Contacts of the helix formed by residues 67 - 80 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51G TYR 4.3 2.4 + - - -
53G SER* 3.4 29.1 + - - +
65G TYR* 3.8 19.5 + - + -
66G ILE* 1.3 79.0 - - - +
68G GLY* 1.3 67.5 + - - +
69G HIS* 3.0 33.2 - - + +
70G ARG* 3.1 30.1 + - + +
71G VAL* 3.1 10.9 + - - +
152G LYS* 5.6 0.2 - - - +
167H LEU 4.9 1.4 - - - +
168H ASP* 5.3 0.2 - - - +
169H LYS* 3.8 31.0 + - - +
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Residues in contact with GLY 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ILE 3.7 1.2 + - - -
67G GLU* 1.3 72.2 - - - +
69G HIS* 1.3 62.9 + - - +
71G VAL* 3.0 5.8 + - - +
72G ILE* 3.0 30.9 + - - +
148G THR* 4.6 16.4 - - - -
152G LYS* 4.5 17.0 - - - +
167H LEU* 5.3 2.5 - - - -
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Residues in contact with HIS 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G GLU* 3.0 31.8 + - + +
68G GLY* 1.3 74.3 + - - +
70G ARG* 1.3 84.9 + - + +
72G ILE* 4.2 2.5 - - - -
73G ASN* 2.9 46.3 + - - -
160H ASN* 5.7 1.3 - - - -
164H ASN* 3.1 38.5 + - - +
165H CYS* 6.0 0.4 - - - -
167H LEU* 3.8 37.1 + - + +
168H ASP* 3.6 30.0 + - + -
169H LYS 5.2 0.2 - - - -
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Residues in contact with ARG 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ASP* 5.0 0.9 - - - +
50G GLU 3.8 14.2 + - - -
51G TYR* 3.7 45.4 + - + +
53G SER* 3.8 5.9 + - - -
66G ILE* 3.8 13.5 - - + -
67G GLU* 3.1 42.0 + - + +
69G HIS* 1.3 97.1 + - + +
71G VAL* 1.3 56.5 + - - +
73G ASN* 3.4 7.4 + - - +
74G LEU* 2.9 35.1 + - - +
168H ASP* 3.9 19.2 + - - -
170H ASP* 4.1 12.1 + - - -
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Residues in contact with VAL 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ILE* 3.6 32.5 - - + +
67G GLU 3.1 13.2 + - - +
68G GLY 3.0 6.4 + - - +
70G ARG* 1.3 72.0 - - - +
72G ILE* 1.3 61.3 + - + +
74G LEU* 3.3 9.5 + - + +
75G ALA* 2.9 28.2 + - - +
151G LEU* 6.0 0.7 - - + -
152G LYS* 4.2 25.8 - - + +
155G LEU* 3.8 27.5 - - + +
162G LEU* 4.3 20.2 - - + +
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Residues in contact with ILE 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G GLY* 3.0 19.7 + - - +
69G HIS* 3.6 4.3 - - - +
71G VAL* 1.3 77.5 - - + +
73G ASN* 1.3 55.6 + - - +
75G ALA* 3.3 6.3 + - - +
76G ASN* 2.9 47.3 + - - +
84G TRP* 4.4 7.5 - - + -
151G LEU* 4.6 20.6 - - + -
155G LEU* 5.5 1.3 - - + -
156H ARG* 5.0 4.3 - - + +
157H SER* 3.7 36.8 - - - +
164H ASN* 3.1 34.1 - - - +
167H LEU* 5.5 4.7 - - + -
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Residues in contact with ASN 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ASP* 3.8 23.2 + - - +
69G HIS* 2.9 35.1 + - - +
70G ARG* 3.7 5.9 - - - +
72G ILE* 1.3 71.9 - - - +
74G LEU* 1.3 66.8 + - - +
76G ASN* 3.3 9.5 + - - +
77G GLU* 2.9 31.5 + - + +
46H ARG* 6.0 1.8 - - - +
159H GLY* 4.8 0.5 - - - -
160H ASN* 3.4 35.4 + - - +
164H ASN* 3.2 16.3 + - - +
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Residues in contact with LEU 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LYS* 3.6 31.4 - - + -
