Contacts of the helix formed by residues 70 - 85 (chain C) in PDB entry 3CUQ
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 PRO 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A GLN* 3.9 8.7 - - - +
17C PHE 3.5 14.4 - - - +
18C THR* 5.4 2.0 - - - -
68C LYS* 3.3 11.8 - - + +
69C LEU* 1.3 93.6 - - + +
71C VAL* 1.3 61.3 + - - +
72C GLU* 3.3 27.4 - - - +
73C SER* 3.3 10.1 + - - +
74C ILE* 2.9 26.0 + - - +
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Residues in contact with VAL 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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51C VAL* 4.6 14.4 - - + -
55C GLN* 3.8 32.4 - - - +
70C PRO* 1.3 70.9 - - - +
72C GLU* 1.3 74.2 + - + +
74C ILE* 3.0 17.6 - - + +
75C GLN* 2.8 35.7 + - + +
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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
----------------------------------------------------------
19C LEU* 5.9 3.6 - - + -
70C PRO* 3.4 24.9 - - - +
71C VAL* 1.3 90.8 - - + +
73C SER* 1.3 77.1 + - - +
75C GLN* 3.1 11.8 + - - +
76C ILE* 3.0 30.0 + - + +
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Residues in contact with SER 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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19C LEU* 3.7 33.8 + - - +
30C LEU* 5.7 0.7 - - - +
69C LEU* 3.1 30.4 - - - +
70C PRO* 3.3 11.7 + - - +
72C GLU* 1.3 88.1 + - - +
74C ILE* 1.3 56.9 + - - +
76C ILE* 2.9 31.8 + - - +
77C VAL* 3.0 11.9 + - - +
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Residues in contact with ILE 74 (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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51C VAL* 5.5 5.6 - - + +
54C ALA* 6.5 0.2 - - + -
55C GLN* 4.3 28.5 - - + +
60C PHE* 3.6 34.1 - - + -
69C LEU* 3.3 37.0 - - + +
70C PRO 2.9 23.0 + - - +
71C VAL* 3.0 32.5 - - + +
73C SER* 1.3 70.3 - - - +
75C GLN* 1.3 62.6 + - + +
76C ILE 2.8 5.3 + - - -
77C VAL* 3.1 6.3 + - + +
78C LEU* 2.8 36.2 + - + +
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Residues in contact with GLN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 3.4 41.0 - - - +
71C VAL* 2.8 27.4 + - + +
72C GLU* 3.3 12.8 - - - +
74C ILE* 1.3 73.2 - - - +
76C ILE* 1.3 57.1 + - + +
78C LEU* 4.1 6.2 - - - +
79C GLU* 3.1 27.5 + - - +
89C TRP* 4.0 19.2 - - - -
94C LYS* 4.9 14.0 + - - +
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Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.9 33.0 - - + -
30C LEU* 4.4 29.2 - - + -
72C GLU* 3.0 18.8 + - + +
73C SER* 2.9 13.2 + - - +
74C ILE 2.8 0.4 - - - -
75C GLN* 1.3 77.7 - - + +
77C VAL* 1.3 60.2 + - - +
79C GLU* 3.3 7.1 + - - +
80C GLU* 3.0 27.4 + - + +
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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
----------------------------------------------------------
30C LEU* 5.0 11.0 - - + +
33C TRP* 4.3 24.7 - - + -
34C CYS* 4.7 6.7 - - - -
37C VAL* 4.7 6.3 - - + -
60C PHE* 4.9 7.9 - - + -
69C LEU* 4.2 14.1 - - + -
73C SER 3.0 17.6 + - - +
74C ILE* 3.2 21.5 - - + +
76C ILE* 1.3 74.8 - - + +
78C LEU* 1.3 71.8 + - + +
80C GLU* 3.0 9.1 + - - +
81C LEU* 3.0 36.0 + - + +
