Contacts of the helix formed by residues 215 - 228 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119W TYR* 4.8 2.2 - - - +
120W GLU* 3.2 40.1 + - - +
213W GLU* 2.8 11.5 + - + +
214W LYS* 1.3 78.4 - - + +
216W LYS* 1.3 57.6 + - - +
218W LYS* 3.4 45.4 + - + +
219W HIS* 2.9 27.5 + - - +
6X LEU* 4.6 12.1 - - + +
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Residues in contact with LYS 216 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ASN* 4.9 6.9 - - - +
14N ASP* 5.6 2.2 + - - -
120W GLU* 3.2 1.4 + - - -
206W ILE* 3.4 30.6 + - + +
207W PRO* 3.1 43.6 - - + +
210W ASP* 5.1 2.3 - - - +
212W GLU* 3.3 37.9 + - - +
213W GLU 3.3 6.5 - - - +
214W LYS* 2.7 14.5 + - - +
215W GLN* 1.3 69.8 - - - +
217W VAL* 1.3 69.0 + - - +
219W HIS* 3.2 4.0 + - - +
220W ASN 2.8 20.8 + - - -
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Residues in contact with VAL 217 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120W GLU* 2.6 14.3 + - - +
123W ASP* 3.1 29.6 - - + +
124W LEU* 3.8 2.2 - - - +
125W ALA 3.5 14.1 - - - +
202W LEU* 3.0 59.6 - - + +
203W ILE 4.2 0.4 - - - +
204W GLY* 3.7 14.8 - - - +
206W ILE* 3.6 33.4 - - + +
216W LYS* 1.3 72.8 - - - +
218W LYS* 1.3 59.2 + - - +
220W ASN* 3.4 1.9 + - - +
221W ILE 3.2 4.7 + - - -
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Residues in contact with LYS 218 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118W LEU* 3.4 47.8 + - + -
119W TYR* 4.3 6.6 - - - +
120W GLU* 2.7 26.8 + - + +
125W ALA* 4.1 10.5 - - + -
215W GLN* 3.4 44.5 + - + +
217W VAL* 1.3 70.8 - - - +
219W HIS* 1.3 69.0 + - - +
221W ILE* 2.8 19.0 + - - +
222W MET* 3.0 10.9 + - - +
233W GLU* 3.3 22.5 + - - -
6X LEU* 3.7 22.3 - - + +
358X ARG* 6.0 2.0 - - - +
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Residues in contact with HIS 219 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207W PRO* 5.2 1.8 - - + -
208W LEU* 3.6 50.1 + - + +
211W GLY* 6.1 1.6 - - - -
212W GLU 5.3 4.9 - - - -
213W GLU* 2.9 30.3 + - + +
215W GLN 2.9 20.1 + - - +
216W LYS* 3.5 7.9 - - - +
218W LYS* 1.3 75.3 - - - +
220W ASN* 1.3 61.8 + - - +
222W MET* 3.4 3.2 + - - +
223W LYS* 3.1 21.9 + - + +
5X LEU* 4.8 18.7 + - - -
6X LEU* 4.1 22.0 - - + +
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Residues in contact with ASN 220 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202W LEU* 3.7 10.9 - - - +
205W SER* 2.7 38.2 + - - +
207W PRO* 3.4 20.8 - - + +
208W LEU* 4.1 10.0 + - - +
216W LYS 2.8 16.0 + - - +
217W VAL 3.5 3.1 - - - +
219W HIS* 1.3 77.2 - - - +
221W ILE* 1.3 58.6 + - - +
223W LYS* 3.2 15.9 + - - +
224W ILE* 2.9 59.3 + - - +
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Residues in contact with ILE 221 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N PHE* 3.3 33.0 - - + -
255N ASP 4.2 2.2 - - - +
118W LEU* 3.6 32.8 - - + -
201W ILE* 4.0 12.3 - - + -
202W LEU* 3.1 46.0 - - + -
217W VAL 3.2 2.0 + - - -
218W LYS* 2.8 18.2 + - - +
220W ASN* 1.3 72.5 - - - +
222W MET* 1.3 60.6 + - - +
224W ILE* 3.1 18.6 + - + +
225W LEU* 2.6 41.6 + - + +
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Residues in contact with MET 222 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118W LEU* 3.7 19.7 - - + -
218W LYS 3.0 5.9 + - - +
219W HIS* 3.7 9.2 - - - +
221W ILE* 1.3 82.4 - - - +
223W LYS* 1.3 53.2 + - - +
225W LEU* 3.2 20.4 + - + -
226W ASN* 2.7 34.3 + - + +
231W ILE* 4.0 19.5 - - + +
232W SER* 3.6 24.0 - - - +
233W GLU* 3.6 22.0 - - - +
236W PHE* 4.3 5.6 - - + -
5X LEU 2.9 33.4 - - - +
6X LEU* 4.2 10.8 - - + -
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Residues in contact with LYS 223 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208W LEU* 3.3 54.8 - - + +
219W HIS* 3.1 7.5 + - + +
220W ASN* 3.3 21.6 + - - +
222W MET* 1.3 79.7 - - - +
224W ILE* 1.3 68.7 + - + +
226W ASN* 2.9 24.8 + - + +
227W GLU* 3.0 46.2 + - + +
5X LEU 5.8 3.3 - - - +
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Residues in contact with ILE 224 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N PHE* 4.2 19.5 - - + +
255N ASP* 3.7 24.0 - - + -
220W ASN* 2.9 47.5 + - - +
221W ILE* 3.1 15.5 + - + +
223W LYS* 1.3 90.3 - - + +
225W LEU* 1.3 64.9 + - + +
226W ASN 3.3 0.5 + - - -
227W GLU* 3.5 19.1 + - - +
228W LYS* 3.6 26.2 + - + +
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Residues in contact with LEU 225 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N PHE* 3.6 53.8 - - + -
118W LEU* 5.9 1.3 - - + -
127W LEU* 6.6 0.2 - - + -
201W ILE* 5.6 5.8 - - + -
221W ILE* 2.6 24.5 + - + +
222W MET* 3.4 16.4 - - + +
224W ILE* 1.3 76.8 - - + +
226W ASN* 1.3 52.6 + - - +
228W LYS* 2.6 23.6 - - + +
229W TYR* 3.6 21.8 - - + -
231W ILE* 3.8 21.8 - - + +
236W PHE* 3.7 31.4 - - + -
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Residues in contact with ASN 226 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222W MET* 2.7 14.4 + - + +
223W LYS* 2.9 18.3 + - - +
225W LEU* 1.3 75.5 - - - +
227W GLU* 1.3 67.0 + - - +
228W LYS 2.8 12.1 - - - +
229W TYR 3.6 7.6 - - - +
230W ASP* 3.8 17.5 - - - +
231W ILE 3.2 24.4 - - - +
5X LEU* 5.5 9.7 - - + +
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Residues in contact with GLU 227 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223W LYS* 3.0 49.0 + - + +
224W ILE* 3.5 12.8 + - - +
226W ASN* 1.3 83.5 - - - +
228W LYS* 1.3 63.8 + - + +
229W TYR 3.7 4.7 + - - +
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Residues in contact with LYS 228 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254N PHE* 4.8 20.8 + - + -
256N ARG* 4.6 16.6 - - - +
163W VAL* 6.0 4.6 - - - +
170W PRO* 5.7 4.9 - - - +
224W ILE* 3.6 21.8 + - + +
225W LEU* 2.6 23.3 - - + +
226W ASN 2.8 8.5 - - - +
227W GLU* 1.3 75.6 - - + +
229W TYR* 1.3 90.7 + - + +
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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