Contacts of the helix formed by residues 63 - 78 (chain F) in PDB entry 4DHX
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 THR 63 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1232D LEU* 3.5 6.1 - - - -
61F HIS 5.1 2.7 - - - +
62F VAL* 1.3 84.0 - - - +
64F VAL* 1.3 67.8 + - - +
65F ASP* 3.7 6.4 + - - +
66F ASP* 3.1 33.5 + - - +
67F LEU* 3.1 18.9 + - - +
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Residues in contact with VAL 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLN 4.5 7.9 - - - +
98B HIS* 5.5 2.9 - - - -
1225D PHE* 3.4 39.7 - - + +
1228D ALA* 4.3 1.3 - - + +
1229D LYS* 4.1 30.1 - - + +
1232D LEU* 3.4 17.9 - - + +
63F THR* 1.3 75.5 - - - +
65F ASP* 1.3 79.5 + - - +
67F LEU* 3.3 5.3 + - - +
68F VAL* 2.9 29.3 + - + +
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Residues in contact with ASP 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS* 2.8 42.7 + - - +
22B GLU* 5.5 1.3 - - - +
23B THR* 5.3 2.0 - - - +
98B HIS* 3.2 32.9 + - - +
1225D PHE* 3.7 7.1 - - - -
63F THR* 3.2 5.4 + - - +
64F VAL* 1.3 88.4 - - - +
66F ASP* 1.3 66.8 + - - +
68F VAL* 3.9 6.7 - - - +
69F ALA* 3.2 23.6 + - - +
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Residues in contact with ASP 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F HIS 3.8 10.7 - - - +
62F VAL* 4.5 7.9 - - + -
63F THR* 3.1 40.1 + - - +
65F ASP* 1.3 78.0 - - - +
67F LEU* 1.3 62.3 + - - +
69F ALA* 3.7 5.5 + - - +
70F GLU* 3.3 24.3 + - - +
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Residues in contact with LEU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228D ALA* 3.8 35.4 - - + +
1231D THR* 5.0 0.4 - - - -
1232D LEU* 4.1 17.9 - - + -
50F CYS* 3.9 24.7 - - + +
53F VAL* 3.6 35.2 - - + -
54F ILE* 4.2 10.1 - - + -
62F VAL* 4.0 8.1 - - + -
63F THR 3.1 11.5 + - - +
64F VAL* 3.6 8.3 - - - +
66F ASP* 1.3 75.6 - - - +
68F VAL* 1.3 66.3 + - - +
70F GLU* 2.9 13.8 + - - +
71F ILE* 3.0 27.0 + - + +
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Residues in contact with VAL 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221D VAL* 5.8 2.9 - - + +
1224D ILE* 4.3 8.7 - - + +
1225D PHE* 3.9 41.7 - - + -
1228D ALA* 4.0 9.2 - - + +
64F VAL 2.9 21.3 + - - +
65F ASP* 3.9 9.2 - - - +
67F LEU* 1.3 77.1 - - - +
69F ALA* 1.3 61.5 + - - +
70F GLU 3.1 0.2 + - - -
71F ILE* 3.2 8.6 + - - +
72F THR* 2.7 43.8 + - - +
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Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ASP 3.2 15.3 + - - +
66F ASP* 3.9 6.7 - - - +
67F LEU 3.2 0.2 - - - -
68F VAL* 1.3 82.6 - - - +
70F GLU* 1.3 61.9 + - - +
72F THR* 4.4 4.5 - - - -
73F PRO* 3.8 14.0 - - - +
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F HIS* 4.2 7.9 - - + -
53F VAL* 4.0 32.3 - - + -
57F LYS* 4.5 18.7 + - - -
66F ASP 3.3 13.5 + - - +
67F LEU* 2.9 12.4 + - - +
69F ALA* 1.3 81.4 - - - +
71F ILE* 1.3 60.0 + - + +
72F THR 3.5 0.6 + - - -
