Contacts of the helix formed by residues 63 - 76 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54E GLN* 3.6 26.4 + - - -
58E GLU* 4.3 14.0 + - - -
61E TYR* 3.2 18.8 + + - -
62E GLU* 1.3 80.3 + - + +
64E LEU* 1.3 65.9 + - - +
65E HIS* 3.2 8.1 - - - -
66E LEU* 2.8 28.8 + - + -
67E GLU* 2.9 41.0 + - + -
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Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ARG* 5.3 2.0 - - - +
61E TYR* 3.5 52.8 + - + +
62E GLU 3.5 2.2 - - - -
63E HIS* 1.3 75.3 - - - +
65E HIS* 1.3 65.0 + - - +
67E GLU* 3.0 5.2 + - - +
68E MET* 2.9 49.6 + - + +
239E PHE* 4.2 17.9 - - + -
380E LEU* 4.2 9.0 - - + -
381E PHE* 4.3 10.3 - - + -
406E PHE* 4.6 4.9 - - + -
485E TYR* 3.7 39.5 - - + -
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Residues in contact with HIS 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLU 3.3 23.5 + - - -
63E HIS* 4.0 1.1 - - - -
64E LEU* 1.3 78.9 - - - +
66E LEU* 1.3 94.9 + - + +
68E MET* 3.8 4.8 + - - +
69E HIS* 3.1 27.4 + - - +
380E LEU* 3.6 33.2 - - + -
406E PHE* 5.5 0.4 - - - -
408E TYR* 3.9 26.5 - + + +
409E SER* 5.1 0.3 + - - -
483E MET* 3.1 43.9 + - + -
485E TYR* 4.0 4.9 - - + -
489E LEU* 3.7 16.7 - - + +
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Residues in contact with LEU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E HIS* 2.8 21.2 + - + +
65E HIS* 1.3 100.8 - - + +
67E GLU* 1.3 64.8 + - - +
69E HIS* 3.6 7.1 - - + +
70E GLN* 3.0 25.5 + - - +
408E TYR* 3.7 26.2 - - + +
482E LYS* 6.5 0.9 - - + -
483E MET 5.3 1.6 - - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E HIS* 4.0 27.8 + - + +
51E ARG* 5.6 1.2 - - - +
54E GLN* 5.3 4.3 + - - -
61E TYR* 2.4 32.5 + - - -
63E HIS* 2.9 35.1 + - + +
64E LEU* 3.4 10.1 - - - +
66E LEU* 1.3 78.4 - - - +
68E MET* 1.3 60.8 + - - +
70E GLN* 3.3 10.0 + - - +
71E THR* 2.6 31.0 + - - +
81E TYR* 5.8 1.2 - - - -
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Residues in contact with MET 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E HIS* 4.3 16.8 - - + -
51E ARG* 4.9 12.6 - - - +
61E TYR* 5.5 0.2 - - - +
64E LEU* 2.9 34.3 + - + +
65E HIS 4.1 3.1 - - - +
67E GLU* 1.3 79.6 - - - +
69E HIS* 1.3 66.3 + - - +
71E THR* 3.1 5.5 + - - -
72E PHE* 3.0 32.4 + - + -
79E PHE* 4.1 17.3 - - + -
81E TYR* 5.2 7.0 - - + -
88E MET* 6.1 2.7 - - - -
90E CYS* 4.3 11.9 - - - -
404E GLN* 5.0 1.8 - - - +
406E PHE* 3.5 60.1 - - + -
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Residues in contact with HIS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E HIS 3.1 21.1 + - - +
66E LEU* 3.6 10.1 - - + +
67E GLU 3.3 0.2 - - - -
68E MET* 1.3 77.6 - - - +
70E GLN* 1.3 57.9 + - - +
72E PHE* 3.3 3.3 + - - +
73E GLN* 3.0 64.6 + - - -
408E TYR* 3.9 17.3 - + + -
409E SER* 3.0 44.3 + - - +
412E ARG* 4.0 28.8 - - + +
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Residues in contact with GLN 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LEU 3.0 16.4 + - - +
67E GLU* 3.6 10.4 + - - +
69E HIS* 1.3 73.9 - - - +
71E THR* 1.3 65.1 + - - +
73E GLN* 3.0 13.9 + - + +
74E GLU* 2.8 61.0 + - + +
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Residues in contact with THR 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E HIS* 3.5 35.8 + - + -
45E PRO* 4.9 4.4 - - + +
67E GLU* 2.6 21.7 + - - +
68E MET 3.1 8.0 + - - -
70E GLN* 1.3 81.2 + - - +
72E PHE* 1.3 50.1 + - - +
74E GLU* 4.4 9.0 - - - +
75E LEU* 2.7 54.7 + - + +
79E PHE* 3.5 24.0 - - + -
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Residues in contact with PHE 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E MET* 3.0 26.8 + - + -
69E HIS 3.7 5.2 - - - +
71E THR* 1.3 72.6 - - - +
73E GLN* 1.3 64.9 + - - +
74E GLU 3.1 0.2 - - - -
76E GLY* 2.9 45.1 + - - +
77E PRO 3.3 17.9 - - - -
79E PHE* 3.6 20.2 - + - -
90E CYS* 3.2 39.7 - - + -
91E VAL 3.7 10.8 - - - -
92E MET* 3.6 27.4 - - + -
406E PHE* 4.0 22.7 - + + -
409E SER* 3.5 21.8 - - - +
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Residues in contact with GLN 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E HIS* 3.0 53.8 + - - +
70E GLN* 3.0 20.1 - - + +
72E PHE* 1.3 80.7 - - - +
74E GLU* 1.3 62.0 + - + +
76E GLY 4.5 1.0 + - - -
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Residues in contact with GLU 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E GLN* 2.8 51.5 + - + +
71E THR* 3.8 7.6 + - - +
73E GLN* 1.3 82.3 - - + +
75E LEU* 1.3 71.8 + - + +
76E GLY 3.8 0.3 + - - -
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Residues in contact with LEU 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PRO* 4.2 25.1 - - + +
43E GLN 3.2 39.5 - - - +
44E HIS* 4.3 0.4 - - - -
45E PRO* 5.0 4.7 - - + -
71E THR* 2.7 40.5 + - + +
74E GLU* 1.3 83.8 - - + +
76E GLY* 1.3 63.0 + - - +
77E PRO* 4.8 0.2 - - - +
78E ILE 4.1 6.8 - - - +
79E PHE* 3.9 14.6 - - + -
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Residues in contact with GLY 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E PHE* 2.9 33.2 + - - +
73E GLN 4.5 1.0 + - - -
74E GLU 3.5 2.6 + - - -
75E LEU* 1.3 81.8 - - - +
77E PRO* 1.3 68.5 - - - +
78E ILE 2.9 14.0 + - - +
79E PHE* 4.5 0.2 - - - -
92E MET* 5.4 0.2 - - - -
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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