Contacts of the helix formed by residues 67 - 80 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51S TYR 4.5 3.2 + - - -
53S SER* 3.7 17.2 + - - +
65S TYR* 3.6 28.6 + - + -
66S ILE* 1.3 78.9 - - - +
68S GLY* 1.3 68.4 + - - +
69S HIS* 3.0 33.1 - - + +
70S ARG* 3.1 25.0 + - + +
71S VAL* 3.3 9.4 + - - +
152S LYS* 5.4 0.2 - - - +
167T LEU 4.4 4.7 - - - +
169T LYS* 3.6 32.3 + - - +
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Residues in contact with GLY 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S ILE 3.7 1.4 + - - -
67S GLU* 1.3 71.9 - - - +
69S HIS* 1.3 63.6 + - - +
71S VAL* 3.0 7.2 + - - +
72S ILE* 2.9 31.2 + - - +
148S THR* 4.4 22.1 - - - +
152S LYS* 4.5 11.2 - - - +
167T LEU* 5.7 2.0 - - - -
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Residues in contact with HIS 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S GLU* 3.0 39.4 + - + +
68S GLY* 1.3 75.5 + - - +
70S ARG* 1.3 90.7 + - + +
72S ILE* 3.3 2.4 + - - +
73S ASN* 2.9 40.9 + - - +
160T ASN* 5.7 1.8 - - - -
164T ASN* 3.0 39.9 + - - +
167T LEU* 3.8 34.7 + - + +
168T ASP* 3.7 30.1 + - + -
169T LYS 5.3 0.2 - - - -
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Residues in contact with ARG 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195R ASP* 6.1 0.2 - - - -
50S GLU 3.6 16.5 + - - -
51S TYR* 3.5 45.7 + - + +
52S ILE 5.2 0.4 + - - -
53S SER* 3.9 14.6 + - - -
66S ILE* 3.9 12.8 - - + -
67S GLU* 3.1 21.6 + - + +
69S HIS* 1.3 103.8 + - + +
71S VAL* 1.3 57.6 + - - +
73S ASN* 3.4 5.2 + - - +
74S LEU* 2.9 34.7 + - - +
168T ASP* 3.9 19.0 + - - -
170T ASP* 4.0 13.3 + - - -
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Residues in contact with VAL 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S ILE* 3.6 34.5 - - + -
67S GLU 3.6 7.2 - - - +
68S GLY 3.0 6.8 + - - +
70S ARG* 1.3 72.6 - - - +
72S ILE* 1.3 67.7 + - + +
74S LEU* 3.3 8.9 + - + +
75S ALA* 2.9 22.9 + - - +
151S LEU* 6.2 0.4 - - + -
152S LYS* 4.3 27.8 - - + -
155S LEU* 3.6 27.6 - - + -
162S LEU* 4.0 23.1 - - + +
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Residues in contact with ILE 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68S GLY 2.9 21.0 + - - +
69S HIS* 3.7 2.0 - - - +
70S ARG 3.3 0.2 - - - -
71S VAL* 1.3 77.2 - - + +
73S ASN* 1.3 56.2 + - - +
75S ALA* 3.2 6.8 + - - +
76S ASN* 2.9 47.5 + - - +
84S TRP* 4.3 7.6 - - + -
151S LEU* 4.6 20.6 - - + -
155S LEU* 5.5 0.9 - - + -
156T ARG* 4.4 4.0 - - + +
157T SER* 3.5 36.1 - - - +
164T ASN* 3.3 34.5 - - - +
167T LEU* 5.9 2.7 - - + -
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Residues in contact with ASN 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195R ASP* 3.8 19.5 - - + +
69S HIS* 2.9 29.6 + - - +
70S ARG* 3.9 5.2 - - - +
72S ILE* 1.3 73.0 - - - +
74S LEU* 1.3 66.9 + - - +
76S ASN* 3.3 5.9 + - - +
77S GLU* 2.9 33.0 + - + +
159T GLY* 4.2 6.7 - - - -
160T ASN* 3.2 46.2 - - - +
164T ASN* 3.3 14.7 + - - +
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Residues in contact with LEU 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192R LYS* 3.7 30.1 - - + -
