Contacts of the helix formed by residues 63 - 76 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B GLN* 3.3 27.4 + - - -
58B GLU* 3.7 17.3 + - - -
61B TYR* 2.9 22.7 + + - -
62B GLU* 1.3 80.6 + - - +
64B LEU* 1.3 55.7 + - - +
65B HIS* 3.2 7.9 - - - -
66B LEU* 2.8 41.9 + - + -
67B GLU* 3.1 32.6 + - + +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ARG* 5.9 0.4 - - - +
61B TYR* 3.2 55.8 + - + +
62B GLU 3.5 1.0 - - - -
63B HIS* 1.3 77.6 - - - +
65B HIS* 1.3 61.9 + - - +
67B GLU* 3.5 3.5 + - - +
68B MET* 3.1 55.2 + - + +
239B PHE* 4.6 11.4 - - + -
380B LEU* 4.3 5.6 - - + -
381B PHE* 4.1 16.4 - - + -
406B PHE* 4.7 2.2 - - + -
485B TYR* 3.4 44.4 - - + +
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Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU 3.6 20.7 + - - -
63B HIS 2.9 1.5 + - - -
64B LEU* 1.3 79.7 - - - +
66B LEU* 1.3 93.1 + - + +
68B MET* 4.2 3.9 - - - +
69B HIS* 3.2 23.4 + - - +
380B LEU* 3.5 32.3 - - + +
406B PHE* 5.7 1.3 - - - -
408B TYR* 3.6 34.4 - + + +
409B SER* 4.9 0.5 + - - -
483B MET* 3.2 43.6 + - + -
485B TYR* 4.2 2.9 - - + -
489B LEU* 3.6 18.7 - - + +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B HIS* 2.8 26.2 + - + +
65B HIS* 1.3 93.8 - - + +
67B GLU* 1.3 64.0 + - - +
69B HIS* 3.4 9.4 + - + +
70B GLN* 3.0 26.0 + - - +
408B TYR* 3.9 24.9 - - + +
483B MET 5.2 1.8 - - - +
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B HIS* 3.7 31.5 + - - +
54B GLN* 5.6 2.1 + - - -
61B TYR* 2.6 38.9 + - - -
63B HIS* 3.1 25.8 + - + +
64B LEU* 3.8 9.2 - - - +
66B LEU* 1.3 75.0 - - - +
68B MET* 1.3 72.9 + - + +
70B GLN* 3.1 12.4 + - + +
71B THR* 3.0 26.7 + - - +
81B TYR* 5.6 0.9 - - - -
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B HIS* 5.2 4.5 - - - +
51B ARG* 5.0 10.3 - - - +
61B TYR* 5.0 0.7 - - - +
64B LEU* 3.1 36.4 + - + +
65B HIS 4.2 2.7 - - - +
67B GLU* 1.3 90.1 - - + +
69B HIS* 1.3 62.4 + - - +
71B THR* 3.4 5.8 + - - -
72B PHE* 3.0 33.9 + - + -
79B PHE* 3.8 23.5 - - + -
81B TYR* 5.3 9.0 - - + -
88B MET* 4.7 14.4 - - + -
90B CYS* 4.7 2.2 - - - -
404B GLN* 5.2 0.2 - - - +
406B PHE* 3.8 52.0 - - + -
409B SER* 5.3 0.4 - - - +
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Residues in contact with HIS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS 3.2 17.8 + - - +
66B LEU* 3.4 13.0 - - + +
67B GLU 3.2 0.2 - - - -
68B MET* 1.3 78.9 - - - +
70B GLN* 1.3 63.0 + - + +
72B PHE* 3.1 7.3 + - - +
73B GLN* 3.1 52.2 + - + +
92B MET* 5.3 3.1 - - + +
408B TYR* 4.1 15.1 - + + -
409B SER* 2.9 44.7 + - - +
412B ARG* 4.2 27.4 - - + -
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU 3.0 14.8 + - - +
67B GLU* 3.1 12.8 + - + +
69B HIS* 1.3 73.4 - - + +
71B THR* 1.3 60.4 + - - +
73B GLN* 2.8 20.6 + - - +
74B GLU* 2.7 58.0 + - + +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B HIS* 3.6 26.8 + - + -
45B PRO* 5.1 2.0 - - + +
67B GLU* 3.0 15.8 + - - +
68B MET* 3.5 9.6 - - - -
70B GLN* 1.3 81.1 - - - +
72B PHE* 1.3 57.1 + - - +
74B GLU* 3.2 12.4 + - - +
75B LEU* 2.8 47.2 + - + +
79B PHE* 3.2 34.5 - - + -
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET* 3.0 28.1 + - + -
69B HIS* 3.1 6.9 + - - +
71B THR* 1.3 73.8 - - - +
73B GLN* 1.3 65.0 + - - +
76B GLY* 3.1 41.1 + - - +
77B PRO 3.8 5.6 - - - -
79B PHE* 3.7 20.6 - + - -
90B CYS* 3.4 30.7 - - + -
91B VAL 3.3 19.1 - - - -
92B MET* 3.3 38.5 - - + +
406B PHE* 4.0 26.2 - + + -
409B SER* 3.5 18.6 - - - -
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B HIS* 3.1 44.8 + - + +
70B GLN* 2.8 20.1 + - - +
72B PHE* 1.3 77.2 - - + +
74B GLU* 1.3 62.4 + - + +
76B GLY 4.6 1.2 + - - -
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PRO* 4.9 12.1 - - - +
70B GLN* 2.7 41.1 + - + +
71B THR* 3.5 15.6 + - - +
73B GLN* 1.3 76.6 - - + +
75B LEU* 1.3 75.7 + - + +
76B GLY 3.6 0.8 + - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PRO* 3.8 28.8 - - + +
43B GLN 3.6 25.8 - - - +
44B HIS* 4.6 1.6 - - - -
45B PRO* 4.7 7.4 - - + -
71B THR* 2.8 39.6 + - + +
74B GLU* 1.3 88.9 - - + +
76B GLY* 1.3 64.0 + - - +
77B PRO* 4.8 0.2 - - - +
78B ILE 3.6 10.0 - - - +
79B PHE* 4.1 16.2 - - + -
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR 4.5 0.2 - - - +
72B PHE* 3.1 33.5 + - - +
73B GLN 4.6 1.0 + - - -
74B GLU 3.6 2.4 + - - -
75B LEU* 1.3 80.1 - - - +
77B PRO* 1.3 68.8 - - - +
78B ILE 3.1 11.3 + - - +
79B PHE* 4.9 0.5 - - - -
92B MET* 5.7 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