Contacts of the helix formed by residues 66 - 75 (chain C) in PDB entry 3HJW
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 HIS 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.8 44.1 - + + -
44B TYR* 3.8 6.5 - - + +
45B ARG* 4.1 25.3 - - + +
37C THR* 4.0 7.4 - - + -
41C THR* 3.0 36.8 + - + +
62C GLU 4.2 6.2 + - - +
63C ILE 3.4 26.8 + - - -
64C VAL* 3.0 1.6 + - - -
65C ALA* 1.3 77.4 + - - +
67C LEU* 1.3 75.6 + - + +
69C PRO* 3.3 5.8 - - - +
70C LEU* 3.2 29.2 + - + +
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Residues in contact with LEU 67 (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 THR* 4.4 4.9 - - + -
40C THR* 4.3 12.1 - - + -
41C THR* 3.9 26.9 - - - +
44C VAL* 4.6 11.9 - - + -
52C VAL* 4.6 4.5 - - + -
54C ILE* 4.0 15.5 - - + -
64C VAL* 3.0 26.7 + - + +
66C HIS* 1.3 87.1 - - + +
68C PRO* 1.4 74.2 - - + +
70C LEU* 3.0 9.0 + - + +
71C CYS* 2.7 29.7 + - - +
99C SER* 3.5 33.9 - - - +
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Residues in contact with PRO 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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7C TYR* 3.7 25.4 - - + +
9C LYS* 4.5 10.8 - - + +
54C ILE* 3.9 11.2 - - + -
64C VAL 3.6 8.3 - - - +
65C ALA* 3.8 6.5 - - - +
67C LEU* 1.4 92.8 - - + +
69C PRO* 1.4 64.0 - - + +
71C CYS* 3.3 2.1 + - - +
72C GLU* 3.0 37.0 + - - +
78C TYR* 3.7 32.0 - - + +
80C TYR* 3.9 8.7 - - + +
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Residues in contact with PRO 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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44B TYR* 3.6 33.4 - - + +
47B ARG* 4.3 22.5 + - + -
48B TRP* 4.1 14.8 - - + +
9C LYS* 5.5 4.3 - - - +
65C ALA 3.5 11.2 - - - +
66C HIS 3.3 16.2 - - - +
68C PRO* 1.4 95.9 - - + +
70C LEU* 1.3 55.6 + - - +
72C GLU* 3.6 11.3 + - + +
73C GLU* 3.1 25.6 + - - +
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Residues in contact with LEU 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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41B TYR* 5.4 1.3 - - + -
44B TYR* 3.6 44.4 - - + +
41C THR* 4.1 24.7 - - + +
44C VAL* 3.5 31.9 - - + -
45C GLU* 4.3 21.1 - - + +
66C HIS* 3.2 22.9 + - + +
67C LEU* 3.0 10.4 + - + +
69C PRO* 1.3 76.9 - - - +
71C CYS* 1.3 60.3 + - - +
73C GLU* 3.4 2.4 - - + +
74C LYS* 3.1 44.7 + - - +
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Residues in contact with CYS 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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44C VAL* 4.2 17.3 - - - -
52C VAL* 4.1 26.0 - - - -
67C LEU* 2.7 23.2 + - - +
68C PRO 3.4 4.9 - - - +
70C LEU* 1.3 74.7 - - - +
72C GLU* 1.3 59.6 - - - +
74C LYS 3.2 1.2 + - - -
75C GLU 2.8 24.8 + - - -
76C ILE* 2.9 32.0 + - - +
78C TYR* 3.5 27.6 - - + -
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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
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51B GLU* 5.8 0.2 - - - +
9C LYS* 4.5 8.3 - - - +
68C PRO* 3.0 24.6 + - - +
69C PRO* 3.9 8.6 - - - +
71C CYS* 1.3 75.1 - - - +
73C GLU* 1.3 61.2 + - - +
75C GLU* 3.5 16.2 + - - +
76C ILE 5.2 0.7 - - - -
78C TYR* 3.0 24.6 + - + -
123C MET* 3.7 26.0 - - + -
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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
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43B GLU* 4.9 1.4 - - - +
44B TYR* 2.8 37.4 + - + +
47B ARG* 4.1 17.0 + - - +
69C PRO 3.1 15.5 + - - +
70C LEU 3.4 9.2 - - - +
72C GLU* 1.3 78.8 - - - +
74C LYS* 1.3 76.5 + - - +
75C GLU* 4.5 5.4 - - - +
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Residues in contact with LYS 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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44B TYR* 4.8 4.0 + - - -
44C VAL* 3.4 22.9 - - + +
45C GLU* 4.3 27.1 + - - +
47C GLY* 5.7 2.9 - - - +
70C LEU* 3.1 27.7 + - + +
71C CYS 3.2 1.5 + - - +
73C GLU* 1.3 92.6 + - + +
75C GLU* 1.3 71.5 + - - +
76C ILE* 3.6 24.8 + - + +
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Residues in contact with GLU 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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71C CYS 2.8 7.4 + - - -
72C GLU* 3.5 13.0 + - - +
73C GLU 3.3 6.1 - - - +
74C LYS* 1.3 82.7 - - - +
76C ILE* 1.3 59.3 + - - +
77C PRO* 4.2 4.7 - - - +
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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