Contacts of the helix formed by residues 215 - 228 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F LEU* 5.0 6.7 - - + +
358F ARG* 6.2 1.0 - - - +
119H TYR* 4.7 2.4 - - - +
120H GLU* 3.2 40.1 + - + +
213H GLU* 2.8 12.9 + - + +
214H LYS* 1.3 80.0 - - + +
216H LYS* 1.3 58.5 + - - +
218H LYS* 3.4 44.1 + - + +
219H HIS* 2.9 27.9 + - - +
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Residues in contact with LYS 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ASP* 5.7 3.2 + - - -
120H GLU* 3.2 1.2 + - - -
206H ILE* 3.3 31.1 + - + +
207H PRO* 3.2 41.2 - - + +
210H ASP* 5.1 3.0 - - - +
212H GLU* 3.3 38.3 + - - +
213H GLU 3.3 6.3 - - - +
214H LYS* 2.7 14.5 + - - +
215H GLN* 1.3 69.2 - - - +
217H VAL* 1.3 68.5 + - - +
219H HIS* 3.0 5.0 + - - +
220H ASN* 2.8 21.3 + - - +
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Residues in contact with VAL 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H GLU* 2.6 15.8 + - - +
123H ASP* 3.1 28.7 - - + +
124H LEU* 3.8 1.8 - - - +
125H ALA 3.6 12.3 - - - +
202H LEU* 3.0 60.9 - - + +
203H ILE 4.1 0.9 - - - +
204H GLY* 3.7 15.7 - - - +
206H ILE* 3.6 34.1 - - + +
216H LYS* 1.3 73.0 - - - +
218H LYS* 1.3 59.7 + - - +
220H ASN* 3.5 2.3 + - - +
221H ILE 3.2 4.2 + - - -
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Residues in contact with LYS 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 4.4 11.1 - - + +
358F ARG* 6.0 2.6 - - - +
118H LEU* 3.4 48.1 + - + -
119H TYR* 4.2 6.5 - - - +
120H GLU* 2.7 27.6 + - + -
125H ALA* 4.1 9.2 - - + -
215H GLN* 3.4 44.9 + - + +
217H VAL* 1.3 70.5 - - - +
219H HIS* 1.3 68.3 + - - +
221H ILE* 2.9 25.5 + - - +
222H MET* 3.0 4.9 + - - +
233H GLU* 3.2 32.5 + - - -
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Residues in contact with HIS 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LEU* 5.6 6.2 - - + +
6F LEU* 3.3 36.1 - - + +
207H PRO* 5.2 2.5 - - + -
208H LEU* 3.6 48.6 + - + +
211H GLY* 6.1 1.8 - - - -
212H GLU 5.3 4.9 - - - -
213H GLU* 2.9 28.0 + - - +
215H GLN 2.9 19.5 + - - +
216H LYS* 3.4 7.4 - - - +
218H LYS* 1.3 76.7 - - - +
220H ASN* 1.3 62.5 + - - +
222H MET* 3.5 2.8 + - - +
223H LYS* 3.2 21.9 + - + +
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Residues in contact with ASN 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E ASP* 4.1 0.2 + - - -
202H LEU* 3.7 10.9 - - - +
205H SER* 2.7 37.7 + - - +
207H PRO* 3.4 28.8 - - + +
208H LEU* 4.0 10.2 + - - +
216H LYS 2.8 9.5 + - - +
217H VAL 3.6 6.5 - - - +
219H HIS* 1.3 72.7 - - - +
221H ILE* 1.3 58.3 + - - +
223H LYS* 3.1 16.8 + - - +
224H ILE* 2.9 58.8 + - - +
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Residues in contact with ILE 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E PHE* 3.2 34.5 - - + -
255E ASP 4.2 1.6 - - - +
118H LEU* 3.6 32.3 - - + -
201H ILE* 4.0 11.7 - - + -
202H LEU* 3.1 45.8 - - + -
217H VAL 3.2 1.8 + - - -
218H LYS* 2.9 18.9 + - - +
220H ASN* 1.3 73.5 - - - +
222H MET* 1.3 60.7 + - - +
224H ILE* 3.1 18.7 + - + +
225H LEU* 2.6 40.9 + - + +
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Residues in contact with MET 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LEU* 3.8 26.5 - - + +
6F LEU* 4.5 9.9 - - + -
118H LEU* 3.6 24.0 - - + -
218H LYS 3.0 7.0 + - - +
219H HIS* 3.8 11.2 - - - +
221H ILE* 1.3 81.5 - - - +
223H LYS* 1.3 53.2 - - - +
225H LEU* 3.3 19.3 + - + -
226H ASN* 2.8 33.1 + - - +
231H ILE* 4.0 18.2 - - + +
232H SER* 3.6 25.1 - - - +
233H GLU* 3.6 23.8 - - + -
236H PHE* 4.2 5.6 - - + -
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Residues in contact with LYS 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LEU* 4.0 7.3 - - + +
208H LEU* 3.3 53.6 - - + +
219H HIS* 3.2 6.5 + - + +
220H ASN* 3.1 22.8 + - - +
222H MET* 1.3 77.1 - - - +
224H ILE* 1.3 71.8 + - + +
226H ASN* 2.9 24.9 + - + +
227H GLU* 3.0 46.2 + - + +
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Residues in contact with ILE 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E PHE* 4.1 19.3 - - + +
255E ASP* 3.7 23.6 - - + -
205H SER* 5.7 0.2 - - - -
220H ASN* 2.9 48.1 + - - +
221H ILE* 3.4 16.4 - - + +
223H LYS* 1.3 89.3 - - + +
225H LEU* 1.3 64.1 + - + +
226H ASN 3.2 0.5 + - - -
227H GLU* 3.4 19.5 + - - +
228H LYS* 3.6 26.7 + - + +
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Residues in contact with LEU 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E PHE* 3.6 54.3 - - + -
118H LEU* 5.8 1.6 - - + -
201H ILE* 5.6 4.5 - - + -
221H ILE* 2.6 26.1 + - + +
222H MET* 3.5 15.9 - - + +
224H ILE* 1.3 74.8 - - + +
226H ASN* 1.3 53.3 + - - +
228H LYS* 2.6 24.1 - - + +
229H TYR* 3.6 21.5 - - + -
231H ILE* 3.8 22.4 - - + +
236H PHE* 3.7 31.0 - - + -
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Residues in contact with ASN 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F LEU* 3.6 25.8 - - + +
222H MET 2.8 13.0 + - - +
223H LYS* 2.9 13.8 + - - +
225H LEU* 1.3 76.1 - - - +
227H GLU* 1.3 69.5 + - - +
228H LYS 2.9 8.6 - - - +
229H TYR 3.6 7.6 - - - +
230H ASP* 3.8 17.5 - - - +
231H ILE 3.3 21.8 - - - +
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Residues in contact with GLU 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H LYS* 3.0 50.0 + - + +
224H ILE* 3.4 13.3 + - - +
226H ASN* 1.3 82.5 - - - +
228H LYS* 1.3 63.1 + - + +
229H TYR 3.7 5.2 + - - +
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Residues in contact with LYS 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E PHE* 4.8 22.2 + - + -
256E ARG* 4.6 16.3 - - - +
163H VAL* 5.9 4.2 - - - +
170H PRO* 5.7 5.1 - - - +
224H ILE* 3.6 21.8 + - + +
225H LEU* 2.6 23.1 - - + +
226H ASN 2.9 3.6 - - - +
227H GLU* 1.3 75.5 - - + +
229H TYR* 1.3 93.5 + - + +
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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