Contacts of the helix formed by residues 214 - 224 (chain B) in PDB entry 3N1Y
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 ASP 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B LYS 4.4 6.1 - - - +
61B TYR* 3.6 19.9 - - + +
64B ASP 4.6 0.3 - - - +
65B SER* 2.8 43.4 + - - -
66B PRO* 3.7 5.0 - - - +
212B ALA 3.4 1.2 - - - -
213B TRP* 1.3 76.3 - - - +
215B TRP* 1.3 62.2 + - - +
216B GLY* 2.9 17.7 + - - -
217B GLU* 3.0 25.1 + - + +
218B ALA* 2.8 27.4 + - - +
288B TRP* 3.4 11.3 - - - -
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Residues in contact with TRP 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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61B TYR 3.0 18.5 + - - +
62B CYS* 3.6 25.4 + - - -
65B SER* 3.6 16.3 + - - -
67B LEU* 3.7 27.4 + - + -
72B TRP* 3.6 38.4 - + - +
142B ILE* 5.2 6.2 - - + +
145B ILE* 3.5 37.2 - - + +
146B ALA* 4.3 7.0 - - + +
147B PRO* 3.5 37.3 - - + +
151B ILE* 4.3 10.8 - - + -
213B TRP 3.2 2.6 + - - -
214B ASP* 1.3 71.8 + - - +
216B GLY* 1.3 69.9 + - - +
218B ALA* 3.6 3.6 - - - +
219B PHE* 3.0 27.1 + - + +
271B LEU* 4.0 22.2 - - + -
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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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65B SER* 4.1 2.5 - - - -
67B LEU* 4.0 12.7 - - - +
214B ASP* 2.9 9.6 + - - -
215B TRP* 1.3 95.0 - - - +
217B GLU* 1.3 60.8 + - - +
219B PHE* 3.6 5.1 + - - +
220B THR* 2.9 27.4 + - - -
288B TRP* 3.3 17.9 - - - -
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Residues in contact with GLU 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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212B ALA* 4.1 19.7 - - + +
214B ASP* 3.0 22.7 + - + +
216B GLY* 1.3 76.1 - - - +
218B ALA* 1.3 55.0 + - - +
220B THR* 3.1 1.2 + - - -
221B ALA* 2.7 37.8 + - - +
288B TRP* 3.6 44.7 + - + -
291B LYS* 2.8 32.8 + - - +
292B TRP* 3.1 22.3 + - - +
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Residues in contact with ALA 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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138B GLY 5.6 0.2 - - - +
141B TYR* 4.2 15.3 - - + -
142B ILE* 3.9 18.6 - - + -
209B ALA 5.5 1.6 - - - +
212B ALA* 3.5 22.3 + - - +
214B ASP 2.8 19.4 + - - +
215B TRP* 3.6 8.1 - - - +
217B GLU* 1.3 71.3 - - - +
219B PHE* 1.3 58.4 + - - +
221B ALA* 4.6 2.0 - - - +
222B ILE* 2.8 41.5 + - + +
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Residues in contact with PHE 219 (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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67B LEU* 5.2 6.1 - - + -
142B ILE* 3.7 16.7 - - + +
215B TRP* 3.0 23.8 + + + +
216B GLY* 3.7 6.7 - - - +
218B ALA* 1.3 77.1 - - - +
220B THR* 1.3 64.3 + - - +
223B ASN* 2.8 45.2 + - + +
224B LEU* 3.3 23.3 + - + -
267B TRP* 3.8 27.4 - + - -
268B SER* 3.5 47.6 - - - -
271B LEU* 3.9 23.6 - - + -
272B VAL* 3.9 11.0 - - + -
285B LEU* 4.8 6.3 - - + -
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Residues in contact with THR 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 2.9 14.5 + - - -
217B GLU 3.1 7.0 + - - -
219B PHE* 1.3 76.9 - - - +
221B ALA* 1.3 62.9 + - - +
224B LEU* 3.1 21.3 + - + +
225B VAL* 2.9 31.3 + - + +
285B LEU* 3.4 22.8 - - + +
288B TRP* 3.6 27.6 - - + +
289B VAL* 3.7 31.2 - - + +
292B TRP* 5.3 0.2 - - + -
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Residues in contact with ALA 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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209B ALA* 4.0 16.6 - - + +
212B ALA* 4.8 2.0 - - + -
217B GLU 2.7 21.2 + - - +
218B ALA* 4.1 4.0 - - - +
220B THR* 1.3 74.0 - - - +
222B ILE* 1.3 54.7 + - + +
225B VAL* 3.9 3.1 - - - +
226B THR* 2.5 40.4 + - - -
292B TRP* 3.8 42.8 - - + +
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Residues in contact with ILE 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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135B LEU* 4.7 9.9 - - + +
138B GLY* 4.3 33.0 - - - +
139B SER 4.3 3.1 - - - +
142B ILE* 3.9 10.1 - - + -
158B GLU* 4.6 1.8 - - - +
162B HIS* 5.5 0.2 - - - +
206B ILE* 3.8 20.2 - - + -
209B ALA* 3.8 33.4 - - + +
210B LEU* 4.8 1.1 - - + -
218B ALA* 2.8 29.7 + - + +
221B ALA* 1.3 74.6 - - + +
223B ASN* 1.3 69.9 + - - +
226B THR* 3.7 2.5 - - - +
227B LYS* 3.0 44.7 + - + +
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Residues in contact with ASN 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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142B ILE* 4.2 5.7 - - - +
158B GLU* 2.7 41.6 + - - +
219B PHE* 2.8 32.7 + - + +
222B ILE* 1.3 82.6 - - - +
224B LEU* 1.3 60.2 + - - +
225B VAL 3.6 0.2 - - - -
227B LYS* 3.4 15.2 - - - +
228B PRO* 3.2 20.6 - - - +
264B HIS 4.2 1.6 + - - -
265B ARG* 5.7 3.1 - - - +
267B TRP* 3.3 17.2 - - - +
268B SER* 2.7 30.2 + - - +
324B VAL* 5.8 0.3 - - - +
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Residues in contact with LEU 224 (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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219B PHE* 3.3 37.0 + - + +
220B THR* 3.1 38.3 + - + +
223B ASN* 1.3 78.0 - - - +
225B VAL* 1.3 61.7 + - + +
228B PRO* 3.4 10.8 - - - +
268B SER* 4.1 7.0 - - - -
272B VAL* 3.9 11.2 - - + -
285B LEU* 4.3 8.7 - - + -
289B VAL* 5.0 5.2 - - + -
324B VAL* 6.0 0.7 - - - -
325B ARG* 2.8 37.0 + - + +
328B MET* 3.7 35.7 - - + -
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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