Contacts of the helix formed by residues 67 - 80 (chain F) in PDB entry 5XS0
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 GLU 67 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F SER* 3.5 24.6 + - - +
65F TYR* 3.7 22.6 + - + -
66F ILE* 1.3 78.0 - - - +
68F GLY* 1.3 67.9 + - - +
69F HIS* 3.0 32.1 + - + -
70F ARG* 3.0 33.7 + - + +
71F VAL* 3.2 9.5 + - - +
152F LYS* 5.3 0.2 - - - +
167G LEU 4.4 3.5 - - - +
169G LYS* 3.3 35.7 + - - +
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Residues in contact with GLY 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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66F ILE 3.7 1.4 + - - -
67F GLU* 1.3 71.8 - - - +
69F HIS* 1.3 64.2 + - - +
71F VAL* 2.9 15.7 + - - +
72F ILE* 2.9 20.8 + - - +
148F THR* 4.3 24.2 - - - +
152F LYS* 4.3 12.5 - - - +
167G LEU* 5.9 1.1 - - - -
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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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67F GLU* 3.0 33.0 + - + -
68F GLY* 1.3 74.5 - - - +
70F ARG* 1.3 88.1 + - + +
72F ILE* 4.3 3.6 - - - -
73F ASN* 3.0 37.8 + - - -
164G ASN* 3.0 37.6 + - - +
165G CYS* 5.8 0.6 - - - -
167G LEU* 3.8 35.3 + - + +
168G ASP* 3.8 36.3 + - + +
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Residues in contact with ARG 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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195E ASP* 5.0 1.1 - - - +
50F GLU 3.5 15.9 + - - -
51F TYR* 2.8 59.2 + - + +
52F ILE 4.6 0.8 + - - -
53F SER* 3.2 19.8 + - - -
66F ILE* 3.6 12.3 - - + -
67F GLU* 3.0 33.4 + - + +
69F HIS* 1.3 100.4 + - + +
71F VAL* 1.3 57.2 + - - +
73F ASN* 3.4 5.4 + - - +
74F LEU* 2.9 35.4 + - - +
168G ASP* 4.8 8.3 + - - -
170G ASP* 5.1 6.1 + - - -
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Residues in contact with VAL 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ILE* 3.7 25.8 - - + -
67F GLU 3.5 13.9 - - - +
68F GLY 2.9 6.2 + - - +
70F ARG* 1.3 72.8 - - - +
72F ILE* 1.3 67.7 + - + +
74F LEU* 3.3 8.3 + - + +
75F ALA* 2.9 24.5 + - - +
151F LEU* 5.7 1.6 - - + -
152F LYS* 4.0 30.1 - - + +
155F LEU* 3.6 33.2 - - + -
162F LEU* 4.3 16.6 - - + +
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Residues in contact with ILE 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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68F GLY 2.9 18.7 + - - +
69F HIS* 3.7 4.0 - - - +
70F ARG 3.3 0.2 - - - -
71F VAL* 1.3 78.8 - - + +
73F ASN* 1.3 56.1 + - - +
75F ALA* 3.3 3.2 + - - +
76F ASN* 2.9 37.4 + - - +
84F TRP* 4.3 10.7 - - + -
151F LEU* 4.5 20.4 - - + -
156G ARG* 4.4 4.0 - - + +
157G SER* 3.4 51.1 - - - +
164G ASN* 3.2 31.9 - - - +
167G LEU* 5.6 4.0 - - + -
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Residues in contact with ASN 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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195E ASP* 3.8 22.4 + - + +
69F HIS* 3.0 30.2 + - - +
70F ARG* 3.9 5.2 - - - +
72F ILE* 1.3 73.4 - - - +
74F LEU* 1.3 66.7 + - - +
76F ASN* 3.3 6.2 + - - +
77F GLU* 2.9 31.3 + - + +
159G GLY* 4.5 4.0 - - - -
160G ASN* 3.3 38.8 + - - +
164G ASN* 3.0 19.5 + - - +
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Residues in contact with LEU 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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192E LYS* 3.6 31.0 - - - -
195E ASP* 3.8 9.2 - - - +
