Contacts of the helix formed by residues 158 - 167 (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 PHE 158 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76F ASN* 3.3 18.0 + - - +
81F TYR* 3.9 18.7 - - + +
43G LEU* 3.2 26.9 - - + +
79G PHE* 4.2 6.1 - + - -
113G VAL* 3.6 32.8 - - + -
115G LEU* 3.5 41.7 - - + -
119G SER* 4.2 5.4 - - - -
120G TYR 4.8 0.4 - - - -
121G HIS* 3.1 38.6 - + + -
154G ALA 4.3 3.8 - - - -
155G LEU* 3.5 25.8 - - + +
156G ARG 3.0 2.0 + - - -
157G SER* 1.3 77.3 - - - +
159G GLY* 1.3 56.4 + - - +
162G LEU* 3.7 22.4 - - + -
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Residues in contact with GLY 159 (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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73F ASN* 4.5 4.3 - - - -
76F ASN* 3.5 12.3 - - - +
43G LEU* 3.9 9.6 - - - +
156G ARG 3.3 6.6 + - - +
157G SER 3.4 1.2 - - - -
158G PHE* 1.3 80.1 - - - +
160G ASN* 1.3 67.0 + - - -
161G ALA 3.3 2.9 - - - -
162G LEU* 3.3 9.5 + - - +
163G GLY 3.5 0.5 + - - -
164G ASN* 3.2 23.8 + - - +
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Residues in contact with ASN 160 (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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73F ASN* 3.3 34.6 + - - +
43G LEU 3.0 4.2 + - - +
44G ARG* 3.4 28.3 + - - +
45G GLN 3.4 14.4 - - - +
46G ARG* 4.4 9.8 + - - +
47G LEU* 3.1 13.7 - - - +
159G GLY* 1.3 72.4 - - - -
161G ALA* 1.3 63.7 + - - +
163G GLY 2.9 12.0 + - - -
164G ASN* 3.5 7.2 + - - +
165G CYS* 3.5 33.5 + - + +
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Residues in contact with ALA 161 (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* 4.8 7.4 - - + -
42G ALA 3.3 27.1 - - - +
43G LEU* 2.8 26.0 + - + +
45G GLN* 3.0 14.2 + - + +
47G LEU* 3.2 25.0 - - + +
74G LEU* 3.6 16.5 - - + +
78G MET* 4.6 9.4 - - + +
159G GLY 3.3 0.4 - - - -
160G ASN* 1.3 72.4 - - - +
162G LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 162 (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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43G LEU* 4.0 11.6 - - + +
47G LEU* 4.8 0.4 - - - -
66G ILE* 4.8 3.8 - - - +
71G VAL* 4.3 22.9 - - + +
74G LEU* 3.8 18.8 - - + +
75G ALA* 3.7 33.9 - - + +
78G MET* 4.6 4.9 - - + -
79G PHE* 3.4 30.7 - - + -
152G LYS 4.9 0.2 - - - +
155G LEU* 3.5 31.8 - - + +
156G ARG* 3.9 14.7 + - - +
158G PHE* 3.7 18.8 - - + -
159G GLY 3.3 7.6 + - - +
160G ASN 3.1 0.8 - - - -
161G ALA* 1.3 77.4 - - - +
163G GLY* 1.3 56.7 + - - +
164G ASN 3.9 0.9 - - - -
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Residues in contact with GLY 163 (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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47G LEU* 4.2 1.8 - - - -
66G ILE* 3.7 23.3 - - - -
156G ARG* 3.4 16.5 - - - -
160G ASN 2.9 7.1 + - - -
161G ALA 3.4 1.2 + - - -
162G LEU* 1.3 80.6 - - - +
164G ASN* 1.3 66.0 + - - +
165G CYS 3.3 2.5 - - - -
166G ILE* 3.1 26.1 - - - +
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Residues in contact with ASN 164 (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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69F HIS* 3.0 28.3 + - - +
72F ILE* 3.2 37.9 - - - +
73F ASN* 3.0 30.6 + - - -
156G ARG* 3.6 14.7 + - - +
159G GLY 3.2 24.8 + - - +
160G ASN* 3.5 3.8 + - - +
162G LEU 3.9 0.2 - - - -
163G GLY* 1.3 78.7 - - - +
165G CYS* 1.3 62.7 + - - +
166G ILE 3.2 0.9 + - - -
167G LEU* 3.3 21.2 + - - +
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Residues in contact with CYS 165 (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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69F HIS* 5.8 0.7 - - - -
73F ASN* 5.9 0.2 - - - +
46G ARG* 3.9 18.6 - - + +
47G LEU* 3.5 47.6 - - - -
52G ILE* 5.9 0.4 - - - -
160G ASN* 3.5 27.5 + - + +
163G GLY 4.8 0.2 - - - -
164G ASN* 1.3 78.0 - - - +
166G ILE* 1.3 59.8 + - - +
167G LEU 3.0 0.9 - - - -
168G ASP* 2.9 28.3 + - + +
171G TYR* 3.3 31.1 - - + -
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Residues in contact with ILE 166 (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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52G ILE* 3.6 33.7 - - + -
64G CYS* 3.7 40.1 - - + +
65G TYR* 4.4 9.2 - - - +
66G ILE* 4.8 10.5 - - + -
156G ARG* 4.5 11.9 - - - +
163G GLY 3.1 22.8 + - - +
164G ASN 3.1 0.8 - - - -
165G CYS* 1.3 80.2 - - - +
167G LEU* 1.3 75.5 + - + +
168G ASP 3.3 0.8 + - - -
171G TYR* 4.2 11.7 - - + -
172G LEU* 3.9 20.3 - - + +
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Residues in contact with LEU 167 (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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67F GLU* 4.4 2.1 - - - +
68F GLY* 5.9 0.9 - - - -
69F HIS* 3.8 43.4 + - + +
72F ILE* 5.6 4.3 - - + -
156G ARG* 4.4 26.0 - - + +
164G ASN* 3.3 15.4 + - - +
165G CYS 3.0 1.0 - - - -
166G ILE* 1.3 91.4 - - + +
168G ASP* 1.3 60.5 + - - +
169G LYS* 3.5 10.7 + - - +
172G LEU* 5.4 2.5 - - - +
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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