Contacts of the helix formed by residues 215 - 228 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A TYR* 4.8 1.8 - - - +
120A GLU* 3.2 38.2 + - - +
213A GLU* 2.8 9.9 + - + +
214A LYS* 1.3 77.4 - - + +
216A LYS* 1.3 59.4 + - - +
218A LYS* 3.4 45.5 + - + +
219A HIS* 2.9 27.9 + - - +
6E LEU* 3.6 19.6 - - + +
358E ARG* 6.3 1.0 - - - +
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 3.2 1.0 + - - -
206A ILE* 3.4 31.0 - - + +
207A PRO* 3.1 42.5 - - + +
210A ASP* 5.1 3.0 - - + +
212A GLU* 3.3 37.6 + - - +
213A GLU 3.3 6.7 - - - +
214A LYS* 2.7 15.4 + - - +
215A GLN* 1.3 68.5 - - - +
217A VAL* 1.3 68.3 + - - +
219A HIS* 3.1 4.5 + - - +
220A ASN* 2.8 21.3 + - - +
10D LYS* 5.6 5.5 - - - +
14D ASP* 6.0 0.8 + - - -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 2.6 15.8 + - - +
123A ASP* 3.2 27.1 - - + +
124A LEU* 3.8 2.5 - - - +
125A ALA* 3.6 12.3 - - + +
202A LEU* 3.0 60.2 - - + +
203A ILE 4.2 0.4 - - - +
204A GLY* 3.6 16.2 - - - +
206A ILE* 3.5 32.8 - - + -
216A LYS* 1.3 72.9 - - - +
218A LYS* 1.3 60.4 + - - +
220A ASN* 3.4 3.1 + - - +
221A ILE 3.2 4.9 + - - -
11D ASN* 5.4 0.2 - - - +
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.4 47.7 + - + -
119A TYR* 4.1 6.9 - - - +
120A GLU* 2.7 26.6 + - + -
125A ALA* 4.1 9.4 - - + -
215A GLN* 3.4 45.3 + - + +
217A VAL* 1.3 70.2 - - - +
219A HIS* 1.3 68.5 + - - +
221A ILE* 2.9 26.0 + - - +
222A MET* 3.0 4.2 + - + +
233A GLU* 3.3 32.2 + - - -
6E LEU* 4.5 11.2 - - + +
358E ARG* 6.0 2.0 - - - +
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Residues in contact with HIS 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A PRO* 5.2 1.8 - - + -
208A LEU* 3.6 48.5 + - + +
211A GLY 6.1 1.8 - - - -
212A GLU 5.3 4.9 - - - -
213A GLU* 2.9 27.4 + - + +
215A GLN 2.9 20.5 + - - +
216A LYS* 3.5 7.0 - - - +
218A LYS* 1.3 75.5 - - - +
220A ASN* 1.3 62.8 + - - +
222A MET* 3.4 3.8 + - - +
223A LYS* 3.1 22.3 + - + +
5E LEU* 5.0 18.3 - - + +
6E LEU* 3.2 25.8 - - + +
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Residues in contact with ASN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 3.8 10.9 - - - +
205A SER* 2.6 38.3 + - - +
207A PRO* 3.4 28.2 - - + +
208A LEU* 4.0 10.2 + - - +
216A LYS 2.8 8.8 + - - +
217A VAL 3.6 3.8 - - - +
219A HIS* 1.3 77.6 - - - +
221A ILE* 1.3 58.1 - - - +
223A LYS* 3.1 16.3 + - - +
224A ILE* 2.9 58.7 + - - +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.6 31.9 - - + -
201A ILE* 4.0 12.3 - - + -
202A LEU* 3.0 46.9 - - + -
217A VAL 3.2 1.6 + - - -
218A LYS* 2.9 18.2 + - - +
220A ASN* 1.3 73.1 - - - +
222A MET* 1.3 60.8 + - - +
224A ILE* 3.1 18.4 + - + +
225A LEU* 2.6 41.9 + - + +
254D PHE* 3.3 34.5 - - + -
255D ASP 4.3 1.6 - - - +
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Residues in contact with MET 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.6 23.1 - - + -
218A LYS* 3.0 7.2 + - + +
219A HIS* 3.7 11.9 - - - +
221A ILE* 1.3 82.1 - - - +
223A LYS* 1.3 53.1 + - - +
225A LEU* 3.2 18.0 + - + -
226A ASN* 2.7 34.6 + - + +
231A ILE* 4.0 19.5 - - + +
232A SER* 3.6 24.9 - - - +
233A GLU* 3.6 23.1 - - + +
236A PHE* 4.3 4.5 - - + -
5E LEU* 4.1 27.6 - - + -
6E LEU* 4.4 6.1 - - + +
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Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.3 52.5 - - + +
219A HIS* 3.1 9.3 + - + +
220A ASN* 3.1 23.1 + - - +
222A MET* 1.3 75.1 - - - +
224A ILE* 1.3 71.5 + - + +
226A ASN* 2.9 25.5 + - + +
227A GLU* 3.0 45.5 + - + +
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A SER* 5.7 0.2 - - - -
220A ASN* 2.9 47.6 + - - +
221A ILE* 3.4 17.5 - - + +
223A LYS* 1.3 89.2 - - + +
225A LEU* 1.3 65.3 + - + +
226A ASN 3.3 0.7 + - - -
227A GLU* 3.4 19.2 + - - +
228A LYS* 3.6 26.7 + - + +
254D PHE* 4.1 19.5 - - + +
255D ASP* 3.7 24.0 - - + -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 5.8 2.5 - - + -
151A ILE* 6.0 0.2 - - + -
201A ILE* 5.6 6.3 - - + -
221A ILE* 2.6 25.3 + - + +
222A MET* 3.4 16.8 - - + +
224A ILE* 1.3 76.1 - - + +
226A ASN* 1.3 52.9 + - - +
228A LYS* 2.6 23.8 - - + +
229A TYR* 3.6 22.2 - - + -
231A ILE* 3.8 22.0 - - + +
236A PHE* 3.7 31.0 - - + -
254D PHE* 3.6 52.9 - - + -
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A MET* 2.7 13.2 + - + +
223A LYS* 2.9 18.1 + - - +
225A LEU* 1.3 75.1 - - - +
227A GLU* 1.3 71.7 + - - +
228A LYS 2.9 8.9 - - - +
229A TYR 3.6 7.3 - - - +
230A ASP* 3.8 17.8 - - - +
231A ILE 3.3 24.4 - - - +
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LYS* 3.0 48.8 + - + +
224A ILE* 3.4 13.4 + - - +
226A ASN* 1.3 83.1 - - - +
228A LYS* 1.3 63.1 + - + +
229A TYR 3.7 5.2 - - - +
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A VAL* 6.0 4.2 - - - +
170A PRO* 5.7 5.3 - - - +
224A ILE* 3.6 21.4 + - + +
225A LEU* 2.6 23.5 - - + +
226A ASN 2.9 3.6 - - - +
227A GLU* 1.3 76.4 - - + +
229A TYR* 1.3 92.5 + - + +
254D PHE* 4.8 22.8 + - + -
256D ARG* 4.7 15.2 - - - +
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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