47F LEU* 4.2 16.2 - - + -
51F TYR* 3.8 26.0 - - + +
66F ILE* 4.9 6.1 - - + -
70F ARG 2.9 26.4 + - - +
71F VAL* 3.6 9.2 - - + +
72F ILE 3.3 0.2 - - - -
73F ASN* 1.3 76.1 - - - +
75F ALA* 1.3 57.2 + - - +
77F GLU* 3.3 5.7 + - + +
78F MET* 2.9 35.1 + - + +
161F ALA* 3.5 22.4 - - + +
162F LEU* 3.7 18.4 - - + -
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Residues in contact with ALA 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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71F VAL 2.9 17.4 + - - +
72F ILE 3.8 1.6 - - - +
74F LEU* 1.3 72.4 - - - +
76F ASN* 1.3 66.8 + - - +
79F PHE* 3.1 32.2 + - + -
84F TRP* 3.7 31.8 - - + -
155F LEU* 3.8 23.3 - - + -
162F LEU* 3.6 11.8 - - + +
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Residues in contact with ASN 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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72F ILE* 2.9 26.5 + - - +
73F ASN* 3.8 7.9 - - - +
75F ALA* 1.3 76.3 - - - +
77F GLU* 1.3 62.1 + - + +
80F GLY* 2.9 29.6 + - - -
81F TYR* 3.6 18.3 - - + +
84F TRP* 2.8 25.1 + - - +
40G GLN* 3.2 11.6 + - - +
121G HIS* 5.0 0.2 - - - -
157G SER 3.2 22.0 + - - +
158G PHE* 3.3 23.5 + - - +
159G GLY* 3.5 8.4 - - - +
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Residues in contact with GLU 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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195E ASP* 3.7 37.5 - - + +
196E LEU* 3.3 17.7 - - - +
197E GLU* 4.5 11.8 + - + +
200E VAL* 4.4 2.8 - - - +
201E GLU* 5.5 0.9 - - - +
204E ARG* 2.8 21.5 + - - -
73F ASN* 2.9 21.6 + - + +
74F LEU* 3.8 4.3 - - - +
76F ASN* 1.3 82.5 - - - +
78F MET* 1.3 60.3 + - + +
40G GLN* 4.2 5.1 + - - +
44G ARG* 2.7 54.1 + - - +
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Residues in contact with MET 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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192E LYS* 5.6 2.2 - - - -
197E GLU* 4.2 15.7 - - + +
200E VAL* 3.3 15.7 - - + +
204E ARG* 2.8 12.2 + - - -
39F ILE* 3.6 45.1 - - + +
42F ALA* 3.8 27.8 - - + -
43F LEU* 3.7 28.5 - - + -
74F LEU* 2.9 25.3 + - + +
75F ALA* 3.3 0.4 + - - -
77F GLU* 1.3 77.1 - - + +
79F PHE* 1.3 76.1 + - + +
161F ALA* 4.4 11.4 - - + +
162F LEU* 4.5 7.0 - - + -
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Residues in contact with PHE 79 (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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81E TYR* 4.1 13.9 - + - -
204E ARG* 3.4 19.8 + - - +
31F TYR* 3.5 20.0 + - - +
35F GLU* 4.7 2.5 - - - +
39F ILE* 4.2 13.9 - - + -
43F LEU* 4.7 3.1 - - + -
75F ALA* 3.1 21.3 + - + +
78F MET* 1.3 86.6 - - + +
80F GLY* 1.3 60.8 + - - +
82F ASN* 4.8 0.5 - - - +
83F GLY* 3.3 34.0 + - - +
84F TRP* 3.8 15.7 - + + +
115F LEU* 3.6 30.7 - - + -
116F LYS* 5.2 2.8 - - - -
155F LEU* 4.7 2.0 - - + -
158F PHE* 4.2 14.6 - + + -
162F LEU* 3.5 33.9 - - + -
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Residues in contact with GLY 80 (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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204E ARG* 3.2 23.5 - - - +
76F ASN 2.9 19.8 + - - -
79F PHE* 1.3 79.8 - - - +
81F TYR* 1.3 67.2 + - - -
82F ASN* 3.0 5.9 + - - -
83F GLY 3.1 8.1 + - - -
84F TRP* 3.4 15.4 - - - -
36G TYR* 4.4 3.4 - - - -
40G GLN* 3.7 3.8 - - - -
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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