Contacts of the helix formed by residues 220 - 234 (chain B) in PDB entry 3UYS
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A HIS 4.4 2.9 + - - +
186A LEU* 3.5 48.0 - - + -
229A SER* 5.4 3.1 - - - +
233A MET* 6.1 0.4 - - - -
218B ALA* 3.8 5.5 - - - +
219B ALA* 1.3 86.9 - - + +
221B LYS* 1.3 65.5 + - - +
222B ARG* 4.0 5.0 + - - +
223B GLN* 2.8 59.2 + - - +
224B LYS* 3.1 10.0 + - - +
234D SER* 4.7 3.4 - - - +
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Residues in contact with LYS 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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170A ASN* 3.1 40.4 + - - +
220B THR* 1.3 73.1 - - - +
222B ARG* 1.3 61.6 + - - +
224B LYS* 3.1 9.5 + - + +
225B TYR* 2.8 68.9 + - + +
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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
----------------------------------------------------------
170A ASN* 2.0 54.5 + - + +
171A LYS* 3.2 19.7 - - - +
172A ASN* 3.4 23.0 + - - +
186A LEU 5.6 1.6 - - - +
187A GLY* 5.6 2.7 - - - -
171B LYS 4.0 5.3 + - - -
172B ASN* 3.1 34.0 - - - +
173B LEU* 4.3 8.1 - - - +
185B HIS 5.9 1.0 + - - -
220B THR* 3.3 6.4 + - - +
221B LYS* 1.3 80.4 - - - +
223B GLN* 1.3 59.8 + - + +
225B TYR* 3.3 18.2 + - - +
226B GLU* 2.9 58.2 + - + +
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Residues in contact with GLN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A HIS 4.1 7.6 - - - +
225A TYR 4.7 1.6 - - - +
226A GLU* 3.1 42.4 + - + +
229A SER* 3.7 25.0 + - - -
230A GLU* 4.4 2.8 + - - -
218B ALA* 4.0 4.9 - - + -
219B ALA* 3.9 11.9 - - - +
220B THR* 2.8 41.1 + - - +
221B LYS 3.1 0.8 - - - -
222B ARG* 1.3 79.7 - - + +
224B LYS* 1.3 66.1 + - - +
226B GLU* 3.1 10.9 + - + +
227B ARG* 3.0 28.5 + - - +
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Residues in contact with LYS 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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177B ALA* 5.6 1.1 - - - -
216B LEU* 3.4 25.2 + - + +
217B LYS* 4.8 3.4 - - - -
218B ALA* 3.6 15.8 - - + +
220B THR 3.1 10.7 + - - +
221B LYS* 3.4 12.6 - - - +
223B GLN* 1.3 75.1 - - - +
225B TYR* 1.3 70.8 + - + +
227B ARG* 2.9 22.9 + - - +
228B ILE* 2.9 32.2 + - + +
295B SO4 3.6 29.7 + - - -
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Residues in contact with TYR 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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170A ASN* 5.3 4.3 - - + -
173B LEU* 3.7 35.7 - - + -
175B GLY 5.4 3.8 + - - -
177B ALA* 3.7 27.9 + - + -
185B HIS* 3.9 9.3 + - + +
221B LYS* 2.8 59.2 + - + +
222B ARG* 3.4 25.6 - - + +
224B LYS* 1.3 94.5 - - + +
226B GLU* 1.3 58.3 + - - +
228B ILE* 3.3 7.2 + - - +
229B SER* 2.9 29.1 + - - -
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Residues in contact with GLU 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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172A ASN* 3.0 22.0 + - - +
222A ARG* 5.5 12.3 - - + +
185B HIS 5.0 9.0 - - - +
222B ARG* 2.9 49.2 + - + +
223B GLN* 3.1 11.6 + - + +
225B TYR* 1.3 79.3 - - - +
227B ARG* 1.3 57.7 + - - +
229B SER* 3.9 10.9 + - - -
230B GLU* 2.9 35.3 + - - +
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Residues in contact with ARG 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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223A GLN* 6.2 0.8 - - - +
