Contacts of the helix formed by residues 215 - 228 (chain G) in PDB entry 2GLJ
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 GLN 215 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119G TYR* 4.8 1.8 - - - +
120G GLU* 3.2 40.3 + - - +
213G GLU* 2.8 13.0 + - + +
214G LYS* 1.3 78.1 - - + +
216G LYS* 1.3 57.3 + - - +
218G LYS* 3.4 46.5 + - + +
219G HIS* 2.9 27.7 + - - +
6H LEU* 5.7 5.4 - - - +
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Residues in contact with LYS 216 (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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120G GLU* 3.2 1.0 + - - -
206G ILE* 3.4 30.2 + - + +
207G PRO* 3.1 41.7 - - + +
210G ASP* 5.1 3.0 - - - +
212G GLU* 3.3 39.0 + - - +
213G GLU 3.3 6.3 - - - +
214G LYS* 2.7 15.2 + - - +
215G GLN* 1.3 69.4 - - - +
217G VAL* 1.3 68.1 + - - +
219G HIS* 3.1 4.4 + - - +
220G ASN 2.8 21.3 + - - -
14J ASP* 5.8 2.6 + - - -
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Residues in contact with VAL 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G GLU* 2.6 16.2 + - - +
123G ASP* 3.2 27.8 - - + +
124G LEU* 3.8 2.5 - - - +
125G ALA* 3.6 12.6 - - + +
202G LEU* 3.0 60.8 - - + +
203G ILE 4.2 0.4 - - - +
204G GLY* 3.6 15.5 - - - +
206G ILE* 3.5 34.1 - - + +
216G LYS* 1.3 73.0 - - - +
218G LYS* 1.3 58.6 + - - +
220G ASN* 3.5 1.7 + - - +
221G ILE 3.2 4.7 + - - -
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Residues in contact with LYS 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G LEU* 3.4 48.1 + - + -
119G TYR* 4.3 6.6 - - - +
120G GLU* 2.7 26.8 + - + -
125G ALA* 4.1 9.4 - - + -
215G GLN* 3.4 45.1 + - + +
217G VAL* 1.3 70.5 - - - +
219G HIS* 1.3 68.3 + - - +
221G ILE* 2.9 25.5 + - - +
222G MET* 3.0 4.2 + - - +
233G GLU* 3.3 32.9 + - - -
6H LEU* 5.2 9.3 - - + +
358H ARG* 6.2 1.2 - - - +
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Residues in contact with HIS 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G PRO* 5.2 2.0 - - + -
208G LEU* 3.6 49.4 + - + +
211G GLY 6.1 1.6 - - - -
212G GLU 5.3 5.4 - - - +
213G GLU* 2.9 30.0 + - + +
215G GLN 2.9 19.8 + - - +
216G LYS* 3.1 8.0 + - - +
218G LYS* 1.3 76.8 - - - +
220G ASN* 1.3 62.1 + - - +
222G MET* 3.4 6.8 + - - +
223G LYS* 3.2 21.9 + - + +
5H LEU* 6.5 0.9 - - - -
6H LEU* 4.2 20.9 - - + +
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Residues in contact with ASN 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G LEU* 3.8 10.9 - - - +
205G SER* 2.6 38.5 + - - +
207G PRO* 3.4 28.8 - - + +
208G LEU* 4.0 9.6 + - - +
216G LYS 2.8 9.8 + - - +
217G VAL 3.6 3.1 - - - +
219G HIS* 1.3 78.0 - - - +
221G ILE* 1.3 58.2 + - - +
223G LYS* 3.2 15.9 + - - +
224G ILE* 2.9 59.1 + - - +
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Residues in contact with ILE 221 (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 LEU* 3.6 32.8 - - + -
201G ILE* 4.0 12.3 - - + -
202G LEU* 3.1 44.9 - - + -
217G VAL 3.2 1.2 + - - -
218G LYS* 2.9 19.3 + - - +
220G ASN* 1.3 74.2 - - - +
222G MET* 1.3 60.2 + - - +
224G ILE* 3.1 19.7 + - + +
225G LEU* 2.6 43.0 + - + +
254J PHE* 3.2 33.4 - - + -