195F ASP* 4.2 5.8 + - - +
47G LEU* 4.4 11.2 - - + -
51G TYR* 3.9 27.6 - - + +
66G ILE* 4.6 14.8 - - + -
70G ARG 2.9 22.8 + - - +
71G VAL* 3.3 14.1 + - + +
73G ASN* 1.3 77.0 - - - +
75G ALA* 1.3 57.3 + - - +
77G GLU* 3.3 3.9 + - - +
78G MET* 2.9 35.9 + - + +
161G ALA 3.6 23.1 - - - +
162G LEU* 3.8 16.6 - - + -
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Residues in contact with ALA 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G VAL 2.9 16.5 + - - +
72G ILE 3.7 3.4 - - - +
74G LEU* 1.3 73.2 - - - +
76G ASN* 1.3 62.0 + - - +
79G PHE* 2.9 38.7 + - + -
84G TRP* 3.7 33.5 - - + -
155G LEU* 4.1 19.5 - - + -
162G LEU* 3.7 11.8 - - + +
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Residues in contact with ASN 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G ILE* 2.9 31.9 + - - +
73G ASN* 3.7 9.4 + - - +
75G ALA* 1.3 76.4 - - - +
77G GLU* 1.3 62.2 + - + +
80G GLY* 2.9 29.6 + - - -
81G TYR* 3.7 17.6 - - - +
84G TRP* 3.0 20.5 + - - +
40H GLN* 3.6 13.2 - - - +
157H SER 3.3 23.1 + - - +
158H PHE* 3.7 18.6 + - - +
159H GLY* 3.8 7.0 - - - +
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Residues in contact with GLU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LYS* 6.0 0.7 - - - -
195F ASP* 3.6 39.0 - - + +
196F LEU* 3.8 17.0 - - - +
197F GLU* 4.6 11.2 + - + +
200F VAL* 4.6 4.2 - - - +
201F GLU* 5.2 4.2 + - - +
204F ARG* 3.5 14.2 + - - -
73G ASN* 2.9 20.6 + - + +
74G LEU* 3.9 3.8 - - - +
76G ASN* 1.3 81.0 - - - +
78G MET* 1.3 64.2 + - + +
40H GLN* 4.1 7.8 + - - -
44H ARG* 3.0 49.9 + - - +
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Residues in contact with MET 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LYS* 5.5 7.0 - - - -
197F GLU* 4.4 14.1 - - + -
200F VAL* 3.6 10.5 - - + +
204F ARG* 2.4 26.1 + - - -
39G ILE* 3.6 49.7 - - + +
42G ALA* 3.8 25.8 - - + -
43G LEU* 3.6 28.5 - - + -
74G LEU* 2.9 24.8 + - + +
75G ALA* 3.9 2.9 - - - +
77G GLU* 1.3 73.3 - - + +
79G PHE* 1.3 70.9 + - + +
161G ALA* 4.6 8.5 - - + -
162G LEU* 4.6 6.3 - - + -
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Residues in contact with PHE 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F TYR* 4.2 3.1 - + - -
204F ARG* 3.3 20.9 + - - +
31G TYR* 3.7 15.9 + - - +
35G GLU* 4.8 1.7 - - - +
39G ILE* 4.1 22.4 - - + -
43G LEU* 4.6 5.2 - - + -
75G ALA* 2.9 21.8 + - + +
78G MET* 1.3 85.6 - - + +
80G GLY* 1.3 60.4 + - - +
83G GLY* 3.2 35.5 + - - +
84G TRP* 3.9 15.3 - + + -
115G LEU* 3.7 35.0 - - + -
116G LYS* 5.3 0.9 - - - -
155G LEU* 4.9 2.5 - - + -
158G PHE* 4.2 14.6 - + + -
162G LEU* 3.4 34.3 - - + -
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Residues in contact with GLY 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F ARG* 3.1 17.5 - - - +
76G ASN 2.9 20.5 + - - -
79G PHE* 1.3 77.8 - - - +
81G TYR* 1.3 66.2 + - - -
82G ASN* 3.0 7.8 + - - -
83G GLY 3.2 8.0 + - - -
84G TRP* 3.2 17.5 - - - -
36H TYR* 4.4 3.1 - - - -
40H GLN* 3.3 6.1 - - - -
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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