Contacts of the helix formed by residues 215 - 228 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119J TYR* 4.8 1.6 - - - +
120J GLU* 3.2 40.5 + - - +
213J GLU* 2.8 12.3 + - + +
214J LYS* 1.3 79.0 - - + +
216J LYS* 1.3 58.5 + - - +
218J LYS* 3.4 44.7 + - + +
219J HIS* 2.9 27.4 + - - +
358K ARG* 6.3 1.2 - - - +
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Residues in contact with LYS 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ASP* 5.8 2.2 + - - -
120J GLU* 3.2 1.4 + - - -
206J ILE* 3.4 28.8 + - + +
207J PRO* 3.1 42.3 - - + +
210J ASP* 5.1 2.8 - - + +
212J GLU* 3.3 38.2 + - - +
213J GLU 3.3 6.5 - - - +
214J LYS* 2.7 15.4 + - - +
215J GLN* 1.3 68.4 - - - +
217J VAL* 1.3 67.2 + - - +
219J HIS* 3.0 5.2 + - - +
220J ASN 2.8 20.8 + - - -
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Residues in contact with VAL 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J GLU* 2.6 16.3 + - - +
123J ASP* 3.1 28.5 - - + +
124J LEU* 3.8 2.5 - - - +
125J ALA 3.5 13.9 - - - +
202J LEU* 3.0 59.6 - - + +
203J ILE 4.2 0.4 - - - +
204J GLY* 3.7 14.8 - - - +
206J ILE* 3.6 33.7 - - + +
216J LYS* 1.3 72.8 - - - +
218J LYS* 1.3 60.3 + - - +
220J ASN* 3.5 1.9 + - - +
221J ILE 3.2 4.3 + - - -
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Residues in contact with LYS 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J LEU* 3.4 49.2 + - + -
119J TYR* 4.1 6.2 - - - +
120J GLU* 2.7 27.0 + - + +
125J ALA* 4.1 8.7 - - + -
215J GLN* 3.4 43.6 + - + +
217J VAL* 1.3 70.8 - - - +
219J HIS* 1.3 69.0 + - - +
221J ILE* 2.8 19.8 + - - +
222J MET* 3.0 11.6 + - + +
233J GLU* 3.3 31.5 + - - -
358K ARG* 6.0 2.6 - - - +
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Residues in contact with HIS 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207J PRO* 5.0 1.8 - - + -
208J LEU* 3.6 49.8 + - + +
211J GLY* 6.1 1.8 - - - -
212J GLU 5.3 5.2 - - - -
213J GLU* 2.9 31.3 + - + +
215J GLN 2.9 18.6 + - - +
216J LYS* 3.0 7.4 + - - +
218J LYS* 1.3 76.0 - - - +
220J ASN* 1.3 62.3 + - - +
222J MET* 3.4 8.0 + - - +
223J LYS* 3.1 22.5 + - + +
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Residues in contact with ASN 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202J LEU* 3.8 10.1 - - - +
205J SER* 2.7 37.5 + - - +
207J PRO* 3.4 28.8 - - + +
208J LEU* 4.0 9.7 + - - +
216J LYS 2.8 9.8 + - - +
217J VAL 3.6 3.1 - - - +
218J LYS 3.0 0.2 + - - -
219J HIS* 1.3 78.6 - - - +
221J ILE* 1.3 57.9 + - - +
223J LYS* 3.2 15.8 + - - +
224J ILE* 2.9 58.8 + - - +
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Residues in contact with ILE 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G PHE* 3.3 33.9 - - + -
255G ASP 4.3 1.8 - - - +
118J LEU* 3.6 32.8 - - + -
201J ILE* 4.0 12.1 - - + -
202J LEU* 3.1 46.0 - - + -
217J VAL 3.2 2.0 + - - -
218J LYS* 2.8 18.6 + - - +
220J ASN* 1.3 73.4 - - - +
222J MET* 1.3 60.6 + - - +
224J ILE* 3.1 18.4 + - + +
225J LEU* 2.7 40.8 + - + +
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Residues in contact with MET 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J LEU* 3.6 25.6 - - + -
218J LYS* 3.0 7.7 + - + +
219J HIS* 3.7 12.1 - - - +
221J ILE* 1.3 82.0 - - - +
223J LYS* 1.3 52.6 + - - +
225J LEU* 3.2 20.3 + - + -
226J ASN* 2.7 34.8 + - + +
231J ILE* 4.0 20.4 - - + +
232J SER* 3.6 25.6 - - - +
233J GLU* 3.7 30.1 - - + +
236J PHE* 4.2 5.8 - - + -
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Residues in contact with LYS 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208J LEU* 3.3 52.7 - - + +
219J HIS* 3.1 7.9 + - + +
220J ASN* 3.3 22.1 + - - +
222J MET* 1.3 80.1 - - - +
224J ILE* 1.3 68.0 + - + +
226J ASN* 2.8 25.8 + - + +
227J GLU* 3.0 44.6 + - + +
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Residues in contact with ILE 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G PHE* 4.2 18.4 - - + +
255G ASP* 3.8 22.9 - - + -
220J ASN* 2.9 47.9 + - - +
221J ILE* 3.4 16.8 - - + +
223J LYS* 1.3 90.2 - - + +
225J LEU* 1.3 64.2 + - + +
226J ASN 3.3 0.7 + - - -
227J GLU* 3.4 19.8 + - - +
228J LYS* 3.6 26.2 + - + +
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Residues in contact with LEU 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G PHE* 3.7 52.9 - - + -
118J LEU* 5.8 1.3 - - + -
151J ILE* 6.0 0.4 - - + -
201J ILE* 5.6 5.8 - - + -
221J ILE* 2.7 25.3 + - + +
222J MET* 3.4 16.6 - - + +
224J ILE* 1.3 75.1 - - + +
226J ASN* 1.3 54.1 + - - +
228J LYS* 2.6 22.8 - - + +
229J TYR* 3.6 22.5 - - + -
231J ILE* 3.8 22.5 - - + +
236J PHE* 3.7 31.4 - - + -
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Residues in contact with ASN 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J MET* 2.7 12.9 + - + +
223J LYS* 2.8 17.8 + - - +
225J LEU* 1.3 75.7 - - - +
227J GLU* 1.3 66.9 + - - +
228J LYS 2.8 12.2 - - - +
229J TYR 3.6 7.3 - - - +
230J ASP* 3.7 17.9 - - - +
231J ILE 3.2 24.9 - - - +
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Residues in contact with GLU 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J LYS* 3.0 48.5 + - + +
224J ILE* 3.4 13.7 + - - +
226J ASN* 1.3 82.7 - - - +
228J LYS* 1.3 64.3 + - + +
229J TYR 3.7 5.0 - - - +
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Residues in contact with LYS 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G PHE* 4.8 22.6 + - + -
256G ARG* 4.6 15.7 - - - +
163J VAL* 5.9 4.0 - - + +
170J PRO* 5.7 5.5 - - - +
224J ILE* 3.6 21.2 + - + +
225J LEU* 2.6 24.0 - - + +
226J ASN 2.8 4.0 - - - +
227J GLU* 1.3 75.5 - - + +
229J TYR* 1.3 93.4 + - + +
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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