Contacts of the helix formed by residues 64 - 83 (chain C) in PDB entry 4HHM
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 SER 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLY 3.5 2.9 + - - -
63C ALA* 1.3 74.6 - - - +
65C ASP* 1.3 53.7 + - - +
66C THR* 3.0 11.8 + - - -
67C GLU* 3.1 33.4 + - - +
68C ARG* 2.7 36.8 + - - +
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Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ALA 5.1 1.2 - - - +
64C SER* 1.3 74.2 - - - +
66C THR* 1.3 63.0 + - - +
68C ARG* 3.1 10.5 - - - +
69C GLU* 3.0 38.6 + - + +
121C ARG* 3.3 28.3 + - - -
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 3.5 10.8 + - - -
65C ASP* 1.3 77.9 - - - +
67C GLU* 1.3 70.2 + - + +
68C ARG 3.0 1.8 + - - -
69C GLU* 3.5 3.6 + - - +
70C ALA* 3.2 20.3 + - + +
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ALA* 3.6 15.5 - - + +
64C SER* 3.1 33.2 + - - +
66C THR* 1.3 80.2 - - + +
68C ARG* 1.3 59.3 + - - +
70C ALA* 3.5 7.9 + - - +
71C HIS* 2.9 41.2 + - + +
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 6.0 3.2 - - - +
59C ILE* 3.6 47.3 - - + +
63C ALA 5.2 3.9 + - - +
64C SER 2.7 17.9 + - - +
65C ASP* 3.1 14.1 - - - +
67C GLU* 1.3 75.1 - - - +
69C GLU* 1.3 69.0 + - + +
71C HIS* 3.0 15.6 + - - +
72C VAL* 3.3 15.3 + - + +
121C ARG* 3.2 70.7 + - - +
122C ASN* 5.3 3.6 + - - +
125C LEU* 4.4 17.6 - - - +
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP* 3.0 23.0 + - - +
66C THR* 4.2 3.1 - - - +
68C ARG* 1.3 83.6 - - + +
70C ALA* 1.3 56.7 + - - +
72C VAL* 3.0 28.0 - - + +
73C LYS* 3.0 16.0 + - - +
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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 THR* 3.2 17.9 + - + +
67C GLU* 3.6 9.9 - - - +
68C ARG 3.1 0.4 - - - -
69C GLU* 1.3 78.1 - - - +
71C HIS* 1.3 59.8 + - + +
73C LYS* 3.4 12.3 - - + +
74C ARG* 3.2 31.4 + - - +
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C LEU* 3.6 24.0 + - - +
59C ILE* 4.5 8.5 - - + -
60C PRO* 3.4 36.4 - - + +
63C ALA* 5.2 0.2 - - + -
67C GLU* 2.9 32.5 + - + +
68C ARG 3.0 7.4 + - - +
70C ALA* 1.3 74.9 - - + +
72C VAL* 1.3 65.1 + - - +
73C LYS 3.1 1.8 - - - -
74C ARG* 3.4 23.1 + - - +
75C PHE* 3.2 22.0 + - - +
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C LEU* 4.1 9.6 - - + -
59C ILE* 4.0 19.3 - - + -
68C ARG* 3.3 11.0 + - + +
69C GLU* 3.0 30.1 - - + +
71C HIS* 1.3 76.9 - - - +
73C LYS* 1.3 57.7 + - - +
75C PHE* 3.6 7.5 - - - +
76C ARG* 3.0 41.3 + - - +
125C LEU* 3.9 29.8 - - + -
128C GLU* 5.3 8.1 - - - +
129C LEU* 5.6 3.2 - - + +
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLU 3.0 20.3 + - - +
70C ALA* 3.4 13.2 - - + +
71C HIS 3.1 0.2 - - - -
72C VAL* 1.3 80.0 - - + +
74C ARG* 1.3 64.2 + - + +
76C ARG* 3.9 4.8 - - - +
77C GLN* 3.1 38.6 + - - +
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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
----------------------------------------------------------
35C ASP* 3.1 39.1 + - - -
36C PRO* 5.4 1.6 - - - +
37C VAL* 3.8 22.6 - - + +
70C ALA* 3.2 19.7 + - - +
71C HIS* 3.4 22.6 + - - +
73C LYS* 1.3 79.8 - - + +
75C PHE* 1.3 61.3 + - - +
77C GLN* 3.4 12.3 - - - +
78C ALA* 3.2 20.6 + - - +
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Residues in contact with PHE 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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15C LEU* 4.0 24.7 - - + -
