Contacts of the helix formed by residues 63 - 76 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H GLN* 3.8 26.5 + - - -
58H GLU* 4.3 9.1 + - - -
61H TYR* 3.0 23.3 + + - -
62H GLU* 1.3 81.4 + - + +
64H LEU* 1.3 64.9 + - - +
65H HIS* 3.2 7.6 - - - -
66H LEU* 2.8 28.0 + - + -
67H GLU* 3.0 36.1 + - + -
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Residues in contact with LEU 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ARG* 5.9 0.7 - - - +
61H TYR* 3.1 58.7 + - + +
62H GLU 3.3 1.8 + - - -
63H HIS* 1.3 78.0 - - - +
65H HIS* 1.3 61.2 + - - +
67H GLU* 3.5 2.8 - - - +
68H MET* 3.1 46.5 + - + +
239H PHE* 4.6 7.4 - - + -
380H LEU* 3.9 9.6 - - + -
381H PHE* 4.3 11.2 - - + -
406H PHE* 4.7 1.8 - - + -
485H TYR* 3.4 43.3 - - + +
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Residues in contact with HIS 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H GLU 3.3 22.1 + - - -
63H HIS* 3.0 3.4 + - - -
64H LEU* 1.3 78.6 - - - +
66H LEU* 1.3 85.2 + - + +
68H MET* 4.0 4.2 - - - +
69H HIS* 3.0 28.1 + - - +
380H LEU* 3.6 34.5 - - + +
408H TYR* 3.7 32.4 - + + +
409H SER* 5.0 0.2 + - - -
483H MET* 3.2 45.1 + - + -
485H TYR* 4.2 2.7 - - + -
489H LEU* 3.6 16.8 - - + +
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Residues in contact with LEU 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H HIS* 2.8 17.5 + - + +
65H HIS* 1.3 98.0 - - + +
67H GLU* 1.3 71.3 + - - +
69H HIS* 3.2 8.7 + - + +
70H GLN* 2.9 22.3 + - - +
408H TYR* 3.4 29.4 - - + +
482H LYS* 6.1 5.6 - - + -
483H MET 5.7 0.7 - - - +
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Residues in contact with GLU 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H HIS* 3.5 33.5 + - + +
51H ARG* 5.5 0.9 - - - -
61H TYR* 2.8 37.7 + - - -
63H HIS* 3.0 27.3 + - + +
64H LEU* 3.5 9.4 - - - +
66H LEU* 1.3 79.5 - - - +
68H MET* 1.3 72.6 + - - +
70H GLN* 2.9 26.1 + - - +
71H THR* 3.1 13.6 + - - +
81H TYR* 5.1 3.6 - - - -
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Residues in contact with MET 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H HIS* 4.6 6.5 - - - -
51H ARG* 4.9 10.1 - - - +
61H TYR* 5.1 0.4 - - - +
64H LEU* 3.1 31.8 + - + +
65H HIS 4.1 3.4 - - - +
67H GLU* 1.3 93.2 - - - +
69H HIS* 1.3 61.3 + - - +
71H THR* 3.4 6.1 + - - -
72H PHE* 3.0 35.8 + - + -
79H PHE* 4.2 16.2 - - + -
81H TYR* 5.3 5.6 - - + -
88H MET* 4.5 6.7 - - + -
90H CYS* 4.3 11.4 - - - -
404H GLN* 4.4 4.0 - - - +
406H PHE* 3.5 55.6 - - + -
409H SER* 5.6 0.2 - - - +
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Residues in contact with HIS 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H HIS 3.0 20.9 + - - +
66H LEU* 3.5 11.4 - - + +
67H GLU 3.0 0.2 + - - -
68H MET* 1.3 75.7 - - - +
70H GLN* 1.3 63.6 + - - +
72H PHE* 3.5 3.6 + - - +
73H GLN* 3.2 49.4 + - + +
92H MET* 5.6 2.9 - - + +
408H TYR* 3.9 18.6 - + + -
409H SER* 2.6 36.0 + - - +
412H ARG* 4.1 34.1 - - + -
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Residues in contact with GLN 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H LEU 2.9 16.4 + - - +
67H GLU* 2.9 22.0 + - - +
69H HIS* 1.3 70.4 - - - +
71H THR* 1.3 62.4 + - - +
73H GLN* 2.8 20.6 + - - +
74H GLU* 2.7 54.9 + - + +
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Residues in contact with THR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H HIS* 3.4 34.5 + - + -
45H PRO* 5.0 3.2 - - + +
67H GLU* 3.1 12.9 + - - +
68H MET* 3.5 10.2 - - - -
70H GLN* 1.3 85.2 + - - +
72H PHE* 1.3 55.4 + - - +
74H GLU* 3.1 11.0 + - - +
75H LEU* 2.7 46.0 + - + +
79H PHE* 3.3 28.9 - - + -
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Residues in contact with PHE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H MET* 3.0 30.0 + - + +
69H HIS 3.8 4.9 - - - +
70H GLN 3.3 0.2 - - - -
71H THR* 1.3 75.2 - - - +
73H GLN* 1.3 57.7 + - + +
76H GLY* 2.8 47.9 + - - -
77H PRO* 4.2 3.4 - - + -
79H PHE* 3.3 24.9 - + - -
90H CYS* 3.5 27.1 - - + -
91H VAL* 3.5 21.1 - - - -
92H MET* 3.4 39.3 - - + +
406H PHE* 3.7 28.5 - + + -
409H SER* 3.8 16.8 - - - -
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Residues in contact with GLN 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H HIS* 3.2 40.1 + - + +
70H GLN* 2.8 23.4 + - - +
72H PHE* 1.3 78.5 - - + +
74H GLU* 1.3 62.7 + - + +
76H GLY* 4.3 2.3 + - - -
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Residues in contact with GLU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H PRO* 5.0 12.3 - - - +
70H GLN* 2.7 39.3 + - + +
71H THR* 3.5 16.6 + - - +
73H GLN* 1.3 76.1 - - + +
75H LEU* 1.3 71.8 + - + +
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Residues in contact with LEU 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H PRO* 4.2 25.7 - - + +
43H GLN 3.3 33.9 - - - +
44H HIS* 4.5 1.3 - - - -
45H PRO* 4.7 5.2 - - + -
71H THR* 2.7 38.6 + - + +
74H GLU* 1.3 89.7 - - + +
76H GLY* 1.3 64.3 + - - +
77H PRO* 4.7 0.2 - - - +
78H ILE* 3.9 7.8 - - - +
79H PHE* 4.4 12.6 - - + -
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Residues in contact with GLY 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H PHE* 2.8 40.6 + - - +
73H GLN 4.3 2.0 + - - -
74H GLU 3.8 1.0 - - - -
75H LEU* 1.3 76.0 - - - +
77H PRO* 1.3 69.5 - - - +
78H ILE 2.9 12.6 + - - +
92H MET* 5.6 0.4 - - - -
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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