78C LEU* 3.2 8.4 + - + -
79C THR* 2.7 44.3 + - + +
101C SO4 5.6 0.9 - - - +
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Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU 2.3 35.0 + - - -
29A TYR* 3.6 12.1 - - - +
25B ARG* 4.6 16.8 + - - +
26B ILE* 4.4 12.5 - - + +
29B TYR* 3.3 43.5 + - + +
72C GLU* 3.1 34.6 + - - +
73C GLN* 4.0 10.8 - - - +
74C ARG 3.3 0.2 - - - -
75C LEU* 1.3 75.4 - - - +
77C VAL* 1.3 58.9 + - + +
79C THR* 3.4 7.2 - - - -
80C LYS* 2.9 23.7 + - - +
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C GLN 3.4 15.5 - - - +
74C ARG* 3.2 9.8 + - - +
75C LEU 3.1 0.4 - - - -
76C ARG* 1.3 76.5 - - + +
78C LEU* 1.3 73.5 + - + +
79C THR 3.1 1.2 + - - -
80C LYS* 3.2 20.7 + - + +
81C ASN 4.6 0.7 + - - -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 5.0 6.8 + - - +
11B LEU* 3.1 37.4 - - + +
14B VAL* 4.2 34.8 - - + -
74C ARG* 3.0 24.9 + - + +
75C LEU* 3.7 10.3 - - + +
77C VAL* 1.3 84.7 - - + +
79C THR* 1.3 60.2 + - + +
81C ASN 5.0 3.4 + - - +
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.6 16.6 - - + -
15B LEU* 4.8 13.2 - - + -
26B ILE* 3.6 26.5 - - + +
29B TYR* 3.2 26.7 - - - -
30B ASN* 2.9 30.8 + - - +
33B LEU* 6.3 3.4 - - + -
75C LEU* 2.7 29.6 + - - +
76C ARG* 3.4 1.6 - - - -
78C LEU* 1.3 78.1 - - + +
80C LYS* 1.3 67.7 + - - +
81C ASN* 3.0 6.4 + - - -
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Residues in contact with LYS 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 3.4 22.3 + - - +
30B ASN* 4.0 8.7 + - - -
76C ARG 2.9 18.8 + - - +
77C VAL* 3.2 14.3 + - + +
79C THR* 1.3 79.1 + - - +
81C ASN* 1.3 84.8 + - - +
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Residues in contact with ASN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 3.2 50.7 - - + +
11B LEU* 6.4 0.2 - - - -
30B ASN* 4.9 5.4 - - - +
77C VAL 4.6 1.0 + - - -
78C LEU 5.0 3.1 + - - +
79C THR* 3.1 7.5 - - - -
80C LYS* 1.3 110.9 + - - +
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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