Contacts of the helix formed by residues 158 - 180 (chain G) in PDB entry 5JGH
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 ASP 158 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G SER 4.5 2.8 - - - +
157G LEU* 1.3 79.0 - - - +
159G GLN* 1.3 66.9 + - - +
160G SER* 4.1 10.5 - - - +
161G ILE* 2.9 29.7 + - + +
162G LYS 2.9 9.9 + - - -
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Residues in contact with GLN 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G LEU 3.7 1.6 + - - -
158G ASP* 1.3 72.4 - - - +
160G SER* 1.3 56.8 + - - +
162G LYS* 3.1 32.2 + - + +
163G ASP* 2.7 62.1 + - - +
166G ILE* 5.2 6.1 - - - +
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Residues in contact with SER 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G ASP* 3.1 8.3 - - - +
159G GLN* 1.3 80.0 - - - +
161G ILE* 1.3 69.4 + - - +
163G ASP* 3.5 11.3 + - - +
164G LYS* 3.4 23.4 + - - +
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Residues in contact with ILE 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G TYR* 6.0 0.7 - - + -
157G LEU* 4.2 18.6 - - + -
158G ASP* 2.9 28.6 + - + +
160G SER* 1.3 79.8 - - - +
162G LYS* 1.3 70.1 + - - +
164G LYS* 3.0 35.3 + - + +
165G TYR* 3.3 27.7 - - + +
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Residues in contact with LYS 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D LYS* 3.4 28.5 - - - +
154G TRP* 3.2 63.4 + - + +
155G GLN* 3.9 4.2 + - - +
157G LEU* 3.4 29.0 + - + +
158G ASP 2.9 5.6 + - - +
159G GLN* 3.2 40.8 - - + +
161G ILE* 1.3 73.6 - - - +
163G ASP* 1.3 65.5 + - - +
165G TYR* 2.8 18.7 + - - +
166G ILE* 3.1 17.6 + - + +
5H T 4.4 6.6 + - - +
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Residues in contact with ASP 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G GLN* 2.7 47.2 + - - +
160G SER* 3.8 9.4 - - - +
161G ILE 3.3 0.2 - - - -
162G LYS* 1.3 71.8 - - - +
164G LYS* 1.3 52.3 + - - +
166G ILE* 3.8 17.8 - - + +
167G GLN* 2.5 39.5 + - + +
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Residues in contact with LYS 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G SER* 3.4 15.6 + - - +
161G ILE* 3.0 33.2 + - + +
162G LYS 2.9 1.0 + - - -
163G ASP* 1.3 76.3 - - - +
165G TYR* 1.3 64.7 + - + +
167G GLN* 3.1 15.2 + - - +
168G GLU* 2.9 37.6 + - - +
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Residues in contact with TYR 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G PRO* 3.7 31.2 - - + +
125G LYS* 4.1 10.4 - - + +
126G TYR* 3.4 54.5 - + + -
129G GLU* 2.9 33.8 + - - +
130G VAL* 5.0 1.6 - - - +
154G TRP* 4.1 12.6 - + + -
157G LEU* 5.0 0.7 - - + -
161G ILE* 3.3 34.6 - - + +
162G LYS 2.8 9.6 + - - +
164G LYS* 1.3 78.4 - - + +
166G ILE* 1.3 57.9 + - - +
168G GLU* 3.4 19.4 + - - +
169G TYR* 3.0 23.0 + - - +
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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
----------------------------------------------------------
122G PRO* 3.8 23.6 - - + -
154G TRP* 4.8 8.1 - - + -
159G GLN* 5.2 5.6 - - - +
162G LYS* 3.1 21.4 + - + +
163G ASP* 3.8 21.1 - - + +
165G TYR* 1.3 73.8 - - - +
167G GLN* 1.3 66.6 + - - +
169G TYR* 4.0 0.2 - - - +
170G LYS* 3.3 33.6 + - + +
5H T 4.8 5.2 - - - +
6H T 3.6 24.0 - - - +
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Residues in contact with GLN 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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163G ASP* 2.5 23.2 + - + +
164G LYS* 3.2 16.6 - - - +
166G ILE* 1.3 71.1 - - - +
168G GLU* 1.3 68.7 + - - +
170G LYS* 3.3 7.7 + - - +
171G LYS* 3.2 46.4 + - + +
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Residues in contact with GLU 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G LYS* 3.1 29.5 - - + +
129G GLU* 4.7 9.8 - - - +
164G LYS* 2.9 28.3 + - - +
165G TYR* 3.4 24.3 + - - +
167G GLN* 1.3 80.3 - - - +
169G TYR* 1.3 50.9 + - - +
171G LYS* 3.2 15.5 + - + +
172G ALA* 2.7 35.5 + - - +
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Residues in contact with TYR 169 (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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119G PRO* 3.7 17.9 - - + -
120G ALA 3.3 17.9 - - - -
121G GLY* 3.8 6.1 - - - -
122G PRO* 3.8 17.0 - - + -
125G LYS* 3.0 16.1 - - - +
