Contacts of the helix formed by residues 64 - 75 (chain C) in PDB entry 6W4E
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 TYR 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.6 23.7 - - + +
59C ALA* 3.9 28.3 - - + +
61C GLN* 5.0 13.3 + - + -
62C GLU* 2.7 29.0 + - - +
63C GLU* 1.3 86.8 - - + +
65C SER* 1.3 59.0 + - - +
66C ALA 3.3 3.4 - - - +
67C MET* 3.5 34.8 - - + -
68C ARG* 3.0 32.3 + - - +
71C TYR* 5.3 2.7 - - - +
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU* 6.0 0.2 + - - -
63C GLU* 2.8 16.5 + - - -
64C TYR* 1.3 72.2 - - - +
66C ALA* 1.3 61.5 + - - +
68C ARG* 3.7 13.6 + - - +
69C ASP* 3.5 9.2 + - - +
99C GLN* 3.4 24.2 + - - +
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Residues in contact with ALA 66 (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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64C TYR* 4.3 0.2 - - - +
65C SER* 1.3 80.5 + - - +
67C MET* 1.3 64.3 + - - +
69C ASP* 3.2 21.3 + - - +
70C GLN* 3.5 6.2 + - - +
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Residues in contact with MET 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.6 33.2 - - + +
37C GLU* 3.9 21.8 - - + +
59C ALA* 4.9 1.6 - - - -
64C TYR* 3.5 50.3 + - + +
66C ALA* 1.3 80.2 - - - +
68C ARG* 1.3 62.6 + - - +
70C GLN* 3.2 28.1 + - - +
71C TYR* 3.4 28.7 - - + +
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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
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9C VAL* 5.2 4.3 - - + -
58C THR* 5.8 1.8 - - - -
59C ALA 5.0 5.6 + - - -
62C GLU* 2.7 34.7 + - - +
64C TYR* 3.0 23.8 + - - +
65C SER* 3.8 14.2 - - - +
66C ALA 3.2 0.2 - - - -
67C MET* 1.3 78.6 - - - +
69C ASP* 1.3 60.7 + - - +
70C GLN 3.2 0.2 + - - -
71C TYR* 3.4 34.0 - - + +
72C MET* 3.0 49.2 + - + +
95C HIS* 5.9 2.0 + - - +
96C TYR* 3.5 42.2 + - - +
99C GLN* 2.9 26.9 + - - +
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Residues in contact with ASP 69 (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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65C SER 3.5 7.4 + - - +
66C ALA* 3.2 14.5 + - - +
68C ARG* 1.3 77.9 - - - +
70C GLN* 1.3 64.7 + - - +
72C MET* 4.1 5.6 - - - -
73C ARG* 3.4 31.2 + - - +
99C GLN* 2.7 28.0 + - - +
102C ARG* 3.9 12.3 + - - -
103C VAL* 3.2 34.8 - - - +
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Residues in contact with GLN 70 (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 GLU* 5.3 6.1 + - - -
66C ALA 3.5 4.9 + - - +
67C MET* 3.2 22.8 + - - +
68C ARG 3.1 0.8 - - - -
69C ASP* 1.3 82.7 - - - +
71C TYR* 1.3 68.5 + - + +
72C MET 3.3 0.2 + - - -
73C ARG* 3.4 18.8 + - - +
74C THR* 3.0 16.3 + - - +
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Residues in contact with TYR 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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7C VAL* 4.0 16.3 - - + +
9C VAL* 5.1 1.1 - - + -
36C ILE 5.4 0.4 - - - -
37C GLU* 5.2 4.5 - - + -
56C LEU* 3.8 28.9 - - + -
57C ASP 5.9 0.2 - - - -
58C THR* 3.5 39.8 - - + +
59C ALA* 4.2 9.2 + - - +
64C TYR* 4.9 2.3 + - - +
67C MET* 3.4 42.7 - - + -
68C ARG* 3.4 48.1 + - + +
70C GLN* 1.3 83.1 - - + +
72C MET* 1.3 61.6 + - + +
73C ARG 3.2 0.2 - - - -
74C THR* 3.5 10.3 - - - +
75C GLY* 2.8 28.8 + - - -
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Residues in contact with MET 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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9C VAL* 5.3 4.9 - - + -
68C ARG* 3.0 44.1 + - + +
69C ASP 3.6 6.3 - - - +
70C GLN 3.2 0.4 - - - -
71C TYR* 1.3 80.3 - - + +
73C ARG* 1.3 60.1 + - - +
75C GLY 3.5 1.0 - - - +
78C PHE* 3.3 35.8 - - + -
96C TYR* 3.9 7.4 - - + +
99C GLN* 3.5 43.7 - - + +
100C ILE* 3.6 28.9 - - + -
103C VAL* 3.7 22.4 - - + -
104C LYS* 3.4 20.1 + - - +
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Residues in contact with ARG 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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69C ASP* 3.4 29.0 + - - +
70C GLN* 3.4 15.8 + - - +
71C TYR 3.2 0.2 - - - -
72C MET* 1.3 81.3 - - - +
74C THR* 1.3 61.8 + - - +
103C VAL* 4.1 19.1 + - + +
104C LYS* 3.4 23.1 + - + -
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Residues in contact with THR 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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5C LYS* 3.8 30.7 - - + +
70C GLN* 3.0 18.9 + - - +
71C TYR* 3.3 10.8 + - - -
73C ARG* 1.3 79.1 - - - +
75C GLY* 1.3 65.0 + - - +
76C GLU* 3.5 6.8 + - - +
104C LYS* 4.8 0.2 + - - -
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Residues in contact with GLY 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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5C LYS* 4.2 9.0 - - - -
7C VAL* 3.4 27.6 - - - +
71C TYR 2.8 15.3 + - - -
72C MET 3.5 5.4 - - - +
74C THR* 1.3 72.5 - - - +
76C GLU* 1.3 57.0 + - - -
77C GLY 3.8 0.4 - - - -
78C PHE* 3.7 5.8 - - - -
104C LYS* 2.7 32.1 + - - -
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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