Contacts of the helix formed by residues 221 - 235 (chain A) in PDB entry 3SPY
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 PHE 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 4.0 28.3 - - + -
117A VAL* 4.4 11.0 - - + -
123A PHE* 3.8 27.1 - + + -
124A PRO* 3.3 37.2 - - + -
126A PRO* 3.9 9.7 - - + +
216A TRP 6.2 0.2 - - - -
217A ASN* 2.9 19.9 + - + +
219A GLU 3.5 0.4 - - - -
220A SER* 1.3 82.1 - - - +
222A ALA* 1.3 74.5 + - + +
223A ILE 3.4 1.6 - - - -
224A PRO* 3.4 3.0 - - - +
225A TYR* 2.9 50.0 + + - +
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Residues in contact with ALA 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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113A PHE* 3.7 27.1 - - + -
114A ASP* 5.3 2.9 - - - +
115A ILE* 4.3 22.0 - - + +
216A TRP 5.8 0.9 - - - +
217A ASN 3.5 2.6 + - - +
218A VAL* 3.4 20.7 + - + -
221A PHE* 1.3 87.0 - - + +
223A ILE* 1.3 57.7 + - - +
225A TYR* 3.8 0.2 - - - +
226A VAL* 2.9 35.2 + - - +
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Residues in contact with ILE 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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113A PHE* 3.8 21.3 - - + -
205A TRP* 6.0 0.2 - - + -
213A LEU* 3.7 20.2 - - + -
218A VAL* 2.7 33.2 + - + +
219A GLU* 4.2 3.6 - - + -
222A ALA* 1.3 73.1 - - - +
224A PRO* 1.4 66.6 - - + +
226A VAL* 3.4 3.0 + - - +
227A TYR* 3.0 24.3 + - + +
242A LEU* 5.0 4.1 - - + +
263A ILE* 4.3 16.2 - - + +
265A LEU* 3.9 30.3 - - + -
270A VAL* 3.7 34.1 - - + -
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Residues in contact with PRO 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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126A PRO* 3.9 14.4 - - + -
127A SER* 6.0 0.2 - - - -
218A VAL 3.6 1.6 - - - +
219A GLU 3.3 27.1 - - - +
220A SER 3.6 14.8 - - - +
221A PHE 3.4 12.6 - - - +
223A ILE* 1.4 93.4 - - + +
225A TYR* 1.3 59.5 + - - +
227A TYR* 4.4 0.2 - - + -
228A ASN* 3.0 35.8 + - - +
261A GLU 4.9 10.3 - - - +
262A ILE* 5.1 0.7 - - - -
263A ILE* 4.0 28.7 - - + +
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Residues in contact with TYR 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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115A ILE* 3.8 12.1 - - + -
117A VAL* 3.4 25.2 - - + +
124A PRO* 4.0 16.6 - - + -
125A GLU 3.9 7.6 - - - -
126A PRO* 3.6 21.2 - - + +
129A ALA* 3.6 25.9 - - + +
130A LYS 3.7 0.3 + - - -
131A HIS* 2.7 48.3 + - - +
133A ILE* 3.7 23.1 - - + -
221A PHE* 2.9 35.2 + + + +
222A ALA 3.8 2.9 - - - +
224A PRO* 1.3 77.4 - - - +
226A VAL* 1.3 57.1 + - - +
229A ARG* 2.9 28.6 + - + +
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Residues in contact with VAL 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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113A PHE* 4.3 10.8 - - + -
115A ILE* 3.9 31.0 - - + -
133A ILE* 3.9 15.5 - - + -
136A ILE* 4.9 4.9 - - + -
198A LEU* 5.1 2.2 - - + -
201A TYR* 4.5 13.9 - - + -
222A ALA 2.9 21.4 + - - +
223A ILE* 4.0 3.6 - - - +
225A TYR* 1.3 74.2 - - - +
227A TYR* 1.3 64.9 + - - +
229A ARG* 3.8 0.5 - - - +
230A ILE* 3.0 45.7 + - + +
242A LEU* 4.2 18.2 - - + -
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Residues in contact with TYR 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 ILE* 3.0 18.7 + - + +
224A PRO* 4.0 4.5 - - + +
226A VAL* 1.3 77.3 - - - +
228A ASN* 1.3 75.3 + - - +
230A ILE* 3.8 0.4 - - - +
231A LYS* 2.9 46.0 + - + +
236A GLU* 4.7 7.4 + - - +
239A ALA* 3.4 44.4 - - + +
240A LYS* 3.7 16.2 + - - +
242A LEU* 3.9 17.7 - - + +
248A THR* 2.9 37.8 + - + -
