Contacts of the helix formed by residues 56 - 69 (chain F) in PDB entry 4R8A
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 PRO 56 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLU 4.2 2.7 - - - +
55F LEU* 1.3 95.8 - - + +
57F GLU* 1.3 65.6 + - - +
58F ALA* 4.4 3.4 - - + +
59F SER* 3.0 33.5 + - - +
60F GLN* 3.1 12.4 + - - +
93F PRO* 4.4 12.3 - - + -
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Residues in contact with GLU 57 (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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20F PHE* 4.5 24.3 - - + -
23F LEU* 3.7 9.2 - - + +
24F HIS* 4.3 9.5 - - - -
27F ARG* 3.0 38.4 + - - +
55F LEU 3.8 1.2 + - - -
56F PRO* 1.3 72.4 - - - +
58F ALA* 1.3 62.6 + - - +
60F GLN* 3.4 10.3 + - - +
61F ALA* 3.1 22.5 + - - +
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Residues in contact with ALA 58 (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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20F PHE* 4.8 4.5 - - + -
56F PRO* 3.3 3.4 - - + +
57F GLU* 1.3 78.4 - - - +
59F SER* 1.3 58.0 + - - +
61F ALA* 3.9 8.6 - - - +
62F LEU* 3.3 24.3 + - - +
83F GLU 5.1 1.6 - - - +
84F ILE* 3.6 34.5 - - - +
90F ALA* 3.8 13.3 - - + +
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Residues in contact with SER 59 (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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55F LEU* 4.1 14.1 - - - -
56F PRO* 3.0 29.0 + - - +
58F ALA* 1.3 77.4 - - - +
60F GLN* 1.3 64.4 + - - +
62F LEU* 3.5 1.2 + - - +
63F LEU* 3.2 23.2 + - - +
90F ALA* 2.9 29.8 + - - -
93F PRO* 3.4 16.2 - - - +
94F LEU* 3.7 13.0 - - - +
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Residues in contact with GLN 60 (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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23F LEU* 3.6 8.5 - - + +
27F ARG* 2.6 44.4 + - - +
52F PHE* 3.0 53.1 + - + +
53F ALA* 3.4 14.3 + - - +
55F LEU* 3.1 23.8 + - + +
56F PRO 3.1 12.0 + - - +
57F GLU* 3.7 6.3 - - - +
59F SER* 1.3 75.7 - - - +
61F ALA* 1.3 61.6 + - - +
63F LEU* 3.4 3.7 + - - +
64F VAL* 3.1 27.7 + - - +
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Residues in contact with ALA 61 (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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20F PHE* 3.5 29.4 - - + -
22F TYR* 3.3 30.8 - - + +
23F LEU* 4.0 6.0 - - + +
57F GLU 3.1 8.5 + - - +
58F ALA 3.9 2.2 - - - +
59F SER 3.2 0.2 - - - -
60F GLN* 1.3 79.9 - - - +
62F LEU* 1.3 62.1 + - - +
64F VAL* 3.3 1.6 + - - -
65F ARG* 3.1 25.5 + - - +
84F ILE* 3.8 9.6 - - + -
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Residues in contact with LEU 62 (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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58F ALA 3.3 16.0 + - - +
59F SER* 3.9 4.3 - - - +
60F GLN 3.4 0.4 - - - -
61F ALA* 1.3 78.8 - - - +
63F LEU* 1.3 64.1 + - - +
65F ARG* 3.3 14.5 + - + +
66F MET* 3.3 21.9 + - - +
79F LEU* 4.3 25.6 - - + +
81F TYR* 4.8 6.7 - - + -
84F ILE* 4.0 21.2 - - + +
87F THR* 3.8 23.8 - - + +
90F ALA* 3.9 6.1 - - + +
91F VAL* 3.7 46.7 - - + +
94F LEU* 4.4 3.1 - - + -
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Residues in contact with LEU 63 (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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26F PHE* 5.6 2.5 - - + -
