Contacts of the helix formed by residues 214 - 223 (chain B) in PDB entry 4GDK
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 THR 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B LEU 4.1 7.6 - - - +
213B HIS* 1.3 79.6 - - - +
215B LEU* 1.3 64.6 + - - +
216B GLY* 3.2 5.0 + - - -
217B ASP* 3.1 31.5 + - - +
218B LEU* 3.1 21.3 + - - +
247B LEU 3.3 12.3 + - - -
248B GLU* 3.6 20.4 - - + +
249B THR 3.3 9.4 - - - +
250B PRO* 4.9 2.0 - - + -
251B LEU* 4.0 6.5 - - - +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B THR* 1.3 72.2 - - - +
216B GLY* 1.3 57.2 + - - +
218B LEU* 3.4 13.2 + - + +
219B LEU* 3.1 37.2 + - + +
238B VAL* 4.2 18.6 - - + -
240B ILE* 4.3 4.9 - - + -
245B PRO* 4.2 15.3 - - + +
246B MET 4.1 14.1 - - - +
247B LEU* 3.6 21.3 - - + +
249B THR* 2.9 15.6 + - - +
251B LEU* 4.3 6.8 - - + +
254B LEU* 4.0 28.0 - - + -
267B ILE* 4.1 26.0 - - + -
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B THR* 3.1 4.0 + - - -
215B LEU* 1.3 75.1 - - - +
217B ASP* 1.3 53.9 + - - +
219B LEU* 3.3 4.0 + - - +
220B LYS* 2.7 36.7 + - - +
227B ILE* 4.0 4.5 - - - +
247B LEU* 2.8 37.6 + - - +
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Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B PHE* 3.9 13.1 - - + -
212B LEU 4.6 0.9 - - - +
213B HIS* 3.6 19.3 - - + -
214B THR* 3.1 42.9 + - - +
216B GLY* 1.3 73.9 - - - +
218B LEU* 1.3 63.3 + - - +
220B LYS* 3.4 7.9 + - - +
221B GLU* 3.0 24.9 + - - +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B PHE* 3.7 46.2 - - + -
189B ILE* 5.0 0.4 - - + -
203B PHE* 3.6 26.8 - - + -
214B THR 3.1 9.9 + - - +
215B LEU* 3.5 12.1 - - + +
217B ASP* 1.3 78.9 - - - +
219B LEU* 1.3 61.5 + - + +
221B GLU* 3.2 2.3 + - - +
222B VAL* 2.9 41.6 + - + +
251B LEU* 3.8 32.5 - - + -
267B ILE* 4.0 25.4 - - + -
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE* 3.6 29.4 - - + -
215B LEU* 3.1 29.2 + - + +
216B GLY 3.8 1.1 - - - +
218B LEU* 1.3 77.2 - - + +
220B LYS* 1.3 61.6 + - - +
222B VAL* 4.7 0.2 - - - -
223B CYS* 2.8 47.0 + - + +
226B ALA* 5.4 2.2 - - + -
227B ILE* 3.7 22.9 - - + -
238B VAL* 3.8 37.5 - - + -
247B LEU* 4.0 13.5 - - + -
267B ILE* 5.1 4.0 - - + -
269B ILE* 4.6 14.4 - - + -
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B GLY 2.7 21.6 + - - +
217B ASP* 3.6 9.2 - - - +
218B LEU 3.3 0.2 - - - -
219B LEU* 1.3 74.0 - - - +
221B GLU* 1.3 60.5 + - - +
224B PRO* 3.7 25.3 - - + +
227B ILE* 3.9 15.8 - - + +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LYS* 5.1 4.0 + - - +
202B LEU 5.8 1.3 - - - +
203B PHE* 3.5 31.6 - - + -
217B ASP 3.0 17.6 + - - +
218B LEU 3.6 0.7 - - - +
219B LEU 3.1 0.2 - - - -
220B LYS* 1.3 79.9 - - - +
222B VAL* 1.3 67.0 + - + +
224B PRO* 4.7 3.9 - - - +
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B PHE* 4.1 18.8 - - + -
189B ILE* 3.6 28.0 - - + -
199B ILE* 3.7 22.1 - - + +
201B LYS* 4.2 37.9 + - + +
202B LEU 5.3 1.6 - - - +
203B PHE* 4.5 4.7 - - + -
218B LEU* 2.9 30.7 + - + +
221B GLU* 1.3 93.3 - - + +
223B CYS* 1.3 62.6 + - - +
224B PRO* 3.9 3.9 - - - +
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Residues in contact with CYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ILE* 4.1 28.0 - - + -
191B GLN* 4.0 17.0 - - - -
199B ILE* 4.3 14.1 - - + -
219B LEU* 2.8 20.2 + - + +
222B VAL* 1.3 83.7 - - - +
224B PRO* 1.3 68.1 - - - +
225B SER* 3.1 15.9 + - - -
226B ALA* 3.2 28.0 + - - +
227B ILE* 4.4 1.0 + - - +
269B ILE* 4.7 1.3 - - - -
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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