195R ASP* 3.9 4.2 + - - +
47S LEU* 4.2 8.1 - - + -
51S TYR* 3.5 38.4 - - + +
66S ILE* 5.1 5.4 - - + -
70S ARG 2.9 24.3 + - - +
71S VAL* 3.4 18.2 - - + +
73S ASN* 1.3 77.0 - - - +
75S ALA* 1.3 57.0 + - - +
77S GLU* 3.8 4.4 - - - +
78S MET* 2.9 35.5 + - + +
161S ALA* 3.4 23.3 - - + +
162S LEU* 3.8 16.4 - - + -
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Residues in contact with ALA 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S VAL 2.9 17.3 + - - +
72S ILE 3.7 3.6 - - - +
74S LEU* 1.3 74.2 - - - +
76S ASN* 1.3 61.1 + - - +
78S MET* 4.3 3.6 - - - -
79S PHE* 2.9 39.3 + - + +
84S TRP* 3.7 30.7 - - + -
155S LEU* 4.1 14.8 - - + -
162S LEU* 3.7 16.1 - - + +
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Residues in contact with ASN 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S ILE* 2.9 30.9 + - - +
73S ASN* 3.8 11.0 - - - +
75S ALA* 1.3 76.0 - - - +
77S GLU* 1.3 62.2 + - + +
80S GLY* 2.9 29.1 + - - -
81S TYR* 3.7 16.9 - - - +
84S TRP* 2.9 20.3 + - - +
40T GLN* 3.1 12.8 + - - +
157T SER 3.1 23.8 + - - +
158T PHE* 3.5 22.7 + - - +
159T GLY* 3.6 6.2 - - - +
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Residues in contact with GLU 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195R ASP* 3.7 38.8 - - + +
196R LEU* 3.8 16.5 - - - +
197R GLU* 4.6 12.2 + - + +
200R VAL* 4.6 0.3 - - - +
201R GLU* 5.3 2.6 + - - +
204R ARG* 3.3 15.1 + - - -
73S ASN* 2.9 23.0 + - + +
74S LEU* 3.8 4.3 - - - +
76S ASN* 1.3 82.2 - - + +
78S MET* 1.3 63.3 + - + +
40T GLN* 4.6 7.0 + - - +
44T ARG* 2.8 52.2 + - - +
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Residues in contact with MET 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192R LYS* 5.4 6.1 - - - -
197R GLU* 4.3 14.8 - - + +
200R VAL* 3.5 13.6 - - + +
204R ARG* 2.7 17.6 + - - -
39S ILE* 3.6 51.3 - - + +
42S ALA* 4.0 20.4 - - + -
43S LEU* 3.7 29.8 - - + -
74S LEU* 2.9 24.9 + - + +
75S ALA* 3.2 4.2 + - - +
77S GLU* 1.3 77.7 - - + +
79S PHE* 1.3 69.6 + - + +
161S ALA* 4.6 10.8 - - + -
162S LEU* 4.8 6.3 - - + -
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Residues in contact with PHE 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R TYR* 4.0 14.6 - + - -
204R ARG* 3.3 20.6 + - - +
31S TYR* 3.4 20.0 + - - +
35S GLU* 4.9 1.8 - - - +
39S ILE* 4.0 14.8 - - + -
43S LEU* 4.6 9.9 - - + -
75S ALA* 2.9 21.5 + - + +
78S MET* 1.3 89.6 - - + +
80S GLY* 1.3 61.0 + - - +
82S ASN* 4.9 0.3 - - - +
83S GLY* 3.3 34.1 - - - +
84S TRP* 4.0 10.8 - + + +
115S LEU* 3.8 35.9 - - + -
116S LYS* 5.3 1.0 - - - -
155S LEU* 5.1 2.0 - - + -
158S PHE* 4.5 11.9 - + - -
162S LEU* 3.7 29.8 - - + -
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Residues in contact with GLY 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204R ARG* 3.6 11.8 - - - -
76S ASN 2.9 20.7 + - - -
79S PHE* 1.3 79.8 - - - +
81S TYR* 1.3 66.7 + - - -
82S ASN* 3.0 5.1 + - - -
83S GLY 3.1 9.1 + - - -
84S TRP* 3.3 14.9 - - - -
36T TYR* 4.6 4.3 - - - -
40T GLN* 3.2 13.7 - - - -
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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