Contacts of the helix formed by residues 220 - 231 (chain B) in PDB entry 5WWT
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B PRO* 4.8 0.7 - - - +
54B THR* 3.4 4.9 - - - -
126B ARG* 2.4 31.1 + - - +
219B GLN* 1.3 73.9 - - - +
221B LEU* 1.3 67.6 + - - +
222B PRO* 3.4 4.3 - - + -
223B SER* 3.0 15.1 + - - +
224B ALA* 3.1 10.4 + - - +
456B ILE* 3.4 37.1 - - + +
72D C 3.5 12.7 + - - -
73D U 2.7 50.3 + - - +
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Residues in contact with LEU 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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54B THR* 3.3 17.9 + - + +
89B HIS* 3.9 8.5 - - + +
92B LEU* 3.6 24.0 - - + +
95B VAL* 3.9 22.4 - - + -
97B LEU* 3.9 16.4 - - + -
219B GLN 4.5 0.2 - - - -
220B ASN* 1.3 69.4 - - - +
222B PRO* 1.4 66.5 - - + +
224B ALA* 3.3 6.7 + - - +
225B LEU* 2.9 26.7 + - - +
403B ILE* 4.6 9.9 - - + -
424B PHE* 5.2 3.6 - - + -
451B ALA* 3.3 28.3 - - + +
452B ASN* 3.6 25.4 - - - +
455B SER* 5.2 4.2 - - - -
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Residues in contact with PRO 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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220B ASN* 3.5 6.1 - - + -
221B LEU* 1.4 94.7 - - + +
223B SER* 1.3 57.8 + - - +
225B LEU* 3.0 11.0 + - + +
226B VAL* 2.9 33.3 + - - +
424B PHE* 3.6 29.8 - - + -
455B SER* 4.4 12.3 - - - +
456B ILE* 3.8 23.3 - - + +
458B PHE* 3.5 32.8 - - + -
460B ILE* 4.0 1.0 - - - +
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Residues in contact with SER 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 GLN* 3.3 22.0 + - - -
220B ASN* 3.0 10.2 + - - +
222B PRO* 1.3 78.0 - - - +
224B ALA* 1.3 61.5 + - - +
226B VAL* 3.5 16.2 + - - +
227B SER* 4.1 2.6 + - - -
248B LYS* 3.7 24.2 - - - +
456B ILE* 4.7 0.2 - - - +
458B PHE* 3.4 19.9 - - - -
72D C 3.5 8.0 + - - +
73D U 2.9 27.8 + - - -
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Residues in contact with ALA 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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56B ARG* 4.8 3.1 - - + -
92B LEU* 4.7 1.3 - - + -
95B VAL* 3.9 27.4 - - + -
219B GLN* 3.7 23.6 - - + +
220B ASN 3.1 11.0 + - - +
221B LEU* 3.7 9.2 - - - +
223B SER* 1.3 74.5 - - - +
225B LEU* 1.3 65.0 + - - +
226B VAL 3.4 0.3 + - - -
227B SER 3.7 2.4 + - - -
228B HIS* 3.2 7.9 - - - -
251B HIS* 3.1 31.8 + - + -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.7 21.7 - - + +
221B LEU 2.9 14.6 + - - +
222B PRO* 3.0 10.1 + - + +
224B ALA* 1.3 77.3 - - - +
226B VAL* 1.3 64.0 + - - +
228B HIS* 3.0 5.7 + - - +
229B VAL* 2.9 25.6 + - + +
401B PRO* 3.6 37.2 - - + +
403B ILE* 3.7 12.3 - - + -
422B GLN* 3.6 18.6 - - - +
424B PHE* 3.4 30.5 - - + -
460B ILE* 3.7 14.8 - - + -
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Residues in contact with VAL 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 PRO 2.9 21.2 + - - +
223B SER 3.6 10.5 - - - +