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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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37C VAL* 5.5 5.4 - - + -
51C VAL* 4.8 7.0 - - + -
54C ALA* 5.7 2.5 - - + -
60C PHE* 4.6 18.2 - - + -
74C ILE* 2.8 35.6 + - + +
75C GLN* 4.1 13.7 - - - +
77C VAL* 1.3 82.1 - - + +
79C GLU* 1.3 58.7 + - - +
81C LEU* 3.3 10.9 + - + +
82C ARG* 2.9 29.1 + - - +
87C LEU* 3.9 28.4 - - + +
89C TRP* 4.5 20.9 - - + -
97C PHE* 4.0 29.6 - - + -
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Residues in contact with GLU 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 GLN 3.1 19.2 + - - +
76C ILE* 3.7 6.3 - - - +
77C VAL 3.2 0.4 - - - -
78C LEU* 1.3 77.8 - - - +
80C GLU* 1.3 61.6 + - + +
82C ARG* 2.7 48.0 + - - +
83C LYS* 3.1 43.5 + - - +
89C TRP* 5.1 3.5 + - + +
94C LYS* 3.7 20.3 + - - +
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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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30C LEU* 4.6 24.2 - - + +
34C CYS* 3.9 15.9 - - - -
76C ILE* 3.0 16.9 + - + +
77C VAL* 3.0 11.4 + - - +
79C GLU* 1.3 76.7 - - + +
81C LEU* 1.3 65.2 + - - +
83C LYS* 3.1 29.7 + - - +
84C LYS* 2.9 36.6 + - - +
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Residues in contact with LEU 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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34C CYS* 3.7 26.7 - - + -
37C VAL* 3.1 38.1 - - + -
38C LEU* 3.8 31.4 - - + -
77C VAL* 3.0 21.1 + - + +
78C LEU* 3.6 13.7 - - + +
80C GLU* 1.3 72.1 - - - +
82C ARG* 1.3 67.3 + - - +
84C LYS* 3.0 10.7 + - - +
85C GLY 2.9 19.4 + - - -
86C ASN* 3.1 16.7 + - + +
87C LEU* 3.9 15.7 - - + -
99C ILE* 4.8 4.5 - - + -
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Residues in contact with ARG 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 19.2 + - - +
79C GLU* 2.7 44.9 + - - +
80C GLU 3.3 0.2 - - - -
81C LEU* 1.3 76.2 - - - +
83C LYS* 1.3 74.4 + - - +
85C GLY* 3.2 12.1 + - - -
87C LEU* 3.3 35.3 - - + +
88C GLU* 5.2 1.6 - - - -
89C TRP* 3.6 28.0 - - + +
94C LYS* 5.0 2.6 - - - +
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Residues in contact with LYS 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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79C GLU* 3.1 38.6 - - - +
80C GLU* 3.1 28.7 + - - +
82C ARG* 1.3 88.6 - - - +
84C LYS* 1.3 59.5 + - - +
85C GLY* 3.1 6.4 + - - -
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Residues in contact with LYS 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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31C ALA* 6.0 1.4 - - - +
34C CYS* 3.7 32.8 - - + +
38C LEU* 5.7 2.9 - - + -
80C GLU* 2.9 25.8 + - - +
81C LEU* 3.6 10.1 - - + +
83C LYS* 1.3 79.2 - - - +
85C GLY* 1.3 56.6 + - - +
86C ASN* 3.5 17.1 + - - +
103C ARG* 3.3 23.1 + - - +
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Residues in contact with GLY 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 LEU 2.9 3.0 + - - -
82C ARG 3.2 8.9 + - - -
83C LYS 3.1 5.3 - - - -
84C LYS* 1.3 79.3 - - - +
86C ASN* 1.3 61.6 + - - +
87C LEU 3.5 5.3 + - - +
100C MET* 4.9 3.6 - - - +
103C ARG* 4.0 16.3 - - - +
104C PRO* 4.2 13.0 - - - +
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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