165G TYR 3.0 13.8 + - - +
166G ILE 4.0 3.1 - - - +
167G GLN 3.3 0.2 - - - -
168G GLU* 1.3 74.9 - - - +
170G LYS* 1.3 78.7 + - + +
172G ALA* 2.9 2.4 + - - +
173G ILE* 2.5 66.2 + - + +
201G ACT 3.6 20.8 + - + +
6H T 2.9 18.3 + - - -
7H A 2.9 40.0 + - - -
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Residues in contact with LYS 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G ILE* 3.3 23.5 + - + +
167G GLN* 3.3 8.0 + - - +
168G GLU 3.3 0.4 - - - -
169G TYR* 1.3 105.1 - - + +
171G LYS* 1.3 53.1 + - - +
173G ILE* 3.2 12.8 - - + +
174G GLN* 2.6 42.4 + - - +
6H T 3.3 28.8 + - - -
7H A 5.4 2.5 - - - +
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Residues in contact with LYS 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G GLN* 3.2 39.6 + - + +
168G GLU* 3.3 14.6 - - + +
170G LYS* 1.3 76.6 - - - +
172G ALA* 1.3 58.3 + - - +
174G GLN* 2.8 9.1 + - - +
175G GLU* 2.8 48.0 + - - +
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Residues in contact with ALA 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G PRO* 3.6 21.7 - - + +
120G ALA 5.5 0.2 - - - +
125G LYS* 3.9 13.7 - - + +
168G GLU 2.7 20.1 + - - +
169G TYR* 2.9 4.9 + - - +
171G LYS* 1.3 72.8 - - - +
173G ILE* 1.3 57.5 + - - +
175G GLU* 3.2 13.2 - - - +
176G TYR* 3.1 28.2 + - - +
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Residues in contact with ILE 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G LYS* 4.9 13.7 - - + -
119G PRO* 3.6 26.0 - - + +
169G TYR* 2.5 61.7 + - + +
170G LYS* 3.2 29.4 - - + +
172G ALA* 1.3 67.3 - - - +
174G GLN* 1.3 65.6 + - - +
176G TYR* 4.3 11.7 - - + -
177G ASN* 3.0 42.6 + - - +
7H A 3.9 11.7 - - - +
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Residues in contact with GLN 174 (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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170G LYS* 2.6 25.9 + - - +
171G LYS* 2.8 7.3 + - - +
173G ILE* 1.3 77.1 - - - +
175G GLU* 1.3 59.8 + - + +
177G ASN* 3.4 8.2 + - - +
178G ALA* 2.9 33.0 + - + +
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Residues in contact with GLU 175 (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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171G LYS* 2.8 40.5 + - - +
172G ALA* 3.2 15.6 - - - +
174G GLN* 1.3 72.4 - - + +
176G TYR* 1.3 53.6 + - - +
178G ALA* 3.3 6.0 + - - +
179G ARG* 2.7 38.7 + - - +
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Residues in contact with TYR 176 (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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31G ARG* 4.5 5.0 - - - -
116G PRO* 3.6 29.9 + - + +
117G LYS 3.6 19.1 - - - -
118G LYS* 3.6 38.8 + - + +
119G PRO* 3.5 23.6 - - + -
172G ALA 3.1 20.1 + - - +
173G ILE* 4.0 7.6 - - + +
175G GLU* 1.3 77.9 - - - +
177G ASN* 1.3 73.6 + - - +
179G ARG* 4.5 4.3 - - - -
180G TYR* 2.7 57.0 + + + +
182G LEU 4.3 13.1 + - - -
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Residues in contact with ASN 177 (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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118G LYS* 5.7 2.4 + - - -
173G ILE* 3.0 38.1 + - - +
174G GLN* 3.7 9.1 + - - +
176G TYR* 1.3 90.6 - - - +
178G ALA* 1.3 62.3 + - - +
180G TYR 3.2 22.3 - - - +
181G PRO* 3.3 13.8 - - + +
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Residues in contact with ALA 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G GLN* 2.9 19.8 + - + +
175G GLU* 3.7 6.5 - - - +
177G ASN* 1.3 78.1 - - - +
179G ARG* 1.3 63.4 + - - +
181G PRO* 3.7 8.8 - - - +
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Residues in contact with ARG 179 (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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175G GLU 2.7 22.3 + - - +
176G TYR* 4.0 2.7 - - - +
178G ALA* 1.3 74.9 - - - +
180G TYR* 1.3 93.9 + - + +
181G PRO* 3.2 7.8 - - - +
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Residues in contact with TYR 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G PRO* 3.4 42.7 - - + +
176G TYR* 2.7 46.6 + + + +
177G ASN* 3.2 9.6 - - - +
179G ARG* 1.3 99.3 - - + +
181G PRO* 1.3 57.4 - - - +
182G LEU* 2.7 28.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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