36C PRO* 4.5 10.5 - - + -
37C VAL* 5.0 3.1 - - - -
40C VAL* 3.7 28.0 - - + -
51C VAL* 3.9 22.0 - - + -
53C PHE* 4.8 8.3 - + - -
58C LEU* 3.4 32.5 - - + -
71C HIS 3.2 15.0 + - - +
72C VAL* 3.6 5.6 - - - +
74C ARG* 1.3 75.6 - - - +
76C ARG* 1.3 67.8 + - - +
77C GLN 3.0 1.1 - - - -
78C ALA* 2.9 16.7 + - + +
79C LEU* 3.0 38.4 + - + +
86C VAL* 3.9 11.2 - - + -
129C LEU* 4.2 16.8 - - + -
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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
----------------------------------------------------------
72C VAL* 3.0 25.5 + - - +
73C LYS* 3.9 5.1 - - - +
75C PHE* 1.3 76.1 - - - +
77C GLN* 1.3 58.1 + - - +
79C LEU* 3.3 13.6 + - - +
80C ASP* 2.9 60.3 + - - +
128C GLU* 3.6 35.9 + - - +
129C LEU* 3.6 26.9 - - + +
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Residues in contact with GLN 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 LYS* 3.1 39.0 + - - +
74C ARG* 3.4 10.9 - - - +
75C PHE 3.0 0.4 - - - -
76C ARG* 1.3 78.0 - - - +
78C ALA* 1.3 60.2 + - - +
80C ASP* 3.8 5.6 + - - +
81C ALA* 3.2 24.6 + - - +
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Residues in contact with ALA 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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37C VAL* 3.8 30.1 - - + +
40C VAL* 4.1 19.5 - - + -
41C GLN* 5.0 4.7 - - + -
74C ARG 3.2 11.8 + - - +
75C PHE* 2.9 9.8 + - - +
77C GLN* 1.3 72.9 - - - +
79C LEU* 1.3 55.5 + - - +
81C ALA* 3.4 4.4 + - - +
82C THR* 2.8 43.1 + - - +
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Residues in contact with LEU 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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40C VAL* 4.1 9.0 - - + -
51C VAL* 3.9 24.0 - - + -
75C PHE* 3.0 46.0 + - + +
76C ARG* 3.7 14.1 - - - +
78C ALA* 1.3 76.7 - - - +
80C ASP* 1.3 56.3 + - - +
82C THR* 3.7 4.9 - - - -
83C GLY* 2.6 32.7 + - - -
84C MET* 3.1 43.8 + - + +
85C THR* 5.6 0.2 - - - -
86C VAL* 3.6 15.7 - - + -
129C LEU* 5.1 6.5 - - + -
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ARG* 2.9 46.5 + - - +
77C GLN* 4.1 5.1 - - - +
79C LEU* 1.3 77.8 - - - +
81C ALA* 1.3 64.8 + - - +
83C GLY* 3.8 6.6 + - - -
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Residues in contact with ALA 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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77C GLN 3.2 18.0 + - - +
78C ALA* 3.8 4.7 - - - +
80C ASP* 1.3 80.1 - - - +
82C THR* 1.3 65.5 + - + +
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Residues in contact with THR 82 (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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40C VAL* 3.3 5.0 - - + +
41C GLN* 4.0 36.3 - - + -
44C ALA* 3.8 22.5 - - + +
78C ALA* 2.8 24.8 + - - +
79C LEU 3.4 1.4 + - - -
81C ALA* 1.3 80.7 - - + +
83C GLY* 1.3 60.7 + - - +
84C MET* 3.2 18.2 - - - +
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Residues in contact with GLY 83 (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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49C TYR* 4.4 4.2 - - - +
79C LEU 2.6 18.0 + - - -
80C ASP 3.8 5.6 + - - -
81C ALA 3.5 1.8 - - - -
82C THR* 1.3 75.9 - - - +
84C MET* 1.3 62.5 + - - +
85C THR* 4.0 1.7 + - - +
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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