Contacts of the helix formed by residues 70 - 82 (chain C) in PDB entry 3QEM
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 ASN 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C ARG 3.6 3.3 - - - +
69C PRO* 1.3 83.1 - - - +
71C ALA* 1.3 61.5 + - - +
72C ILE* 2.9 15.8 + - - +
73C GLN* 3.0 26.4 + - - +
74C MET* 3.0 28.5 + - - +
321D CYS 3.2 26.6 + - - +
322D TYR* 3.7 2.2 - - - +
323D ASN 3.2 30.4 - - - +
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Residues in contact with ALA 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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70C ASN* 1.3 75.2 + - - +
72C ILE* 1.3 61.2 + - - +
73C GLN 2.9 6.0 + - - -
74C MET* 3.0 11.9 + - - +
75C ALA* 3.1 15.9 + - - +
106C PRO* 4.0 22.7 - - + +
114D PHE* 3.9 5.6 - - + -
118D GLN* 3.0 34.1 - - - +
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Residues in contact with ILE 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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70C ASN* 2.9 9.7 + - - +
71C ALA* 1.3 76.0 - - - +
73C GLN* 1.3 59.6 + - - +
75C ALA* 4.3 1.7 - - - +
76C LEU* 3.3 30.4 + - + +
82D ILE* 4.5 14.5 - - + +
86D CYS* 4.9 1.1 - - - -
114D PHE* 4.2 14.3 - - + -
115D ILE* 6.2 2.9 - - + -
118D GLN* 4.7 17.0 - - + +
119D THR* 5.4 3.8 - - + -
321D CYS* 4.2 26.5 - - + +
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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
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68C ARG* 3.9 10.6 - - + +
69C PRO* 3.2 28.7 - - - +
70C ASN* 3.0 27.6 + - - +
71C ALA 2.9 0.6 - - - -
72C ILE* 1.3 80.9 - - + +
74C MET* 1.3 64.7 + - - +
76C LEU* 3.5 10.8 + - + +
77C SER* 3.1 21.7 + - - -
321D CYS* 4.8 5.6 - - + +
322D TYR* 3.5 30.7 - - - +
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Residues in contact with MET 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL* 4.2 12.3 - - + -
65C VAL* 4.3 17.3 - - + -
66C THR 4.4 0.9 - - - +
67C HIS* 3.9 16.2 - - + -
68C ARG* 3.7 29.4 - - + +
70C ASN 3.0 18.6 + - - +
71C ALA* 3.0 6.2 + - - +
73C GLN* 1.3 77.0 - - - +
75C ALA* 1.3 62.7 + - - +
77C SER* 3.1 26.3 + - - +
78C VAL* 3.2 12.6 + - + +
103C THR 5.6 1.8 - - - +
106C PRO* 4.2 11.7 - - + -
107C ILE* 4.0 31.0 - - + -
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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
----------------------------------------------------------
71C ALA 3.1 14.6 + - - +
72C ILE 4.4 2.2 - - - +
74C MET* 1.3 77.5 - - - +
76C LEU* 1.3 65.1 + - - +
78C VAL* 3.1 17.2 + - - +
79C CYS* 3.4 8.6 + - - +
106C PRO* 4.1 15.4 - - + +
110C THR* 3.6 26.1 + - - +
82D ILE* 4.4 11.2 - - + -
114D PHE* 4.2 18.6 - - + -
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Residues in contact with LEU 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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72C ILE* 3.3 21.9 + - + +
73C GLN* 3.5 12.5 + - + +
74C MET 3.3 0.4 - - - -
75C ALA* 1.3 78.9 - - - +
77C SER* 1.3 62.5 + - - +
79C CYS* 3.0 17.6 + - - +
80C GLU* 3.0 15.9 + - - +
79D LYS* 4.0 38.2 + - + +
82D ILE* 4.0 31.8 - - + +
83D THR* 4.0 13.7 - - - +
86D CYS* 5.5 6.7 - - + -
321D CYS* 6.4 0.4 - - + -
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Residues in contact with SER 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 4.0 17.7 - - - +
66C THR 5.4 0.3 + - - -
68C ARG* 4.8 5.8 - - - +
73C GLN 3.1 13.4 + - - -
74C MET* 3.1 22.3 + - - +
76C LEU* 1.3 76.4 - - - +
78C VAL* 1.3 55.3 + - - +
80C GLU* 4.4 2.9 - - - +
81C ASP* 2.7 56.2 + - - +
82C LEU* 4.7 1.1 - - - +
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Residues in contact with VAL 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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74C MET* 3.2 16.1 + - + +
75C ALA* 3.1 10.2 + - - +
77C SER* 1.3 77.5 - - - +
79C CYS* 1.3 58.0 + - - +
82C LEU* 3.3 22.9 + - + -
83C ILE* 2.8 52.6 + - + +
90C ILE* 4.0 16.2 - - + -
107C ILE* 4.1 33.0 - - + -
110C THR* 3.7 16.4 - - + -
111C ALA 4.8 2.2 - - - +
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Residues in contact with CYS 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 ALA 3.4 4.7 + - - -
76C LEU* 3.0 12.2 + - - +
78C VAL* 1.3 80.6 - - - +
80C GLU* 1.3 57.1 - - - +
83C ILE* 4.1 2.1 - - - +
84C SER* 3.2 24.6 + - - -
110C THR* 3.7 17.9 - - - -
329C CYS* 2.0 58.1 + - + -
78D PRO* 4.4 3.4 - - - -
79D LYS* 3.9 32.6 - - + +
82D ILE* 6.4 0.4 - - - -
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Residues in contact with GLU 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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76C LEU 3.0 13.9 + - - +
77C SER* 4.3 2.2 - - - +
79C CYS* 1.3 77.3 - - - +
81C ASP* 1.3 72.9 + - - +
84C SER* 3.5 17.4 + - - -
79D LYS* 4.1 20.6 - - - +
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Residues in contact with ASP 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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63C THR* 3.6 20.7 - - + +
65C VAL* 3.7 24.4 - - + +
77C SER* 2.7 37.6 + - - +
80C GLU* 1.3 90.6 - - - +
82C LEU* 1.3 61.0 + - + +
84C SER* 4.6 2.5 - - - -
85C SER* 3.7 10.3 + - - -
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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
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30C GLY* 4.5 2.0 - - - -
31C ALA 3.5 30.1 - - - +
32C VAL* 3.6 26.9 - - + -
63C THR* 4.3 5.6 - - + -
64C SER* 3.9 20.6 - - - +
65C VAL* 4.5 5.6 - - + +
77C SER 3.7 1.1 + - - +
78C VAL* 3.3 23.9 + - + +
81C ASP* 1.3 85.1 - - + +
83C ILE* 1.3 63.7 + - - +
84C SER 3.3 0.7 - - - -
85C SER* 3.2 12.9 + - - -
87C VAL* 3.1 33.5 - - + +
90C ILE* 3.8 26.7 - - + -
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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
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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