Contacts of the helix formed by residues 215 - 228 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B TYR* 4.8 1.8 - - - +
120B GLU* 3.2 39.9 + - + +
213B GLU* 2.8 13.4 + - + +
214B LYS* 1.3 78.9 - - + +
216B LYS* 1.3 57.1 + - - +
218B LYS* 3.4 45.6 + - + +
219B HIS* 2.9 27.9 + - - +
6C LEU* 5.6 5.6 - - + +
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU* 3.2 1.4 + - - -
206B ILE* 3.4 32.0 + - + +
207B PRO* 3.1 41.6 - - + +
210B ASP* 5.1 3.0 - - - +
212B GLU* 3.3 40.1 + - - +
213B GLU 3.3 5.8 - - - +
214B LYS* 2.7 16.5 + - - +
215B GLN* 1.3 68.9 - - - +
217B VAL* 1.3 66.9 + - - +
219B HIS* 3.1 3.7 + - - +
220B ASN 2.8 21.5 + - - -
10K LYS* 5.2 9.7 - - - +
14K ASP* 5.7 3.0 + - - -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 2.6 16.2 + - - +
123B ASP* 3.1 27.6 - - + +
124B LEU* 3.8 2.0 - - - +
125B ALA 3.6 12.1 - - - +
202B LEU* 3.0 61.5 - - + +
203B ILE 4.1 0.7 - - - +
204B GLY* 3.7 15.5 - - - +
206B ILE* 3.6 33.9 - - + +
216B LYS* 1.3 72.2 - - - +
218B LYS* 1.3 59.4 + - - +
220B ASN* 3.5 1.6 + - - +
221B ILE 3.2 5.0 + - - -
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Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.4 50.8 + - + -
119B TYR* 4.3 6.4 - - - +
120B GLU* 2.7 27.0 + - + -
125B ALA* 4.1 9.4 - - + -
215B GLN* 3.4 44.9 + - + +
217B VAL* 1.3 70.1 - - - +
219B HIS* 1.3 68.5 + - - +
221B ILE* 2.9 25.6 + - - +
222B MET* 3.0 4.6 + - - +
233B GLU* 3.3 30.0 + - - -
6C LEU* 4.6 9.2 - - + +
7C LYS 5.5 0.4 + - - -
358C ARG* 6.3 0.6 - - - +
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B PRO* 5.1 2.2 - - + -
208B LEU* 3.6 43.9 + - + +
211B GLY* 6.1 1.8 - - - -
212B GLU 5.3 4.7 - - - +
213B GLU* 2.9 28.9 + - + +
215B GLN 2.9 19.4 + - - +
216B LYS* 3.5 7.2 - - - +
218B LYS* 1.3 76.2 - - - +
220B ASN* 1.3 62.0 + - - +
222B MET* 3.4 4.9 + - - +
223B LYS* 3.1 21.8 + - - +
5C LEU* 3.9 24.1 - - + +
6C LEU* 3.3 24.4 - - + +
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Residues in contact with ASN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LEU* 3.7 11.1 - - - +
205B SER* 2.7 36.5 + - - +
207B PRO* 3.4 28.4 - - + +
208B LEU* 4.0 10.0 + - - +
216B LYS 2.8 9.8 + - - +
217B VAL 3.6 3.4 - - - +
218B LYS 3.0 0.2 + - - -
219B HIS* 1.3 77.8 - - - +
221B ILE* 1.3 57.8 + - - +
223B LYS* 3.1 15.6 + - - +
224B ILE* 2.9 59.0 + - - +
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Residues in contact with ILE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.6 32.1 - - + -
201B ILE* 4.0 12.6 - - + -
202B LEU* 3.1 46.4 - - + -
217B VAL 3.2 1.8 + - - -
218B LYS 2.9 15.0 + - - +
220B ASN* 1.3 76.6 - - - +
222B MET* 1.3 60.1 + - - +
224B ILE* 3.1 18.9 + - + +
225B LEU* 2.6 41.3 + - + +
254K PHE* 3.3 34.1 - - + -
255K ASP 4.2 1.8 - - - +
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Residues in contact with MET 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.7 20.0 - - + -
218B LYS 3.0 5.2 + - - +
219B HIS 3.7 6.5 - - - +
221B ILE* 1.3 82.1 - - - +
223B LYS* 1.3 52.9 + - - +
225B LEU* 3.2 20.2 + - + -
226B ASN* 2.7 34.1 + - - +
231B ILE* 4.0 19.5 - - + +
232B SER* 3.6 25.6 - - - +
233B GLU* 3.6 19.7 - - - -
236B PHE* 4.2 6.1 - - + -
5C LEU* 3.5 20.0 - - + +
6C LEU* 3.4 29.8 - - + -
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.3 53.2 - - + +
219B HIS 3.1 8.4 + - - +
220B ASN* 3.3 19.0 + - - +
222B MET* 1.3 74.9 - - - +
224B ILE* 1.3 74.4 + - + +
226B ASN* 2.9 25.6 + - - +
227B GLU* 3.0 46.0 + - + +
5C LEU* 4.3 8.6 - - + +
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Residues in contact with ILE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B ASN* 2.9 45.9 + - - +
221B ILE* 3.4 16.4 - - + +
223B LYS* 1.3 90.2 - - + +
225B LEU* 1.3 64.5 + - + +
226B ASN 3.0 0.9 + - - -
227B GLU* 3.4 18.8 + - - +
228B LYS* 3.6 26.1 + - + +
254K PHE* 4.1 18.8 - - + +
255K ASP* 3.7 23.8 - - + -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 5.8 1.3 - - + -
151B ILE* 6.0 0.2 - - + -
201B ILE* 5.6 5.6 - - + -
221B ILE* 2.6 25.3 + - + +
222B MET* 3.4 16.8 - - + +
224B ILE* 1.3 75.3 - - + +
226B ASN* 1.3 52.9 + - - +
228B LYS* 2.6 22.6 - - + +
229B TYR* 3.6 22.1 - - + -
231B ILE* 3.8 22.0 - - + +
236B PHE* 3.7 31.6 - - + -
254K PHE* 3.6 54.1 - - + -
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Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B MET 2.7 13.7 + - - +
223B LYS* 2.9 15.7 + - - +
225B LEU* 1.3 75.8 - - - +
227B GLU* 1.3 68.0 + - - +
228B LYS 2.8 11.4 - - - +
229B TYR 3.5 7.6 - - - +
230B ASP* 3.8 17.3 - - - +
231B ILE 3.2 21.1 - - - +
5C LEU* 3.8 20.5 - - + +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LYS* 3.0 49.6 + - + +
224B ILE* 3.4 12.9 + - - +
226B ASN* 1.3 82.3 - - - +
228B LYS* 1.3 63.8 + - + +
229B TYR 3.6 5.4 - - - +
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Residues in contact with LYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL* 6.0 4.4 - - - +
170B PRO* 5.7 4.8 - - - +
224B ILE* 3.6 22.3 + - + +
225B LEU* 2.6 23.1 - - + +
226B ASN 2.8 4.0 - - - +
227B GLU* 1.3 75.9 - - + +
229B TYR* 1.3 96.1 + - + +
254K PHE* 4.8 22.1 + - + -
256K ARG* 4.6 16.8 - - - +
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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