48F PHE* 4.4 10.3 - - + -
52F PHE* 3.7 25.6 - - + -
59F SER 3.2 15.6 + - - +
60F GLN* 3.6 4.3 - - - +
62F LEU* 1.3 76.6 - - - +
64F VAL* 1.3 67.4 + - - +
66F MET* 3.1 9.7 + - - +
67F VAL* 3.0 31.2 + - + +
94F LEU* 3.9 21.7 - - + +
99F TRP* 3.7 30.5 - - + -
100F VAL* 4.2 6.7 - - + -
166F LEU* 3.7 30.3 - - + -
168F CYS* 4.1 8.3 - - - -
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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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22F TYR* 3.6 23.8 - - + +
23F LEU* 3.8 13.9 - - + -
26F PHE* 3.6 38.8 - - + -
52F PHE* 4.1 3.6 - - + -
60F GLN 3.1 16.9 + - - +
61F ALA 3.6 4.9 - - - +
63F LEU* 1.3 75.9 - - + +
65F ARG* 1.3 57.6 + - - +
67F VAL* 3.2 8.3 + - + +
68F MET* 2.9 58.9 + - + +
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Residues in contact with ARG 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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19F PRO 4.9 0.8 + - - -
21F TYR* 4.5 15.2 + - - -
22F TYR* 3.2 49.5 + - + +
61F ALA 3.1 20.5 + - - +
62F LEU* 3.4 11.9 - - + +
63F LEU 3.2 0.4 - - - -
64F VAL* 1.3 76.0 - - - +
66F MET* 1.3 58.9 + - + +
68F MET* 3.9 6.5 - - - +
69F ARG* 3.0 39.1 + - - +
79F LEU* 5.2 0.7 - - + -
81F TYR* 3.2 59.4 + - + +
83F GLU* 3.6 14.1 + - - -
84F ILE* 5.6 0.7 - - + -
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Residues in contact with MET 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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62F LEU* 3.3 27.1 - - - +
63F LEU* 3.1 9.1 + - - +
65F ARG* 1.3 73.7 - - - +
67F VAL* 1.3 65.7 + - - +
69F ARG 3.4 13.9 - - - +
74F PHE* 3.5 44.9 - - + -
79F LEU* 4.3 24.5 - - + -
91F VAL* 5.3 1.3 - - - -
94F LEU* 5.0 0.9 - - - -
100F VAL* 3.7 41.7 - - + -
164F TYR* 4.0 17.3 - - + +
166F LEU* 3.7 24.2 - - + +
169F MET* 3.8 3.5 - - - +
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Residues in contact with VAL 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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26F PHE* 4.7 9.0 - - + -
63F LEU* 3.0 28.4 + - + +
64F VAL* 3.2 10.7 + - + +
66F MET* 1.3 77.3 - - - +
68F MET* 1.3 63.5 + - + +
69F ARG 3.5 1.6 - - - +
166F LEU* 3.7 20.9 - - + -
168F CYS* 5.0 0.2 - - - -
169F MET* 3.3 21.9 - - - +
172F CYS* 4.0 32.1 - - + -
187F TRP* 3.6 36.9 - - + -
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Residues in contact with MET 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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22F TYR* 3.5 44.4 - - + +
25F ASN* 5.2 2.7 - - + +
26F PHE* 4.9 2.9 - - + +
64F VAL* 2.9 34.5 + - + +
65F ARG* 4.0 8.7 - - - +
67F VAL* 1.3 79.7 - - + +
69F ARG* 1.3 60.9 + - + +
70F LYS* 3.9 0.3 + - - -
187F TRP* 3.6 57.5 - - + +
191F VAL* 6.6 0.4 - - + -
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Residues in contact with ARG 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 ARG* 3.0 23.8 + - - +
66F MET 3.4 5.8 + - - +
67F VAL 3.4 5.0 - - - +
68F MET* 1.3 83.0 - - + +
70F LYS* 1.3 68.5 + - - +
71F GLY 3.4 8.9 - - - +
74F PHE* 3.3 33.2 - - + -
78F LYS* 2.6 43.6 + - - +
79F LEU* 3.7 5.8 - - - +
81F TYR* 2.8 30.2 + - - -
169F MET* 4.3 1.4 - - - +
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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