Contacts of the helix formed by residues 63 - 76 (chain C) in PDB entry 4DVQ
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 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C GLN* 5.7 5.2 - - + -
58C GLU* 4.2 22.8 + - - -
61C TYR* 3.1 19.1 + + - -
62C GLU* 1.3 82.4 + - + +
64C LEU* 1.3 67.1 + - - +
65C HIS* 3.1 8.1 - - - -
66C LEU* 2.8 30.9 + - + +
67C GLU* 2.9 43.1 + - + -
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Residues in contact with LEU 64 (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 TYR* 3.3 56.8 + - + +
62C GLU 3.4 1.6 - - - -
63C HIS* 1.3 78.8 - - - +
65C HIS* 1.3 62.8 + - - +
67C GLU* 3.3 3.4 + - - +
68C MET* 3.0 45.8 + - + +
239C PHE* 4.1 11.4 - - + -
380C LEU* 4.0 10.8 - - + -
381C PHE* 4.4 8.3 - - + -
406C PHE* 4.6 4.5 - - + -
485C TYR* 3.6 40.4 - - + +
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Residues in contact with HIS 65 (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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62C GLU 3.1 23.0 + - - -
63C HIS* 3.8 2.2 - - - -
64C LEU* 1.3 79.1 - - - +
66C LEU* 1.3 92.8 + - + +
68C MET* 3.5 4.4 + - - +
69C HIS* 3.0 29.5 + - - +
380C LEU* 3.6 35.3 - - + +
406C PHE* 5.6 0.4 - - - -
408C TYR* 3.8 25.6 - + + +
483C MET* 2.9 44.0 + - + -
485C TYR* 4.2 4.0 - - + -
489C LEU* 3.7 16.4 - - + +
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Residues in contact with LEU 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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63C HIS* 2.8 25.3 + - + +
65C HIS* 1.3 94.7 - - + +
67C GLU* 1.3 55.4 + - - +
69C HIS* 3.2 7.5 + - + +
70C GLN* 2.8 39.8 + - - +
408C TYR* 3.7 26.2 - - + +
482C LYS* 6.3 2.9 - - + -
483C MET 5.3 1.8 - - - +
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Residues in contact with GLU 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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44C HIS* 3.3 27.5 + - + +
51C ARG* 5.8 0.2 - - - -
61C TYR* 3.1 27.9 + - - -
63C HIS* 2.9 38.3 + - + +
64C LEU* 3.6 9.0 - - - +
66C LEU* 1.3 75.3 - - - +
68C MET* 1.3 58.0 + - + +
70C GLN* 3.5 11.2 + - - +
71C THR* 2.7 42.2 + - - +
81C TYR* 5.4 1.9 - - - -
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Residues in contact with MET 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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44C HIS* 4.4 17.7 - - + -
64C LEU* 3.0 40.6 + - + +
65C HIS 4.1 3.1 - - - +
67C GLU* 1.3 78.5 - - - +
69C HIS* 1.3 63.5 + - - +
71C THR* 3.3 4.1 + - - -
72C PHE* 2.9 34.9 + - + -
79C PHE* 3.5 20.6 - - + -
81C TYR* 5.9 3.4 - - + -
88C MET* 5.5 1.8 - - + -
90C CYS* 3.4 23.1 - - - -
404C GLN* 4.8 0.9 - - - +
406C PHE* 3.4 50.0 - - + -
409C SER* 4.6 0.4 - - - +
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Residues in contact with HIS 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 HIS 3.0 19.3 + - - +
66C LEU* 3.2 8.7 + - + +
68C MET* 1.3 74.6 - - - +
70C GLN* 1.3 64.3 + - - +
72C PHE* 3.2 13.5 + - - +
73C GLN* 3.2 38.7 + - + +
92C MET* 5.4 4.6 - - + +
408C TYR* 4.0 21.3 - + + -
409C SER* 3.0 34.7 + - - +
412C ARG* 4.3 30.3 - - + +
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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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66C LEU 2.8 18.1 + - - +
67C GLU* 3.7 9.8 - - - +
69C HIS* 1.3 78.0 - - - +
71C THR* 1.3 60.8 + - - +
73C GLN* 3.4 20.7 + - + +
74C GLU* 3.3 46.7 + - + +
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Residues in contact with THR 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 HIS* 3.8 22.8 + - + -
45C PRO* 4.8 5.9 - - + +
67C GLU* 2.7 25.6 + - - +
68C MET* 3.5 7.9 - - - -
69C HIS 3.2 0.4 - - - -
70C GLN* 1.3 76.1 - - - +
72C PHE* 1.3 56.9 + - - +
74C GLU* 3.2 7.6 + - - +
75C LEU* 2.9 43.6 + - + +
79C PHE* 3.4 35.4 - - + -
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Residues in contact with PHE 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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68C MET* 2.9 31.5 + - + -
69C HIS* 3.2 5.1 + - - +
71C THR* 1.3 71.7 - - - +
73C GLN* 1.3 62.7 + - - +
76C GLY* 2.8 52.0 + - - +
77C PRO 3.4 12.6 - - - -
79C PHE* 3.6 24.2 - + - -
90C CYS* 3.6 18.4 - - + -
91C VAL 3.5 20.6 - - - -
92C MET* 3.3 41.7 - - + -
406C PHE* 4.0 23.6 - + + -
409C SER* 3.7 15.5 - - - +
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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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69C HIS* 3.2 40.8 + - + +
70C GLN* 3.4 19.5 - - + +
72C PHE* 1.3 80.4 - - - +
74C GLU* 1.3 63.3 + - + +
76C GLY* 4.2 2.1 + - - -
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Residues in contact with GLU 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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70C GLN* 3.3 39.5 + - + +
71C THR* 3.2 8.4 + - - +
73C GLN* 1.3 82.0 - - + +
75C LEU* 1.3 72.6 + - + +
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Residues in contact with LEU 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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42C PRO* 4.0 31.0 - - + +
43C GLN 3.2 39.7 - - - +
44C HIS* 3.9 8.3 - - - +
45C PRO* 4.4 5.8 - - + -
71C THR* 2.9 27.2 + - + +
74C GLU* 1.3 88.5 - - + +
76C GLY* 1.3 59.7 + - - +
77C PRO* 4.6 1.2 - - - +
78C ILE 4.3 3.0 - - - +
79C PHE* 4.4 13.5 - - + -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 2.8 41.9 + - - +
73C GLN 4.2 1.9 + - - -
74C GLU 3.5 1.6 - - - -
75C LEU* 1.3 82.3 - - - +
77C PRO* 1.3 70.8 - - - +
78C ILE* 3.3 3.3 + - - -
79C PHE* 4.5 2.1 - - - -
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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