Contacts of the helix formed by residues 215 - 228 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C TYR* 4.7 2.0 - - - +
120C GLU* 3.2 39.8 + - - +
213C GLU* 2.8 12.0 + - + +
214C LYS* 1.3 78.9 - - + +
216C LYS* 1.3 57.5 + - - +
218C LYS* 3.4 44.6 + - + +
219C HIS* 2.9 27.2 + - - +
6D LEU* 4.8 9.9 - - + +
358D ARG* 6.3 1.0 - - - +
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Residues in contact with LYS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C GLU* 3.2 1.2 + - - -
206C ILE* 3.3 30.4 + - + +
207C PRO* 3.1 43.3 - - + +
210C ASP* 5.1 2.5 - - + +
212C GLU* 3.3 38.2 + - - +
213C GLU 3.3 6.1 - - - +
214C LYS* 2.6 15.1 + - - +
215C GLN* 1.3 69.4 - - - +
217C VAL* 1.3 67.5 + - - +
219C HIS* 3.1 4.8 + - - +
220C ASN 2.8 21.1 + - - -
11F ASN* 5.4 1.8 + - - -
14F ASP* 5.7 3.4 + - - -
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Residues in contact with VAL 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLU* 2.6 15.1 + - - +
123C ASP* 3.2 28.7 - - + +
124C LEU* 3.8 2.2 - - - +
125C ALA* 3.6 12.1 - - + +
202C LEU* 3.0 61.8 - - + +
203C ILE 4.2 0.4 - - - +
204C GLY* 3.6 15.5 - - - +
206C ILE* 3.5 34.7 - - + +
216C LYS* 1.3 72.8 - - - +
218C LYS* 1.3 60.5 + - - +
220C ASN* 3.5 1.7 + - - +
221C ILE 3.2 4.7 + - - -
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Residues in contact with LYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 3.5 47.5 + - + -
119C TYR* 4.3 6.7 - - - +
120C GLU* 2.7 26.7 + - + -
125C ALA* 4.1 9.9 - - + -
215C GLN* 3.4 45.8 + - + +
217C VAL* 1.3 70.2 - - - +
219C HIS* 1.3 69.1 + - - +
221C ILE* 2.8 19.1 + - - +
222C MET* 3.0 11.3 + - - +
233C GLU* 3.3 32.7 + - - -
6D LEU* 4.5 11.3 - - + +
358D ARG* 6.0 2.2 - - - +
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Residues in contact with HIS 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C PRO* 5.0 2.5 - - + -
208C LEU* 3.6 49.1 + - + +
211C GLY* 6.1 2.0 - - - -
212C GLU 5.3 4.9 - - - -
213C GLU* 2.9 28.8 + - + +
215C GLN 2.9 17.2 + - - +
216C LYS* 3.1 7.4 + - - +
218C LYS* 1.3 79.0 - - - +
220C ASN* 1.3 61.5 + - - +
222C MET* 3.4 3.1 + - - +
223C LYS* 3.1 22.1 + - + +
5D LEU* 6.1 3.6 - - + -
6D LEU* 3.7 30.3 - - + +
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Residues in contact with ASN 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C LEU* 3.7 11.1 - - - +
205C SER* 2.7 36.5 + - - +
207C PRO* 3.4 28.8 - - + +
208C LEU* 4.0 10.3 + - - +
216C LYS 2.8 9.0 + - - +
217C VAL 3.6 3.6 - - - +
219C HIS* 1.3 77.7 - - - +
221C ILE* 1.3 58.4 + - - +
223C LYS* 3.2 14.9 + - - +
224C ILE* 2.9 58.9 + - - +
255F ASP* 4.0 0.2 + - - -
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Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 3.6 32.5 - - + -
201C ILE* 4.0 8.5 - - + -
202C LEU* 3.1 45.5 - - + -
217C VAL 3.2 1.4 + - - -
218C LYS* 2.8 20.4 + - - +
220C ASN* 1.3 74.6 - - - +
222C MET* 1.3 58.4 + - - +
224C ILE* 3.0 20.1 + - + +
225C LEU* 2.6 42.1 + - + +
254F PHE* 3.2 37.0 - - + -
255F ASP 4.1 1.6 - - - +
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Residues in contact with MET 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 3.6 24.7 - - + -
218C LYS 3.0 5.2 + - - +
219C HIS 3.7 4.5 - - - +
221C ILE* 1.3 81.8 - - - +
223C LYS* 1.3 52.3 + - - +
225C LEU* 3.1 22.0 + - + +
226C ASN* 2.7 34.2 + - + +
231C ILE* 4.0 17.5 - - + +
232C SER* 3.6 25.4 - - - +
233C GLU* 3.6 23.6 - - - +
236C PHE* 4.2 4.9 - - + -
5D LEU* 4.2 9.4 - - - +
6D LEU* 3.6 33.7 - - + -
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Residues in contact with LYS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C LEU* 3.3 52.7 - - + +
219C HIS* 3.1 7.3 + - + +
220C ASN* 3.3 22.3 + - - +
221C ILE 3.1 0.4 - - - -
222C MET* 1.3 77.7 - - - +
224C ILE* 1.3 71.8 + - + +
226C ASN* 2.9 25.1 + - + +
227C GLU* 3.0 44.8 + - + +
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Residues in contact with ILE 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C SER* 5.7 0.2 - - - -
220C ASN* 2.9 48.1 + - - +
221C ILE* 3.0 16.1 + - + +
223C LYS* 1.3 88.9 - - + +
225C LEU* 1.3 65.0 + - + +
226C ASN 3.0 0.9 + - - -
227C GLU* 3.4 20.3 + - - +
228C LYS* 3.5 26.5 + - + +
254F PHE* 4.1 19.1 - - + +
255F ASP* 3.7 24.2 - - + -
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Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 5.8 1.6 - - + -
151C ILE* 6.0 0.4 - - + -
201C ILE* 5.6 5.8 - - + -
221C ILE* 2.6 25.5 + - + +
222C MET* 3.4 17.0 - - + +
224C ILE* 1.3 75.1 - - + +
226C ASN* 1.3 53.0 + - - +
228C LYS* 2.6 23.9 - - + +
229C TYR* 3.6 22.1 - - + -
231C ILE* 3.8 22.7 - - + +
236C PHE* 3.6 31.4 - - + -
254F PHE* 3.6 53.4 - - + -
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Residues in contact with ASN 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C MET* 2.7 12.4 + - + +
223C LYS* 2.9 18.0 + - - +
225C LEU* 1.3 76.5 - - - +
227C GLU* 1.3 69.9 + - - +
228C LYS 2.9 7.8 - - - +
229C TYR 3.6 7.4 - - - +
230C ASP* 3.8 17.7 - - - +
231C ILE 3.3 25.0 - - - +
5D LEU 5.1 8.1 + - - +
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Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C LYS* 3.0 46.9 + - + +
224C ILE* 3.4 13.3 + - - +
226C ASN* 1.3 83.2 - - - +
228C LYS* 1.3 64.0 + - + +
229C TYR 3.6 5.4 + - - +
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Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C VAL* 6.0 4.9 - - - +
170C PRO* 5.7 5.5 - - - +
224C ILE* 3.5 22.0 + - + +
225C LEU* 2.6 24.1 - - + +
226C ASN 2.9 4.0 - - - +
227C GLU* 1.3 76.3 - - + +
229C TYR* 1.3 94.3 + - + +
254F PHE* 4.9 20.0 + - + -
256F ARG* 4.5 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