226A GLU* 2.6 48.1 + - - +
216B LEU* 3.5 30.2 - - + +
217B LYS 3.1 26.7 + - - +
218B ALA* 3.7 10.8 - - - +
223B GLN* 3.0 17.6 + - - +
224B LYS* 2.9 11.3 + - - +
226B GLU* 1.3 78.2 - - - +
228B ILE* 1.3 60.0 + - - +
230B GLU* 3.3 7.5 + - - +
231B LYS* 3.0 23.2 + - - +
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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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177B ALA* 3.5 41.7 - - + +
178B ARG* 4.8 1.3 - - - +
185B HIS* 4.0 9.2 - - + +
213B TRP* 3.9 32.0 - - + +
216B LEU* 3.9 19.3 - - + -
224B LYS* 2.9 44.5 + - + +
225B TYR* 3.7 6.1 - - - +
227B ARG* 1.3 73.9 - - - +
229B SER* 1.3 61.2 + - - +
231B LYS* 3.3 1.6 + - - +
232B LYS* 2.8 35.8 + - - +
295B SO4 4.2 10.3 - - - +
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B HIS* 3.4 38.2 + - - +
186B LEU* 5.0 0.3 - - - +
225B TYR 2.9 17.3 + - - -
226B GLU* 3.9 14.1 + - - -
228B ILE* 1.3 77.4 - - - +
230B GLU* 1.3 59.2 + - - +
232B LYS* 3.9 1.1 - - - +
233B MET* 2.6 63.8 + - - +
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Residues in contact with GLU 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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220A THR* 6.1 4.8 - - - +
222A ARG* 4.7 18.2 - - + +
223A GLN* 6.2 1.8 - - - +
226B GLU* 2.9 24.0 + - - +
227B ARG* 3.4 9.6 - - + +
228B ILE 3.1 0.6 - - - -
229B SER* 1.3 80.6 + - - +
231B LYS* 1.3 62.0 + - - +
233B MET* 3.3 10.3 + - - +
234B SER* 2.7 37.3 + - - +
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B PRO* 3.0 40.2 + - - +
213B TRP* 4.0 14.4 - - + -
216B LEU* 4.3 12.8 - - + -
227B ARG 3.0 13.8 + - - +
228B ILE 4.1 1.8 - - - +
230B GLU* 1.3 79.7 - - - +
232B LYS* 1.3 57.6 + - - +
234B SER* 3.3 8.4 + - - -
235B THR* 2.8 45.6 + - - +
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Residues in contact with LYS 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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177B ALA 2.9 26.3 + - - -
178B ARG 3.3 6.9 + - - -
180B ALA 2.8 27.5 + - - +
182B ILE* 4.4 15.2 - - + +
185B HIS* 3.0 22.9 + - + -
201B TYR* 4.2 17.9 - - + +
213B TRP* 3.4 53.2 - - + +
228B ILE* 2.8 23.0 + - - +
229B SER* 3.9 4.3 - - - +
231B LYS* 1.3 78.0 - - - +
233B MET* 1.3 61.3 + - + +
234B SER 3.1 1.6 + - - -
235B THR* 3.4 17.3 + - - +
256B ARG* 5.0 3.0 + - - +
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Residues in contact with MET 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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182B ILE* 3.5 39.7 - - + -
185B HIS* 4.8 2.2 - - + -
186B LEU* 3.9 28.3 - - + -
229B SER* 2.6 51.2 + - - +
230B GLU* 3.3 13.7 + - - +
232B LYS* 1.3 76.8 - - + +
234B SER* 1.3 59.6 + - - +
235B THR 3.4 1.6 + - - -
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Residues in contact with SER 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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230B GLU* 2.7 25.6 + - - +
231B LYS* 3.6 10.5 - - - -
232B LYS 3.1 0.6 - - - -
233B MET* 1.3 79.4 - - - +
235B THR* 1.3 57.9 + - - +
236B PRO* 3.3 12.9 - - - +
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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