Contacts of the helix formed by residues 221 - 232 (chain A) in PDB entry 1YRP
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A GLY 4.0 2.0 - - - -
220A GLU* 1.3 81.7 - - + +
222A LYS* 1.3 64.6 + - - +
223A GLN* 3.6 14.0 + - - +
224A GLU* 3.1 25.3 + - - +
225A THR* 3.1 25.6 + - - -
47B ARG* 5.4 3.6 - - - -
57B SER* 5.0 0.2 - - - -
59B GLU* 3.3 30.5 - - + +
60B GLU* 3.8 21.1 - - + +
63B ARG* 5.6 3.4 - - - +
166B HIS* 6.2 1.6 - - - -
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PRO* 3.8 35.0 - - + -
221A THR* 1.3 69.5 - - - +
223A GLN* 1.3 67.5 + - - +
225A THR* 3.1 17.4 + - - -
226A LEU* 3.1 25.7 + - + +
23B GLN* 4.6 16.0 - - - +
24B PHE* 4.9 10.5 - - - -
47B ARG* 5.2 9.1 - - - +
60B GLU* 2.9 22.6 + - - +
176B ASN* 4.5 10.8 - - - +
177B ILE 5.0 12.5 + - - +
178B PHE* 5.8 5.9 - - + +
278B DTT 5.1 11.0 + - - +
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Residues in contact with GLN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A THR* 3.6 12.0 + - - +
222A LYS* 1.3 78.5 - - - +
224A GLU* 1.3 59.8 + - - +
226A LEU* 3.4 3.9 + - - +
227A THR* 3.0 34.9 + - - +
166B HIS* 4.5 7.3 + - - +
173B GLU 3.8 20.2 + - - -
174B PHE* 3.4 30.6 - - + +
175B LYS 3.5 17.1 + - - +
176B ASN* 3.8 24.5 - - - +
191B TYR* 4.5 1.6 + - - -
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLY* 4.1 6.5 - - - -
220A GLU* 3.2 31.7 + - - +
221A THR* 3.1 19.3 + - - +
223A GLN* 1.3 78.5 - - + +
225A THR* 1.3 68.5 + - - +
227A THR* 3.2 10.0 + - + -
228A ASN* 2.9 43.2 + - - +
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Residues in contact with THR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PRO* 4.2 13.0 - - + -
182A GLU* 4.2 22.0 - - + +
217A PHE 3.5 22.1 - - - +
218A LEU* 3.8 12.0 - - + +
219A GLY 3.2 17.2 + - - +
221A THR 3.1 15.7 + - - -
222A LYS* 3.1 11.4 + - - -
224A GLU* 1.3 78.6 - - - +
226A LEU* 1.3 61.4 + - - +
228A ASN* 3.5 0.5 + - - +
229A ILE* 3.3 35.2 + - + +
47B ARG* 5.3 2.1 + - - -
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PRO* 4.2 29.2 - - + -
184A VAL* 4.6 2.0 - - + -
189A VAL* 3.9 29.3 - - + +
222A LYS* 3.1 18.2 + - + +
223A GLN 3.7 4.7 - - - +
225A THR* 1.3 74.6 - - - +
227A THR* 1.3 64.3 + - - +
229A ILE* 3.2 8.8 + - + +
230A SER* 3.1 25.6 + - - -
176B ASN* 3.8 14.6 - - + -
177B ILE* 3.7 43.7 - - + +
191B TYR* 3.6 12.8 + - + +
278B DTT 5.3 5.6 - - - -
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Residues in contact with THR 227 (chain A).
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* 3.0 23.0 + - - +
224A GLU* 3.5 15.1 - - + -
226A LEU* 1.3 76.4 - - - +
228A ASN* 1.3 61.2 + - - +
230A SER* 3.5 2.3 + - - -
231A ALA* 2.9 38.9 + - + +
175B LYS 5.4 0.5 + - - -
191B TYR* 3.5 13.2 + - - -
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Residues in contact with ASN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PHE* 3.2 28.9 + - + +
218A LEU 4.5 1.0 + - - -
219A GLY* 4.4 6.1 - - - +
224A GLU* 2.9 41.8 + - - +
225A THR 3.6 6.3 - - - +
227A THR* 1.3 80.3 - - - +
229A ILE* 1.3 53.6 + - - +
231A ALA* 4.4 0.2 - - - -
232A VAL* 2.7 12.5 + - - -
233A ASN* 2.7 70.4 + - - +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PRO 3.0 30.5 - - - +
182A GLU 4.2 6.3 - - - +
184A VAL* 3.3 27.6 - - + +
186A PRO* 3.4 25.5 - - - +
189A VAL* 3.6 16.8 - - + -
201A TRP* 3.8 8.3 - - + -
217A PHE* 3.7 26.7 - - + -
225A THR* 3.3 24.2 + - + +
226A LEU* 3.2 10.0 + - + +
227A THR 3.2 0.6 - - - -
228A ASN* 1.3 74.8 - - - +
230A SER* 1.3 66.9 + - - +
232A VAL* 3.1 13.7 + - - +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PRO* 4.2 6.1 - - - -
189A VAL* 4.5 4.0 - - - -
190A ASN* 2.9 31.1 + - - -
226A LEU 3.1 13.8 + - - -
227A THR* 4.0 2.7 - - - -
229A ILE* 1.3 79.8 - - - +
231A ALA* 1.3 59.7 + - - +
232A VAL 3.6 0.2 + - - -
258A LYS* 3.1 39.4 + - - +
191B TYR* 4.2 15.7 - - - -
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A THR* 2.9 26.0 + - + +
228A ASN 4.0 2.5 - - - +
230A SER* 1.3 75.6 - - - +
232A VAL* 1.3 70.4 + - - +
233A ASN* 4.2 13.6 - - + +
258A LYS* 6.0 0.2 - - - -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A TRP* 4.2 12.6 - - + -
217A PHE* 4.0 6.1 - - - -
228A ASN 2.7 13.8 + - - -
229A ILE 3.1 14.6 + - - +
231A ALA* 1.3 79.0 - - - +
233A ASN* 1.3 57.3 + - - +
234A TYR* 3.3 25.8 + - + +
256A LEU 3.6 23.6 - - - +
258A LYS* 3.7 39.0 - - + +
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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