Contacts of the helix formed by residues 59 - 69 (chain F) in PDB entry 5ITZ
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 59 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F ALA 3.1 24.5 - - - -
23F ARG 3.0 18.8 + - - -
24F ALA 3.5 5.4 - - - -
25F GLY* 3.2 23.8 + - - -
27F ASP* 5.7 0.7 - - - +
54F ALA* 2.9 18.3 + - + +
57F TYR* 3.4 28.4 + - + +
58F GLY* 1.3 74.1 + - - +
60F LEU* 1.3 66.1 + - - +
61F GLU* 3.3 4.7 - - - -
62F ILE* 3.3 16.0 + - + +
63F VAL* 3.0 23.7 + - - +
95F ILE* 3.9 2.2 - - - -
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Residues in contact with LEU 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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58F GLY 3.2 7.0 + - - +
59F HIS* 1.3 74.7 - - - +
61F GLU* 1.3 81.9 + - - +
63F VAL* 3.2 2.2 + - + +
64F GLU* 3.0 46.8 + - + +
94F GLU* 3.4 37.0 - - + +
95F ILE* 3.8 31.4 - - + +
98F VAL* 3.8 20.0 - - + -
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Residues in contact with GLU 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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27F ASP* 3.6 18.9 + - + +
59F HIS* 3.3 1.6 - - - -
60F LEU* 1.3 93.8 + - - +
62F ILE* 1.3 58.6 + - - +
64F GLU* 3.4 14.7 + - - +
65F VAL* 3.0 35.0 + - + +
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Residues in contact with ILE 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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21F ALA 4.0 2.9 - - - +
22F ALA* 4.2 5.8 - - + +
25F GLY* 3.5 39.5 - - - +
26F GLN 3.7 5.2 - - - +
27F ASP* 3.2 22.9 + - + +
30F VAL* 3.7 34.1 - - + -
54F ALA* 3.8 11.7 - - + -
59F HIS* 3.3 12.4 + - + +
60F LEU 3.3 0.6 - - - -
61F GLU* 1.3 75.0 - - - +
63F VAL* 1.3 65.1 + - - +
65F VAL* 3.1 7.0 + - + +
66F LEU* 2.8 45.6 + - + +
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Residues in contact with VAL 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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51F LEU* 4.0 16.6 - - + +
54F ALA* 3.8 6.3 - - + -
55F ALA* 3.7 31.6 - - - +
59F HIS 3.0 17.8 + - - +
60F LEU* 3.2 10.5 + - + +
62F ILE* 1.3 77.0 - - - +
64F GLU* 1.3 64.6 + - - +
66F LEU* 3.2 2.1 + - - +
67F LEU* 3.0 42.9 + - + +
95F ILE* 4.0 23.1 - - + -
98F VAL* 4.0 14.6 - - + -
99F LEU* 4.4 3.4 - - + -
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Residues in contact with GLU 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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60F LEU* 3.0 43.1 + - + +
61F GLU* 3.8 13.0 - - - +
63F VAL* 1.3 76.6 - - - +
65F VAL* 1.3 59.0 + - + +
67F LEU* 3.4 5.7 + - - +
68F LYS* 2.9 29.1 + - - +
98F VAL* 3.7 25.5 - - + +
102F HIS* 5.5 3.2 + - + -
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Residues in contact with VAL 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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30F VAL* 4.3 10.1 - - + -
31F ARG* 5.8 4.9 - - + -
34F MET* 4.0 19.5 - - - +
61F GLU* 3.0 23.5 + - + +
62F ILE* 3.1 7.2 + - + +
64F GLU* 1.3 75.7 - - + +
66F LEU* 1.3 65.0 + - - +
68F LYS* 3.2 11.6 + - + +
69F HIS* 2.8 42.7 + - + +
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Residues in contact with LEU 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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18F LEU* 4.6 8.3 - - + -
22F ALA* 4.5 0.2 - - + -
30F VAL* 4.6 5.8 - - + -
34F MET* 4.4 20.4 - - - -
40F VAL* 4.0 18.3 - - + +
50F PRO* 3.5 26.9 - - + +
51F LEU* 3.4 35.9 - - + +
54F ALA* 4.3 3.1 - - + -
62F ILE* 2.8 40.7 + - + +
63F VAL 3.7 3.1 - - - +
65F VAL* 1.3 70.6 - - - +
67F LEU* 1.3 58.3 + - - +
69F HIS 3.1 18.5 + - - +
71F ALA* 3.2 29.7 + - + +
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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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51F LEU* 3.7 26.9 - - + -
63F VAL* 3.0 29.3 + - + +
64F GLU 3.9 3.1 - - - +
66F LEU* 1.3 72.1 - - - +
68F LYS* 1.3 65.0 + - - +
69F HIS 3.1 2.5 + - - -
70F GLY* 3.9 5.9 + - - -
71F ALA* 4.0 14.4 + - + +
73F VAL* 3.8 21.8 - - + -
98F VAL* 3.8 28.0 - - + +
99F LEU* 4.1 12.8 - - + -
102F HIS* 3.9 37.3 - - + +
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Residues in contact with LYS 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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64F GLU 2.9 17.6 + - - +
65F VAL* 3.2 10.3 + - + +
67F LEU* 1.3 76.3 - - - +
69F HIS* 1.3 82.9 + - + +
70F GLY 3.7 1.6 + - - -
102F HIS* 5.1 3.1 + - - -
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Residues in contact with HIS 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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34F MET* 3.4 29.5 - - + +
40F VAL* 3.6 17.0 - - + +
65F VAL* 2.8 32.1 + - + +
66F LEU 3.1 5.4 + - - +
67F LEU 3.1 1.0 - - - -
68F LYS* 1.3 109.3 + - + +
70F GLY* 1.3 60.0 + - - +
71F ALA 3.5 1.2 + - - -
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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