255J ASP 4.2 1.3 - - - +
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Residues in contact with MET 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G LEU* 3.6 26.2 - - + -
218G LYS 3.0 7.0 + - - +
219G HIS* 3.7 11.4 - - - +
221G ILE* 1.3 82.2 - - - +
223G LYS* 1.3 52.5 + - - +
225G LEU* 3.2 21.0 + - + +
226G ASN* 2.7 33.9 + - + +
231G ILE* 4.0 18.8 - - + +
232G SER* 3.6 26.7 - - - +
233G GLU* 3.6 20.2 - - + -
236G PHE* 4.2 6.3 - - + -
5H LEU 3.7 20.9 - - - +
6H LEU* 4.7 8.3 - - + -
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Residues in contact with LYS 223 (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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208G LEU* 3.3 51.8 - - + +
219G HIS* 3.2 6.7 + - + +
220G ASN* 3.2 23.1 + - - +
221G ILE 3.1 0.2 - - - -
222G MET* 1.3 77.7 - - - +
224G ILE* 1.3 71.8 + - + +
226G ASN* 2.9 23.8 + - + +
227G GLU* 3.0 46.1 + - + +
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Residues in contact with ILE 224 (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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220G ASN* 2.9 47.0 + - - +
221G ILE* 3.4 17.0 - - + +
223G LYS* 1.3 90.9 - - + +
225G LEU* 1.3 65.8 + - + +
226G ASN 3.1 0.9 + - - -
227G GLU* 3.5 18.8 + - - +
228G LYS* 3.6 27.0 + - + +
254J PHE* 4.2 16.8 - - + +
255J ASP* 3.8 23.1 - - + -
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Residues in contact with LEU 225 (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 LEU* 5.8 1.1 - - + -
127G LEU* 6.6 0.2 - - + -
151G ILE* 6.0 0.2 - - + -
201G ILE* 5.6 6.3 - - + -
221G ILE* 2.6 28.4 + - + +
222G MET* 3.4 16.4 - - + +
224G ILE* 1.3 75.5 - - + +
226G ASN* 1.3 52.5 + - - +
228G LYS* 2.6 24.0 - - + +
229G TYR* 3.6 21.7 - - + -
231G ILE* 3.8 20.8 - - + +
236G PHE* 3.7 31.2 - - + -
254J PHE* 3.7 50.5 - - + -
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Residues in contact with ASN 226 (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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222G MET* 2.7 13.6 + - + +
223G LYS* 2.9 16.9 + - - +
225G LEU* 1.3 75.3 - - - +
227G GLU* 1.3 72.1 + - - +
228G LYS 2.9 8.2 - - - +
229G TYR 3.6 7.8 - - - +
230G ASP* 3.7 17.5 - - - +
231G ILE 3.3 25.0 - - - +
23R GLU* 4.7 11.4 + - - +
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Residues in contact with GLU 227 (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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223G LYS* 3.0 50.0 + - + +
224G ILE* 3.5 13.0 + - - +
226G ASN* 1.3 82.7 - - - +
228G LYS* 1.3 63.6 + - + +
229G TYR 3.7 5.2 - - - +
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Residues in contact with LYS 228 (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 VAL* 6.0 4.2 - - + +
170G PRO* 5.7 5.7 - - - +
224G ILE* 3.6 22.0 + - + +
225G LEU* 2.6 23.7 - - + +
226G ASN 2.9 3.6 - - - +
227G GLU* 1.3 75.8 - - + +
229G TYR* 1.3 93.9 + - + +
254J PHE* 4.9 21.4 + - + -
256J ARG* 4.6 15.2 - - - +
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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