250A VAL* 5.5 4.7 - - + +
263A ILE* 4.1 32.3 - - + -
265A LEU* 4.6 1.3 - - + -
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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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126A PRO 2.9 27.2 + - - +
127A SER* 3.5 20.9 + - - +
129A ALA* 3.8 7.6 - - + -
224A PRO* 3.0 24.0 + - - +
227A TYR* 1.3 84.0 - - - +
229A ARG* 1.3 60.0 + - - +
231A LYS* 3.2 29.8 + - - +
232A ASN* 2.8 37.9 + - - +
263A ILE* 4.8 8.6 - - - +
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Residues in contact with ARG 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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129A ALA* 3.0 31.0 + - + +
130A LYS* 3.3 19.6 + - - +
131A HIS 3.3 18.2 + - - -
132A PRO* 3.7 16.4 - - - +
133A ILE* 3.7 21.5 - - + -
194A GLU* 2.8 41.9 + - - +
198A LEU* 4.2 3.6 - - + -
225A TYR* 2.9 21.0 + - + +
226A VAL 3.8 1.1 - - - +
228A ASN* 1.3 76.4 - - - +
230A ILE* 1.3 57.1 + - - +
232A ASN* 3.3 8.0 + - - +
233A ILE* 3.0 46.2 + - + +
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Residues in contact with ILE 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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198A LEU* 4.1 32.8 - - + +
201A TYR* 5.4 2.0 - - + -
202A LEU* 3.9 29.8 - - + -
226A VAL* 3.0 38.7 + - + +
227A TYR 3.8 2.9 - - - +
229A ARG* 1.3 74.0 - - + +
231A LYS* 1.3 57.3 - - - +
233A ILE* 3.1 0.9 + - - -
234A PHE* 2.7 52.0 + - + -
235A GLY 3.6 0.3 + - - -
238A THR* 3.9 10.5 - - + -
239A ALA* 3.5 28.3 - - - +
242A LEU* 4.8 5.6 - - + -
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Residues in contact with LYS 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 TYR* 2.9 31.7 + - + +
228A ASN* 3.2 28.1 + - - +
230A ILE* 1.3 76.5 - - - +
232A ASN* 1.3 70.6 + - - +
235A GLY* 2.7 37.1 + - - -
236A GLU* 3.7 36.6 - - + +
239A ALA* 3.6 8.2 - - + +
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Residues in contact with ASN 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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128A GLN 2.9 28.5 + - - +
129A ALA* 3.3 15.9 + - - +
130A LYS* 5.1 0.6 - - - +
228A ASN* 2.8 28.0 + - - +
229A ARG* 3.5 9.4 - - - +
231A LYS* 1.3 87.3 + - - +
233A ILE* 1.3 64.7 + - + +
235A GLY 4.7 0.3 + - - -
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Residues in contact with ILE 233 (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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194A GLU* 3.4 32.8 - - + +
195A LYS* 3.7 35.5 - - + -
198A LEU* 3.9 12.1 - - + -
229A ARG* 3.0 40.6 + - - +
232A ASN* 1.3 80.6 - - + +
234A PHE* 1.3 82.8 + - + +
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Residues in contact with PHE 234 (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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195A LYS* 3.8 26.7 - - + -
198A LEU* 4.0 24.5 - - + -
199A MET* 3.7 37.7 - - + -
202A LEU* 5.6 0.9 - - + -
230A ILE* 2.7 34.8 + - + +
233A ILE* 1.3 99.3 - - + +
235A GLY* 1.3 55.9 + - - +
237A SER* 5.5 1.0 + - - -
238A THR* 3.7 32.8 + - + +
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Residues in contact with GLY 235 (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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230A ILE 3.9 0.7 - - - +
231A LYS* 2.7 38.2 + - - -
232A ASN 4.7 0.6 + - - -
233A ILE 3.8 0.4 - - - -
234A PHE* 1.3 76.6 - - - +
236A GLU* 1.3 65.0 + - - -
237A SER* 3.5 2.2 - - - -
238A THR* 3.6 2.8 + - - -
239A ALA 3.4 10.9 + - - -
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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