Contacts of the helix formed by residues 74 - 87 (chain C) in PDB entry 3E2A
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 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C ASN* 4.8 0.5 + - - -
69C GLN 5.1 0.5 - - - +
71C ILE* 2.9 33.1 + - + +
72C HIS 3.6 0.4 - - - -
73C THR* 1.3 75.4 - - - +
75C PHE* 1.3 58.4 + - - +
76C ASN* 3.2 16.6 + - - +
77C CYS* 3.2 22.0 + - + +
78C LEU* 3.0 30.3 + - - +
119C TRP* 3.6 13.3 - - + -
73D THR* 6.5 0.4 - - - -
74E ASP* 4.2 2.9 - - - +
75E PHE* 5.8 0.9 - - - +
76E ASN* 2.8 37.4 + - - +
75F PHE* 4.4 0.2 - - - -
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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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73C THR 3.3 5.6 + - - +
74C ASP* 1.3 73.2 + - - +
76C ASN* 1.3 57.7 + - - +
78C LEU* 4.5 2.7 - - - -
79C SER* 2.8 64.4 + - - -
115D LEU* 5.3 1.6 - - + -
74E ASP* 5.8 1.3 - - - +
115E LEU* 3.7 37.7 - - + -
118E ASN* 3.7 20.0 - - + -
119E TRP* 4.2 5.6 - + + -
72F HIS 4.1 4.5 - - - -
73F THR* 3.2 56.8 - - + +
75F PHE* 3.8 30.3 - + + -
78F LEU* 4.4 16.4 - - + -
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Residues in contact with ASN 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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63C HIS* 3.3 13.4 + - - -
74C ASP* 3.2 12.6 + - - +
75C PHE* 1.3 82.3 - - - +
77C CYS* 1.3 60.4 + - - +
79C SER* 3.5 2.6 - - - -
80C VAL* 3.0 25.6 + - - +
63E HIS* 3.3 29.5 + - - -
65E ASN* 3.5 13.0 - - - +
66E VAL 5.2 0.2 + - - -
74E ASP* 2.9 33.4 + - - +
76E ASN* 3.7 11.4 - - - +
119E TRP* 3.6 26.3 - - + -
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Residues in contact with CYS 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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40C ILE* 4.0 22.2 - - - -
63C HIS* 3.7 26.2 - - - +
69C GLN 4.0 17.9 - - - +
70C VAL* 4.1 16.4 - - + -
71C ILE 5.5 0.7 - - - +
74C ASP* 3.2 22.2 + - + +
76C ASN* 1.3 76.9 + - - +
78C LEU* 1.3 65.3 + - - +
80C VAL* 3.4 9.8 + - - +
81C VAL* 3.1 32.1 + - - +
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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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70C VAL* 5.7 3.5 - - + +
71C ILE 5.3 1.6 - - - +
72C HIS 4.2 10.3 - - - +
74C ASP 3.0 23.3 + - - +
75C PHE* 4.2 2.9 - - - +
77C CYS* 1.3 72.9 - - - +
79C SER* 1.3 57.8 + - - +
81C VAL* 3.4 7.6 + - + +
82C GLN* 2.9 25.3 + - - +
161C THR* 3.5 28.7 - - + -
163C ILE* 2.7 45.2 - - + +
115D LEU* 4.3 1.8 - - + -
118D ASN* 4.0 17.3 - - - +
115E LEU* 4.0 15.9 - - + -
75F PHE* 3.6 30.7 - - + -
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Residues in contact with SER 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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75C PHE* 2.8 47.6 + - - -
76C ASN 3.5 4.7 - - - -
78C LEU* 1.3 78.8 - - - +
80C VAL* 1.3 57.1 + - - +
82C GLN* 3.3 3.3 + - - +
83C TYR* 2.9 30.3 + - - +
66E VAL* 5.9 0.4 - - - -
115E LEU* 4.1 12.2 + - - +
116E ILE* 3.7 21.7 - - - +
119E TRP* 3.7 14.9 - - - +
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Residues in contact with VAL 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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38C LEU* 4.2 13.0 - - + -
61C PHE* 3.1 39.9 - - + -
63C HIS* 4.0 23.3 - - + +
76C ASN* 3.0 20.9 - - - +
77C CYS* 3.7 12.1 - - - +
79C SER* 1.3 72.9 - - - +
81C VAL* 1.3 56.9 + - + +
83C TYR* 3.9 4.3 - - - +
84C ALA* 2.8 36.3 + - - +