224B ALA 3.2 0.4 - - - -
225B LEU* 1.3 76.1 - - - +
227B SER* 1.3 57.7 + - - +
229B VAL* 3.1 6.2 + - - +
230B LEU* 2.9 27.4 + - + +
248B LYS* 3.9 16.2 - - + -
321B LEU* 3.5 33.7 - - + -
369B VAL* 4.1 9.8 - - + +
371B SER* 4.0 8.1 - - - +
458B PHE* 3.5 25.6 - - + -
460B ILE* 3.7 15.7 - - + -
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Residues in contact with SER 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 SER 4.1 3.1 + - - -
224B ALA 3.7 1.4 + - - -
225B LEU 3.3 0.2 - - - -
226B VAL* 1.3 79.0 - - - +
228B HIS* 1.3 60.7 + - - +
230B LEU* 3.6 6.1 + - - +
231B ASN 3.2 15.1 + - - -
232B PRO* 3.4 14.6 - - - +
248B LYS* 3.6 20.8 + - - +
251B HIS* 3.2 41.7 + - - +
252B ILE* 4.0 17.7 - - - +
255B LEU* 3.5 9.5 - - - +
321B LEU* 5.7 0.4 - - - -
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Residues in contact with HIS 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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65A GLN* 3.8 3.1 - - - +
91B ASP 5.1 0.6 + - - -
92B LEU* 3.7 20.0 - - + +
93B GLN* 3.4 28.6 + - + -
94B ASP* 2.9 37.3 + - - -
224B ALA* 3.2 23.8 - - + -
225B LEU 3.0 8.2 + - - +
227B SER* 1.3 76.6 - - - +
229B VAL* 1.3 62.9 + - - +
231B ASN* 3.1 19.0 + - - +
251B HIS* 3.5 10.3 + + - -
255B LEU* 4.1 19.8 - - + +
400B GLU 3.6 8.7 - - - +
401B PRO* 3.9 16.9 - - + +
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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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65A GLN* 4.8 1.7 + - - +
225B LEU* 2.9 40.7 + - + +
226B VAL* 3.1 9.4 + - - +
228B HIS* 1.3 74.0 - - - +
230B LEU* 1.3 65.5 + - - +
231B ASN* 3.3 4.5 + - - +
369B VAL* 4.5 5.8 - - + -
399B GLN* 3.5 33.9 - - + +
400B GLU 3.5 15.2 + - - +
401B PRO 4.3 0.2 - - - +
422B GLN* 3.8 16.4 - - - +
460B ILE* 4.1 11.7 - - + -
462B LYS* 3.6 27.4 - - + -
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Residues in contact with LEU 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 VAL 2.9 16.0 + - - +
227B SER* 3.7 6.5 - - - +
228B HIS 3.3 0.2 - - - -
229B VAL* 1.3 75.4 - - - +
231B ASN* 1.3 68.1 + - - +
232B PRO* 4.6 3.4 - - + -
238B ILE* 3.9 17.3 - - + -
252B ILE* 3.6 32.5 - - + -
319B ARG* 2.9 44.6 + - + -
320B ILE 4.2 4.5 - - - +
321B LEU* 3.9 18.2 - - + +
367B VAL* 4.1 18.1 - - + +
369B VAL* 3.6 29.3 - - + +
462B LYS* 5.1 0.5 - - - -
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Residues in contact with ASN 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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63A SER* 2.7 34.9 + - - -
65A GLN* 3.5 38.3 - - - +
66A HIS* 3.9 7.1 - - - +
227B SER 3.2 0.6 + - - -
228B HIS* 3.1 16.0 + - - +
229B VAL 3.1 5.5 - - - +
230B LEU* 1.3 77.4 - - - +
232B PRO* 1.3 72.3 - - - +
233B GLN* 3.5 8.7 + - - +
319B ARG* 2.9 29.6 + - - +
462B LYS* 5.7 2.5 - - - -
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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