Contacts of the helix formed by residues 216 - 226 (chain B) in PDB entry 3V98
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 ASN 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B ILE 4.0 0.8 + - - -
215B SER* 1.3 73.9 - - - +
217B THR* 1.3 67.0 + - - +
218B ILE 3.5 1.7 + - - -
219B SER* 2.8 42.3 + - - -
220B GLU* 2.9 26.9 + - - +
558B TYR* 3.6 24.8 - - + +
559B ASP* 2.9 25.6 + - - +
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Residues in contact with THR 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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216B ASN* 1.3 80.0 - - - +
218B ILE* 1.3 69.8 + - + +
220B GLU* 3.9 6.6 - - - +
221B ARG* 3.3 25.3 + - - +
657B LEU* 5.3 8.1 - - + -
658B PRO* 6.4 1.6 - - + -
660B TYR* 6.0 0.9 - - - -
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Residues in contact with ILE 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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216B ASN* 3.4 2.8 + - - -
217B THR* 1.3 80.7 - - + +
219B SER* 1.3 62.9 + - - +
221B ARG* 3.0 9.7 + - - +
222B VAL* 2.8 29.4 + - + +
559B ASP* 3.6 38.1 - - + +
560B TRP* 4.0 24.7 - - + +
657B LEU* 4.2 22.9 - - + -
658B PRO* 4.4 11.4 - - + +
660B TYR* 3.5 36.1 - - + +
661B TYR* 3.8 9.9 - - + +
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Residues in contact with SER 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.5 16.7 - - - -
215B SER* 3.6 7.8 - - - -
216B ASN* 2.8 41.4 + - - -
218B ILE* 1.3 77.3 - - - +
220B GLU* 1.3 55.8 + - - +
222B VAL* 3.3 5.6 + - - +
223B MET 2.9 22.5 + - - -
558B TYR* 4.0 2.2 - - - -
559B ASP 3.2 15.6 + - - -
562B SER* 3.0 27.5 + - - -
563B TRP* 4.4 1.6 - - - +
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Residues in contact with GLU 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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211B PHE* 4.4 4.5 - - - -
215B SER* 4.1 14.3 + - - +
216B ASN 2.9 21.0 + - - +
217B THR* 3.9 6.4 - - - +
219B SER* 1.3 75.7 + - - +
221B ARG* 1.3 65.8 + - - +
223B MET* 3.3 20.2 + - + +
224B ASN* 3.0 41.4 + - - +
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Residues in contact with ARG 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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217B THR* 3.3 19.1 + - - +
218B ILE 3.0 10.5 + - - +
220B GLU* 1.3 79.5 - - - +
222B VAL* 1.3 62.1 + - - +
224B ASN* 3.1 3.3 + - - +
225B HIS* 3.0 56.4 + - + +
231B MET* 4.5 8.7 - - + -
656B GLN* 3.0 38.0 + - - +
657B LEU* 3.5 36.8 - - + +
658B PRO* 6.0 0.4 - - - +
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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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218B ILE* 2.8 20.3 + - + +
219B SER* 3.5 8.5 - - - +
220B GLU 3.2 0.2 - - - -
221B ARG* 1.3 76.6 - - + +
223B MET* 1.3 58.0 + - - +
226B TRP* 2.8 38.9 + - + +
231B MET* 3.9 11.0 - - + -
559B ASP 3.9 12.3 - - - +
560B TRP* 3.6 37.0 - - + +
563B TRP* 3.9 13.7 - - + -
566B ASN* 3.7 36.8 - - + +
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Residues in contact with MET 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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208B GLU* 3.7 32.5 - - - +
211B PHE* 3.6 28.9 - - + -
212B VAL* 4.1 15.9 - - + -
215B SER* 5.6 0.7 - - - +
219B SER 2.9 14.4 + - - +
220B GLU* 3.5 29.4 - - + +
221B ARG 3.3 0.2 - - - -
222B VAL* 1.3 75.3 - - - +
224B ASN* 1.3 74.0 + - - +
226B TRP* 3.3 18.7 + - - -
563B TRP* 3.8 30.7 - - + -
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Residues in contact with ASN 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 GLU* 3.0 34.2 + - - +
221B ARG* 3.1 3.0 + - - +
222B VAL 3.1 0.6 - - - -
223B MET* 1.3 93.5 - - - +
225B HIS* 1.3 84.0 + - + +
226B TRP* 3.9 1.1 - - - -
228B GLU* 4.4 1.4 - - - +
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Residues in contact with HIS 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 ARG* 3.0 51.7 + - + +
222B VAL 3.7 0.2 - - - -
224B ASN* 1.3 95.4 + - + +
226B TRP* 1.3 66.3 + - - +
227B GLN* 3.1 3.1 - - - -
228B GLU* 2.7 53.8 + - - +
231B MET* 3.4 22.5 - - + +
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Residues in contact with TRP 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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204B PHE* 3.8 28.0 - + - -
222B VAL* 2.8 25.8 + - + +
223B MET 3.3 23.1 + - - -
224B ASN 5.1 0.4 - - - -
225B HIS* 1.3 76.7 - - - +
227B GLN* 1.3 88.0 + - + +
228B GLU 3.3 5.5 + - - +
231B MET* 4.2 12.6 - - - +
232B PHE* 5.3 6.1 + - - +
348B LEU* 3.8 29.4 - - + +
351B LYS* 5.2 2.1 + - - -
352B ILE* 3.8 27.1 - - + -
563B TRP* 3.2 30.0 - - + +
565B PRO* 3.7 28.3 - - + -
566B ASN* 4.4 12.1 - - - +
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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