Contacts of the helix formed by residues 213 - 225 (chain B) in PDB entry 5HNK
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 GLY 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B MET* 3.8 18.4 - - - +
212B ILE* 1.3 74.6 - - - +
214B ALA* 1.3 59.8 + - - -
217B GLY* 2.9 27.2 + - - -
5X G 2.8 36.6 + - - -
6X C 4.7 1.3 - - - -
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Residues in contact with ALA 214 (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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185B ASN* 5.4 14.2 - - + +
195B LEU* 4.3 10.6 - - + +
199B MET* 3.7 24.1 - - + +
213B GLY* 1.3 71.5 - - - -
215B LYS* 1.3 63.0 + - + +
218B TYR* 3.1 31.4 + - - +
5X G 3.4 5.3 + - - +
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Residues in contact with LYS 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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173A ARG* 4.5 9.5 + - - +
182A GLU* 2.7 33.5 + - + +
183A HIS* 3.0 22.4 + - - +
184A HIS* 4.2 0.8 - - - +
185A ASN* 4.6 12.3 + - - +
185B ASN* 6.1 0.6 - - - -
214B ALA* 1.3 79.9 - - + +
216B ARG* 1.3 67.1 + - + +
218B TYR* 4.0 4.1 - - - +
219B ASN* 3.1 23.3 + - - +
4X A 3.7 47.3 - - + +
5X G 3.3 16.2 + - - +
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Residues in contact with ARG 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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211B GLY* 2.8 39.3 + - - -
212B ILE* 4.3 7.4 - - + -
215B LYS* 1.3 78.2 - - + +
217B GLY* 1.3 57.1 + - - +
219B ASN* 3.3 7.1 + - - +
220B ILE* 2.9 37.7 + - + +
242B TYR* 3.5 52.3 - - + +
3X A 4.9 11.3 + - - -
4X A 3.6 28.5 + - - +
5X G 3.0 31.4 + - - +
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Residues in contact with GLY 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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195B LEU* 3.7 15.5 - - - -
198B ILE* 4.6 4.6 - - - +
212B ILE* 3.6 15.3 - - - +
213B GLY 2.9 20.9 + - - -
216B ARG* 1.3 78.4 - - - +
218B TYR* 1.3 56.6 + - - +
220B ILE* 3.5 4.5 + - - +
221B ILE* 3.0 33.4 + - - +
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Residues in contact with TYR 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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182A GLU* 3.7 25.6 - - + -
181B TYR* 3.4 26.5 + + - -
185B ASN* 3.2 27.6 - - + +
186B VAL* 4.3 6.3 - - + -
187B ASP* 3.3 18.7 + - - -
191B GLN* 3.6 26.0 - - - -
195B LEU* 3.8 9.0 - - + +
214B ALA 3.1 19.7 + - - +
215B LYS* 4.0 2.9 - - - +
217B GLY* 1.3 72.0 - - - +
219B ASN* 1.3 62.5 + - - +
221B ILE* 3.8 6.7 - - + -
222B ARG* 2.9 74.3 + - + +
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Residues in contact with ASN 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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173A ARG* 3.4 46.9 + - - +
182A GLU* 5.1 1.3 - - - +
215B LYS 3.1 19.0 + - - +
216B ARG* 3.3 8.2 + - - +
218B TYR* 1.3 80.7 - - - +
220B ILE* 1.3 64.6 + - - +
222B ARG* 4.0 12.7 + - - +
223B GLU* 3.2 32.9 + - - +
242B TYR* 5.7 2.2 + - - -
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Residues in contact with ILE 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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198B ILE* 5.1 7.0 - - + -
212B ILE* 4.1 24.5 - - + -
216B ARG* 2.9 24.6 + - - +
217B GLY* 3.7 4.7 - - - +
219B ASN* 1.3 78.2 - - + +
221B ILE* 1.3 59.9 + - - +
223B GLU* 4.7 0.9 - - - -
224B PHE* 2.9 50.6 + - + +
225B GLY 4.4 0.3 - - - +
230B ILE* 4.1 18.8 - - + -
236B LEU* 4.4 1.3 - - + -
242B TYR* 4.1 24.5 - - + -
243B ILE* 4.2 15.9 - - + -
246B LEU* 4.3 16.4 - - + -
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Residues in contact with ILE 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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186B VAL* 5.6 1.8 - - + -
191B GLN* 3.9 36.1 + - + +
194B SER* 3.7 11.9 - - - -
195B LEU* 3.3 45.8 - - + +
198B ILE* 3.8 16.2 - - + -
217B GLY 3.0 20.9 + - - +
218B TYR* 3.8 9.2 - - + +
220B ILE* 1.3 76.1 - - - +
222B ARG* 1.3 60.0 + - - +
225B GLY* 2.9 45.2 + - - +
226B ASN* 4.4 5.8 - - - +
230B ILE* 4.5 0.9 - - + -
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Residues in contact with ARG 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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173A ARG* 3.7 12.7 - - - +
179A ASP* 4.3 14.5 + - - -
182A GLU* 3.2 35.0 + - - -
181B TYR* 5.0 0.8 + - - -
187B ASP* 5.6 3.6 - - - +
191B GLN* 4.9 9.4 - - - +
218B TYR* 2.9 52.1 + - + +
219B ASN* 4.0 12.0 + - - +
221B ILE* 1.3 78.8 - - - +
223B GLU* 1.3 62.5 + - - +
225B GLY* 4.8 0.7 + - - -
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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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219B ASN* 3.2 28.1 + - - +
220B ILE* 5.6 0.3 - - - -
222B ARG* 1.3 79.4 - - - +
224B PHE* 1.3 100.6 + - + +
225B GLY 3.9 0.2 + - - -
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Residues in contact with PHE 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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220B ILE* 2.9 32.2 + - + +
223B GLU* 1.3 105.8 - - + +
225B GLY* 1.3 58.7 + - - +
229B ASP* 3.9 5.4 - - - +
230B ILE* 4.0 15.8 - - + +
233B GLN* 2.9 45.9 + - - +
236B LEU* 3.7 34.8 - - + -
237B PRO* 4.1 32.3 - - + -
243B ILE* 5.9 3.4 - - + -
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Residues in contact with GLY 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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221B ILE* 2.9 28.9 + - - +
222B ARG 4.7 0.8 + - - -
223B GLU 3.6 1.4 + - - -
224B PHE* 1.3 77.7 - - - +
226B ASN* 1.3 64.9 + - - -
229B ASP* 4.2 6.7 - - - -
230B ILE* 3.1 21.0 - - - +
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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