Contacts of the helix formed by residues 221 - 234 (chain B) in PDB entry 4ND1
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 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B ILE* 3.6 4.9 - - - -
220B ILE* 1.3 77.5 - - - +
222B GLN* 1.3 65.7 + - - +
223B GLU* 3.4 22.2 + - - +
224B GLN* 2.9 51.8 + - - +
225B ILE* 3.0 13.9 + - - +
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Residues in contact with GLN 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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216B ILE* 3.4 18.0 - - + +
221B THR* 1.3 73.2 - - - +
223B GLU* 1.3 58.1 + - + +
225B ILE* 3.3 27.1 + - - +
226B ASP* 2.9 64.1 + - - +
403B GOL 5.0 7.9 + - - -
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Residues in contact with GLU 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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221B THR* 3.1 23.0 + - - +
222B GLN* 1.3 79.5 - - + +
224B GLN* 1.3 58.1 + - + +
226B ASP* 3.2 12.2 + - - +
227B GLU* 2.9 27.9 + - - +
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Residues in contact with GLN 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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179B HIS* 3.5 31.0 + - + +
220B ILE* 3.5 12.2 - - + -
221B THR* 2.9 45.5 + - - +
223B GLU* 1.3 73.4 - - + +
225B ILE* 1.3 64.9 + - - +
227B GLU* 3.4 8.6 + - - +
228B ILE* 3.1 31.0 + - + +
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Residues in contact with ILE 225 (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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172B PHE* 6.4 0.2 - - + -
203B THR* 3.7 31.0 - - + -
212B LEU* 4.1 32.8 - - + -
216B ILE* 3.9 27.4 - - + -
220B ILE* 3.6 20.0 - - + -
221B THR 3.0 12.3 + - - +
222B GLN* 3.5 27.6 - - - +
223B GLU 3.3 0.2 - - - -
224B GLN* 1.3 76.8 - - - +
226B ASP* 1.3 58.3 + - - +
228B ILE* 3.3 8.6 + - + +
229B VAL* 3.0 28.7 + - + +
403B GOL 5.5 0.7 - - - -
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Residues in contact with ASP 226 (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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222B GLN* 2.9 45.9 + - - +
223B GLU* 3.2 12.1 + - - +
225B ILE* 1.3 72.7 - - - +
227B GLU* 1.3 60.9 + - - +
229B VAL* 3.4 8.0 + - - +
230B CYS* 3.0 29.3 + - - +
233B ARG* 5.4 0.7 + - - -
403B GOL 5.1 7.6 - - - -
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Residues in contact with GLU 227 (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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223B GLU 2.9 12.7 + - - +
224B GLN* 3.6 11.7 - - - +
225B ILE 3.3 0.2 - - - -
226B ASP* 1.3 77.2 - - - +
228B ILE* 1.3 64.5 + - - +
230B CYS* 3.3 6.5 + - + +
231B HIS* 2.8 51.9 + - - +
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Residues in contact with ILE 228 (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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172B PHE* 3.7 29.2 - - + -
175B PHE* 3.9 37.6 - - + +
176B ILE* 4.0 17.7 - - + -
179B HIS* 4.2 16.4 - - + +
220B ILE* 4.4 15.3 - - + -
224B GLN* 3.1 19.0 + - + +
225B ILE* 3.5 9.9 - - + +
227B GLU* 1.3 85.1 - - - +
229B VAL* 1.3 62.6 + - - +
231B HIS* 3.6 5.1 - - - +
232B THR* 2.8 30.5 + - - -
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Residues in contact with VAL 229 (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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172B PHE* 4.5 3.6 - - + -
201B PRO* 3.9 22.5 - - + +
203B THR* 3.4 31.9 - - + -
225B ILE* 3.0 23.4 + - + +
226B ASP* 3.7 8.3 - - - +
228B ILE* 1.3 77.4 - - - +
230B CYS* 1.3 62.5 + - - +
232B THR* 3.4 6.9 + - - -
233B ARG* 3.2 39.6 + - - +
403B GOL 3.9 26.2 - - - -
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Residues in contact with CYS 230 (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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226B ASP 3.0 17.4 + - - +
227B GLU* 3.7 6.3 - - - +
229B VAL* 1.3 76.1 - - - +
231B HIS* 1.3 66.0 + - - +
233B ARG* 3.0 44.3 + - - +
234B ILE* 3.2 28.8 + - - +
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Residues in contact with HIS 231 (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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64A LEU* 6.4 0.7 - - + -
175B PHE* 3.2 45.3 - + + +
178B GLN* 5.4 1.6 - - - -
227B GLU* 2.8 40.0 + - - +
228B ILE* 3.6 6.7 - - - +
230B CYS* 1.3 73.7 - - - +
232B THR* 1.3 56.7 + - - +
234B ILE* 3.6 15.3 + - + -
235B ALA* 3.0 27.9 + - - +
238B GLU* 2.8 33.9 + - - -
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Residues in contact with THR 232 (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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168B ASP* 3.6 26.1 - - - +
171B ARG* 4.6 5.0 + - + -
172B PHE* 3.5 33.3 - - + +
175B PHE* 3.7 11.6 - - - -
191B VAL* 3.9 13.5 - - + -
199B MET* 4.0 13.3 - - - +
201B PRO* 4.0 9.6 - - + -
228B ILE 2.8 19.5 + - - -
229B VAL 3.5 8.5 - - - -
230B CYS 3.2 0.2 - - - -
231B HIS* 1.3 76.6 - - - +
233B ARG* 1.3 62.5 + - - +
234B ILE 3.3 0.5 + - - -
235B ALA* 3.3 15.1 + - - +
236B TRP 5.1 0.2 + - - -
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Residues in contact with ARG 233 (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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109B ARG* 4.9 0.9 + - - -
196B GLY 4.6 2.1 - - - +
197B ASP* 3.7 26.6 + - - +
199B MET* 3.7 50.3 - - + +
201B PRO* 4.4 3.4 - - + -
226B ASP 5.4 0.8 + - - -
229B VAL* 3.2 35.2 + - - +
230B CYS* 3.0 34.9 + - - +
232B THR* 1.3 79.9 - - - +
234B ILE* 1.3 66.4 + - + +
235B ALA 3.9 0.2 + - - -
236B TRP* 4.2 11.3 + - - -
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Residues in contact with ILE 234 (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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197B ASP* 5.5 8.3 - - - +
230B CYS* 3.2 30.6 + - - +
231B HIS* 4.0 16.8 - - + +
233B ARG* 1.3 84.5 - - + +
235B ALA* 1.3 66.3 + - - +
236B TRP* 3.2 9.0 - - - -
237B LYS* 3.1 42.2 + - + +
238B GLU* 3.6 11.1 + - + +
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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