73F PRO* 3.9 8.0 - - - +
74F LYS 5.2 0.3 + - - -
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Residues in contact with ILE 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224D ILE* 3.9 32.0 - - + +
1228D ALA* 4.1 8.1 - - + -
46F LEU* 4.0 15.6 - - + +
49F HIS* 3.6 26.7 - - + +
50F CYS* 3.3 34.1 - - - -
53F VAL* 4.5 2.5 - - + -
67F LEU* 3.0 34.5 + - + +
68F VAL* 3.6 4.9 - - - +
70F GLU* 1.3 80.4 - - + +
72F THR* 1.3 62.6 + - - +
73F PRO 3.4 2.0 - - - -
74F LYS* 3.1 5.9 + - - +
75F GLY* 2.8 26.2 + - - -
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224D ILE* 3.9 19.5 - - + +
68F VAL* 2.7 35.7 + - - +
69F ALA* 4.4 4.1 - - - -
71F ILE* 1.3 78.4 - - - +
73F PRO* 1.3 71.9 - - + +
75F GLY* 3.1 1.9 + - - -
76F ARG* 3.0 64.5 + - + +
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Residues in contact with PRO 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ALA 3.8 13.2 - - - +
70F GLU 3.9 7.0 - - - +
71F ILE 3.6 2.5 - - - -
72F THR* 1.3 100.0 - - + +
74F LYS* 1.3 61.7 + - - +
76F ARG* 3.5 11.2 + - + +
77F ALA* 3.1 24.1 + - - +
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Residues in contact with LYS 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLN* 5.3 2.7 - - - -
46F LEU* 4.7 5.2 - - + -
49F HIS* 3.6 50.3 - - + +
70F GLU 5.2 0.4 + - - +
71F ILE 3.1 9.5 + - - +
73F PRO* 1.3 75.8 - - - +
75F GLY* 1.3 67.0 + - - +
77F ALA* 3.3 7.1 + - + -
78F LEU* 3.0 53.7 + - + +
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Residues in contact with GLY 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220D LEU* 4.5 2.2 - - - -
1224D ILE* 4.2 6.3 - - - -
42F TRP* 2.9 36.6 + - - -
46F LEU* 3.9 18.3 - - - +
71F ILE 2.8 14.2 + - - -
72F THR 3.1 3.1 + - - -
74F LYS* 1.3 76.5 - - - +
76F ARG* 1.3 60.5 + - - +
78F LEU* 3.3 6.6 + - - -
79F VAL* 3.5 3.3 - - - +
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Residues in contact with ARG 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217D ASP* 6.2 3.4 - - - +
1220D LEU* 3.7 24.2 - - + +
1221D VAL* 5.7 7.9 - - - +
1224D ILE* 4.5 2.8 - - + +
72F THR* 3.0 44.3 + - + +
73F PRO* 3.8 10.7 - - - +
75F GLY* 1.3 76.2 - - - +
77F ALA* 1.3 62.1 + - - +
78F LEU 3.1 1.0 + - - -
79F VAL* 3.3 19.6 + - - +
84F LYS* 4.6 7.6 + - - -
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Residues in contact with ALA 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F PRO 3.1 14.7 + - - +
74F LYS* 3.9 8.3 - - + +
76F ARG* 1.3 77.9 - - - +
78F LEU* 1.3 61.6 + - + +
79F VAL 3.3 5.0 + - - +
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F TRP* 3.4 36.1 - - + +
45F GLN* 3.5 49.5 - - + +
46F LEU* 3.8 13.9 - - + +
74F LYS* 3.0 48.4 + - + +
75F GLY* 3.5 1.1 - - - +
76F ARG 3.0 0.6 - - - -
77F ALA* 1.3 79.3 - - - +
79F VAL* 1.3 63.6 + - - +
80F PRO* 3.2 11.4 - - - +
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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