43E SER* 4.2 11.2 - - - +
66E VAL* 3.9 17.5 - - + +
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Residues in contact with VAL 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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38C LEU* 3.8 18.8 - - + -
40C ILE* 4.4 3.1 - - + -
70C VAL* 5.4 1.6 - - + -
77C CYS* 3.1 32.8 + - - +
78C LEU* 3.6 10.5 - - + +
80C VAL* 1.3 74.8 - - + +
82C GLN* 1.3 58.1 + - - +
84C ALA* 3.4 0.9 + - - +
85C VAL* 2.9 36.7 + - + +
93C ILE* 4.2 10.8 - - + -
158C LEU* 3.9 32.8 - - + -
161C THR* 4.7 1.8 - - - +
163C ILE* 3.9 22.2 - - + -
164C VAL* 4.2 6.5 - - + -
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Residues in contact with GLN 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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78C LEU 2.9 17.0 + - - +
79C SER 3.7 2.5 - - - +
80C VAL 3.2 0.2 - - - -
81C VAL* 1.3 74.9 - - - +
83C TYR* 1.3 58.8 + - - +
86C ASP* 2.7 73.3 + - - +
87C VAL* 4.6 0.2 - - - +
163C ILE* 3.8 26.0 - - + -
113E LEU 2.8 23.4 + - - -
114E GLY* 3.7 3.4 - - - -
115E LEU* 3.5 28.1 - - + +
116E ILE* 2.9 37.1 + - - +
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Residues in contact with TYR 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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61C PHE* 3.5 35.4 - + - -
79C SER 2.9 17.6 + - - +
80C VAL* 3.9 2.2 - - - +
82C GLN* 1.3 81.3 + - - +
84C ALA* 1.3 58.8 + - - +
87C VAL* 3.0 37.3 + - + +
88C LEU* 2.9 47.2 + - + +
44E ASP* 4.9 4.3 + - + +
66E VAL* 4.6 14.6 - - + -
102E GLY* 3.8 25.9 + - - -
103E GLY 5.3 0.4 - - - -
106E ALA* 4.3 19.8 - - + +
113E LEU* 4.5 2.2 - - + -
116E ILE* 3.7 32.3 - - + -
120E LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 84 (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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38C LEU* 3.7 23.3 - - + -
61C PHE* 3.9 7.9 - - + -
80C VAL 2.8 23.7 + - - +
81C VAL 3.7 1.6 - - - +
83C TYR* 1.3 76.0 - - - +
85C VAL* 1.3 58.1 + - + +
88C LEU* 3.5 13.3 - - - +
89C LYS 3.0 9.5 + - - -
90C ILE* 3.0 47.0 + - + -
93C ILE* 5.6 0.2 - - + -
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Residues in contact with VAL 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 VAL* 2.9 22.4 + - + +
84C ALA* 1.3 79.1 - - + +
86C ASP* 1.3 76.5 + - - +
89C LYS* 3.6 11.1 - - - +
90C ILE 4.4 5.2 - - - +
93C ILE* 3.7 27.4 - - + -
163C ILE* 4.2 13.5 - - + -
164C VAL* 5.0 0.2 - - + -
167C ALA* 3.7 21.5 - - + -
172C GLN* 2.9 38.3 + - - +
174C LEU* 3.8 18.8 - - + -
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Residues in contact with ASP 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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82C GLN* 2.7 53.4 + - - +
85C VAL* 1.3 83.6 - - - +
87C VAL* 1.3 60.4 + - + +
89C LYS* 3.6 18.9 - - - -
163C ILE* 4.5 8.6 - - - +
170C ARG* 3.0 31.1 + - - +
172C GLN* 5.1 0.4 - - - -
113E LEU 4.9 0.7 - - - +
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Residues in contact with VAL 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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83C TYR* 3.0 44.1 + - + +
86C ASP* 1.3 83.9 - - + +
88C LEU* 1.3 68.5 + - + +
89C LYS* 3.3 9.8 + - - +
113E LEU* 3.7 55.2 - - + +
116E ILE* 4.5 0.4 - - + -
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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
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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