Contacts of the helix formed by residues 215 - 228 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.8 12.6 - - + +
119I TYR* 4.8 2.0 - - - +
120I GLU* 3.2 40.3 + - - +
213I GLU* 2.8 11.0 + - + +
214I LYS* 1.3 78.5 - - + +
216I LYS* 1.3 58.1 + - - +
218I LYS* 3.4 45.7 + - + +
219I HIS* 2.9 27.0 + - - +
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Residues in contact with LYS 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I GLU* 3.2 1.0 + - - -
206I ILE* 3.4 30.0 + - + +
207I PRO* 3.2 40.2 - - + +
210I ASP* 5.1 2.8 - - + +
212I GLU* 3.3 38.8 + - - +
213I GLU 3.3 6.3 - - - +
214I LYS* 2.6 15.6 + - - +
215I GLN* 1.3 69.2 - - - +
217I VAL* 1.3 67.0 + - - +
219I HIS* 3.1 5.4 + - - +
220I ASN* 2.8 21.5 + - - +
14L ASP* 5.8 2.8 + - - -
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Residues in contact with VAL 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I GLU* 2.6 15.2 + - - +
123I ASP* 3.2 28.7 - - + +
124I LEU* 3.8 1.8 - - - +
125I ALA* 3.6 14.8 - - + +
202I LEU* 3.0 59.3 - - + +
203I ILE 4.2 0.7 - - - +
204I GLY* 3.6 15.3 - - - +
206I ILE* 3.5 33.9 - - + +
216I LYS* 1.3 73.5 - - - +
218I LYS* 1.3 60.6 - - - +
220I ASN* 3.5 2.1 + - - +
221I ILE 3.2 4.7 + - - -
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Residues in contact with LYS 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 5.1 10.8 - - + +
358A ARG* 6.2 0.8 - - - +
118I LEU* 3.4 46.2 + - + -
119I TYR* 4.3 7.1 - - - +
120I GLU* 2.7 26.5 + - + +
125I ALA* 4.1 8.5 - - + -
215I GLN* 3.4 45.3 + - + +
217I VAL* 1.3 70.3 - - - +
219I HIS* 1.3 68.3 + - - +
221I ILE* 2.9 18.8 + - - +
222I MET* 3.0 11.4 + - - +
233I GLU* 3.2 33.5 + - - -
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Residues in contact with HIS 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.8 17.9 - - + -
6A LEU* 3.8 28.2 - - + +
207I PRO* 5.2 2.0 - - + -
208I LEU* 3.6 49.6 + - + +
211I GLY* 6.1 1.8 - - - -
212I GLU 5.3 4.9 - - - -
213I GLU* 2.9 28.8 + - + +
215I GLN 2.9 19.5 + - - +
216I LYS* 3.4 7.4 - - - +
218I LYS* 1.3 75.7 - - - +
220I ASN* 1.3 62.3 + - - +
222I MET* 3.4 1.9 + - - +
223I LYS* 3.2 22.4 + - + +
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Residues in contact with ASN 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I LEU* 3.7 11.1 - - - +
205I SER* 2.6 37.9 + - - +
207I PRO* 3.5 27.3 - - + +
208I LEU* 4.1 9.3 + - - +
216I LYS 2.8 5.2 + - - +
217I VAL 3.6 6.7 - - - +
218I LYS 3.1 0.2 - - - -
219I HIS* 1.3 77.3 - - - +
221I ILE* 1.3 58.0 + - - +
223I LYS* 3.2 16.6 + - - +
224I ILE* 2.9 57.4 + - - +
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Residues in contact with ILE 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I LEU* 3.7 31.9 - - + -
201I ILE* 4.0 12.6 - - + -
202I LEU* 3.1 45.3 - - + -
217I VAL 3.2 1.6 + - - -
218I LYS* 2.9 19.3 + - - +
220I ASN* 1.3 73.8 - - - +
222I MET* 1.3 58.6 + - - +
224I ILE* 3.1 19.1 + - + +
225I LEU* 2.6 41.0 + - + +
254L PHE* 3.2 35.0 - - + -
255L ASP 4.2 0.4 - - - +
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Residues in contact with MET 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.0 21.1 - - + +
6A LEU* 4.0 20.6 - - + -
118I LEU* 3.7 21.5 - - + -
218I LYS 3.0 7.2 + - - +
219I HIS* 3.7 7.9 - - - +
221I ILE* 1.3 81.6 - - - +
223I LYS* 1.3 53.9 + - - +
225I LEU* 3.2 19.1 + - + -
226I ASN* 2.7 34.1 + - + +
231I ILE* 4.0 19.7 - - + +
232I SER* 3.6 23.6 - - - +
233I GLU* 3.5 21.5 - - + -
236I PHE* 4.2 6.1 - - + -
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Residues in contact with LYS 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I LEU* 3.3 54.3 - - + +
219I HIS* 3.2 7.5 + - + +
220I ASN* 3.3 23.2 + - - +
222I MET* 1.3 78.1 - - - +
224I ILE* 1.3 71.0 + - + +
226I ASN* 2.9 26.0 + - + +
227I GLU* 3.0 46.0 + - + +
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Residues in contact with ILE 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220I ASN* 2.9 47.6 + - - +
221I ILE* 3.4 16.8 - - + +
223I LYS* 1.3 90.2 - - + +
225I LEU* 1.3 64.5 + - + +
226I ASN 3.0 0.6 + - - -
227I GLU* 3.4 19.2 + - - +
228I LYS* 3.6 26.1 + - - +
254L PHE* 4.1 19.1 - - + +
255L ASP* 3.8 23.6 - - + -
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Residues in contact with LEU 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I LEU* 5.8 1.8 - - + -
151I ILE* 6.0 0.7 - - + -
201I ILE* 5.6 5.4 - - + -
221I ILE* 2.6 26.5 + - + +
222I MET* 3.4 16.2 - - + +
224I ILE* 1.3 75.1 - - + +
226I ASN* 1.3 53.7 + - - +
228I LYS* 2.6 23.0 - - + +
229I TYR* 3.6 21.7 - - + -
231I ILE* 3.8 22.2 - - + +
236I PHE* 3.7 30.7 - - + -
254L PHE* 3.6 53.4 - - + -
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Residues in contact with ASN 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222I MET* 2.7 13.5 + - + +
223I LYS* 2.9 18.3 + - - +
225I LEU* 1.3 75.1 - - - +
227I GLU* 1.3 70.0 + - - +
228I LYS 2.8 8.3 - - - +
229I TYR 3.6 7.6 - - - +
230I ASP* 3.7 18.0 - - - +
231I ILE 3.3 25.1 - - - +
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Residues in contact with GLU 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I LYS* 3.0 48.2 + - + +
224I ILE* 3.4 13.4 + - - +
226I ASN* 1.3 83.2 - - - +
228I LYS* 1.3 64.0 + - + +
229I TYR 3.6 4.7 - - - +
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Residues in contact with LYS 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163I VAL* 6.0 4.4 - - - +
170I PRO* 5.7 5.7 - - - +
224I ILE* 3.6 21.0 + - + +
225I LEU* 2.6 23.5 - - + +
226I ASN 2.8 3.8 - - - +
227I GLU* 1.3 74.8 - - + +
229I TYR* 1.3 94.7 + - + +
254L PHE* 4.9 21.8 + - + -
256L ARG* 4.7 14.8 - - - +
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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