Contacts of the helix formed by residues 72 - 88 (chain C) in PDB entry 4NH1
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 ILE 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C HIS* 4.6 16.3 - - + +
48C GLN* 4.2 25.1 - - + +
49C ALA* 5.0 1.6 - - - +
52C MET* 3.9 23.1 - - + -
66C PRO* 3.3 37.5 - - + +
69C SER* 2.8 25.0 + - - +
70C ASP 3.2 0.2 - - - -
71C LEU* 1.3 103.9 - - + +
73C GLU* 1.3 55.1 + - - +
74C GLN 3.3 0.7 - - - -
75C ALA* 3.0 6.5 + - - +
76C ALA* 2.7 31.9 + - - +
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Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TRP* 3.1 36.8 + - - -
12C TRP* 4.1 15.3 - - - -
52C MET* 3.7 21.8 - - + +
69C SER* 2.4 36.6 + - - +
70C ASP* 5.1 1.1 - - - +
72C ILE* 1.3 70.1 - - - +
74C GLN* 1.3 61.5 + - + +
75C ALA 3.1 0.2 - - - -
76C ALA* 3.1 3.5 + - - +
77C GLU* 3.0 41.9 + - - +
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Residues in contact with GLN 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C SER 3.8 0.2 + - - -
70C ASP* 3.1 42.4 + - - +
73C GLU* 1.3 76.6 - - + +
75C ALA* 1.3 58.8 + - - +
77C GLU* 3.7 33.1 - - - +
78C MET* 3.8 13.3 + - - +
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 4.8 3.3 - - - +
44C PRO* 4.0 32.1 - - + +
45C HIS* 4.5 1.3 - - + +
49C ALA* 3.6 11.1 - - + +
70C ASP 4.4 0.2 + - - -
71C LEU* 3.3 26.0 - - - +
72C ILE* 3.0 10.2 + - - +
74C GLN* 1.3 76.9 - - - +
76C ALA* 1.3 62.4 + - - +
77C GLU 3.3 0.4 - - - -
78C MET* 3.5 11.6 - - - +
79C LEU* 3.5 14.0 + - - +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TRP* 4.3 5.4 - - + -
49C ALA* 3.6 30.5 - - - +
52C MET* 4.2 17.0 - - - -
53C ILE* 3.8 14.5 - - + +
72C ILE 2.7 11.2 + - - +
73C GLU 3.3 11.0 - - - +
75C ALA* 1.3 76.9 - - - +
77C GLU* 1.3 63.1 + - - +
78C MET 3.2 0.4 - - - -
79C LEU* 3.4 2.8 + - - +
80C TYR* 3.2 24.3 + - - +
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TRP* 4.3 11.2 - - + -
12C TRP* 5.2 4.9 - - - -
13C PHE* 3.8 38.0 - - + -
16C LEU* 5.6 1.9 - - - +
73C GLU* 3.0 30.0 + - - +
74C GLN* 3.7 30.3 - - - +
76C ALA* 1.3 78.2 - - - +
78C MET* 1.3 62.0 + - - +
80C TYR* 4.0 1.4 - - - +
81C GLY* 3.1 21.3 + - - -
158C TYR* 4.4 7.6 - - + -
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Residues in contact with MET 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLN* 3.4 24.2 - - + +
43C VAL* 3.7 16.6 - - + -
44C PRO* 3.9 19.7 - - + -
74C GLN 3.8 9.5 + - - +
75C ALA* 3.5 14.7 + - - +
76C ALA 3.2 0.2 - - - -
77C GLU* 1.3 81.0 - - - +
79C LEU* 1.3 60.7 - - - +
81C GLY 3.6 0.3 + - - -
82C LEU* 3.3 32.5 + - + +
128C PRO* 4.8 22.0 - - + -
158C TYR* 3.5 24.6 - - + +
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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
----------------------------------------------------------
36C LEU* 5.7 0.7 - - + -
39C LEU* 4.3 14.8 - - + -
43C VAL* 3.8 27.8 - - + +
46C TYR* 4.1 20.2 - - + +
49C ALA* 3.5 43.7 - - + +
50C LEU* 3.6 22.2 - - + +
53C ILE* 4.2 7.0 - - + -
75C ALA 3.5 3.1 + - - +
76C ALA 3.4 8.4 + - - +
77C GLU 3.3 0.8 - - - -
78C MET* 1.3 76.2 - - - +
80C TYR* 1.3 61.0 + - - +
82C LEU* 3.0 7.6 + - + +
83C ILE* 2.9 42.8 + - + +
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Residues in contact with TYR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TRP* 4.0 18.2 - + + -
10C ILE* 3.3 24.2 - - + +
13C PHE* 3.8 37.0 - + - -
14C CYS* 3.2 14.8 - - - -
22C PHE* 4.4 11.0 - + - -
23C CYS 2.8 24.3 + - - -
25C VAL* 3.2 36.5 + - + -
30C ILE* 4.6 7.4 - - + -
53C ILE* 4.1 17.7 - - + +
76C ALA 3.2 13.1 + - - +
77C GLU 4.2 2.2 - - - +
79C LEU* 1.3 79.4 - - - +
81C GLY* 1.3 59.1 + - - +
83C ILE* 3.6 10.5 - - + +
84C HIS* 2.9 27.1 + - + +
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 4.5 7.9 - - - -
77C GLU 3.1 16.0 + - - -
78C MET 3.9 0.2 - - - -
79C LEU 3.1 0.4 - - - -
80C TYR* 1.3 79.0 - - - +
82C LEU* 1.3 59.4 + - - +
84C HIS* 3.3 5.2 + - - +
85C ALA 3.3 15.2 + - - -
158C TYR* 3.3 46.2 - - - +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 4.6 17.5 - - + -
42C GLN* 3.8 31.0 - - + +
43C VAL* 3.8 28.0 - - + -
78C MET* 3.3 17.0 + - + +
79C LEU* 3.0 7.9 + - - +
81C GLY* 1.3 73.4 - - - +
83C ILE* 1.3 65.1 + - - +
85C ALA* 3.2 19.5 + - + +
86C ARG* 3.4 13.2 + - - +
126C ASP 5.6 1.3 - - - +
128C PRO* 4.1 18.8 - - + -
157C ALA* 4.2 11.0 - - + +
158C TYR* 3.8 21.3 - - + -
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Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL* 4.5 9.6 - - + -
29C TYR* 4.2 23.5 - - + -
30C ILE* 4.3 20.9 - - + -
35C ASN 5.8 1.1 - - - +
36C LEU* 4.4 22.2 - - + -
39C LEU* 4.6 10.8 - - + -
53C ILE* 4.0 19.5 - - + -
79C LEU* 2.9 43.3 + - + +
80C TYR* 3.6 8.7 - - + +
82C LEU* 1.3 76.2 - - - +
84C HIS* 1.3 58.2 + - - +
86C ARG* 3.2 9.4 + - - +
87C TYR* 2.9 26.0 + - - +
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Residues in contact with HIS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 4.1 15.4 - + + -
23C CYS* 3.0 59.4 + - - +
25C VAL* 4.5 11.2 - - + +
80C TYR* 2.9 20.5 + - + +
81C GLY* 3.4 10.1 - - - +
83C ILE* 1.3 77.2 - - - +
85C ALA* 1.3 60.2 + - - +
87C TYR* 4.1 5.4 - + - -
88C ILE* 3.1 41.6 + - + +
97C MET* 4.2 5.4 - - - -
158C TYR 3.2 17.6 + - - +
159C PHE* 3.7 28.1 - + - -
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Residues in contact with ALA 85 (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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81C GLY 3.3 3.7 + - - +
82C LEU* 3.2 12.5 + - + +
83C ILE 3.1 0.4 - - - -
84C HIS* 1.3 81.9 - - - +
86C ARG* 1.3 62.5 + - + +
87C TYR 3.5 0.2 + - - -
88C ILE* 3.5 11.1 - - - +
89C LEU* 3.4 23.0 - - - +
157C ALA 3.6 23.8 - - - +
158C TYR 3.6 12.8 + - - +
159C PHE 4.2 7.0 - - - +
160C GLY* 4.5 3.8 - - - +
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Residues in contact with ARG 86 (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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71A LYS* 5.0 9.1 + - - +
72A PRO* 5.3 11.8 - - - +
29C TYR* 3.2 20.2 + - + +
35C ASN 3.3 26.0 + - - -
36C LEU* 3.7 3.6 - - - +
37C THR* 2.8 37.6 + - - +
38C GLY* 4.5 3.8 + - - -
39C LEU* 3.4 31.0 - - - +
42C GLN* 4.9 1.0 + - - -
82C LEU 3.4 11.0 + - - +
83C ILE* 3.2 9.7 + - - +
85C ALA* 1.3 78.1 - - + +
87C TYR* 1.3 62.3 + - - +
89C LEU* 3.7 18.7 + - - +
90C THR* 3.7 8.7 - - - +
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Residues in contact with TYR 87 (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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23C CYS* 4.0 15.3 - - - -
25C VAL* 4.0 22.0 - - + -
26C ASP* 2.9 34.8 + - + -
29C TYR* 3.7 41.7 - + + -
83C ILE 2.9 17.1 + - - +
84C HIS* 3.8 7.0 - + - +
85C ALA 3.2 0.4 - - - -
86C ARG* 1.3 75.8 - - - +
88C ILE* 1.3 59.4 + - + +
89C LEU 3.1 7.1 + - - -
90C THR* 2.5 32.0 + - - -
92C ARG* 3.7 8.5 - - + +
93C GLY* 3.3 25.2 - - - -
96C GLN* 2.3 42.7 + - - -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C CYS* 4.0 6.1 - - - -
84C HIS* 3.1 50.4 + - + +
85C ALA 3.5 9.4 - - - +
87C TYR* 1.3 77.6 - - + +
89C LEU* 1.3 58.6 + - + +
90C THR 3.4 0.4 - - - -
93C GLY* 4.1 7.2 - - - +
94C ILE* 3.2 20.7 - - - +
97C MET* 3.8 17.7 - - + -
159C PHE* 3.2 41.3 - - + +
163C PHE* 3.3 42.4 - - + -
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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