Contacts of the helix formed by residues 219 - 228 (chain A) in PDB entry 4FE1
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 VAL 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER 3.6 18.2 - - - +
151A GLY* 3.9 4.7 - - - +
215A HIS* 2.8 30.8 + - + +
216A GLN 3.6 0.4 + - - -
217A ILE 3.6 0.2 - - - -
218A HIS* 1.3 84.2 - - + +
220A SER* 1.3 69.0 + - - +
221A LEU 3.5 0.4 - - - -
222A PRO* 3.6 2.9 - - - -
223A ILE* 3.2 49.0 + - + +
239A PRO* 3.6 28.9 - - + +
243A ILE* 5.7 4.0 - - + -
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Residues in contact with SER 220 (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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149A ALA 3.1 19.7 + - - -
150A SER 4.4 8.3 + - - -
151A GLY 4.6 0.2 - - - +
212A TRP* 5.7 0.2 - - - -
215A HIS* 3.4 4.8 + - - -
216A GLN* 3.0 34.4 + - - +
219A VAL* 1.3 80.2 - - - +
221A LEU* 1.3 63.6 + - - +
224A ASN* 2.9 33.3 + - - +
294A LEU* 3.0 24.9 - - - +
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Residues in contact with LEU 221 (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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216A GLN* 2.6 29.6 + - + +
217A ILE* 3.7 13.9 - - - +
220A SER* 1.3 77.4 + - - +
222A PRO* 1.4 71.5 - - + +
224A ASN* 4.1 1.6 - - - +
225A LYS* 2.9 20.4 + - - +
253A TYR* 2.9 34.1 + - + +
278A PHE* 4.0 15.9 - - + +
294A LEU* 3.4 29.8 - - + +
295A SER* 3.3 32.5 - - - +
298A ALA* 4.2 6.3 - - + -
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Residues in contact with PRO 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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217A ILE 3.3 14.8 - - - +
218A HIS 3.7 10.1 - - - +
219A VAL 3.5 13.5 - - - +
221A LEU* 1.4 94.2 - - + +
223A ILE* 1.3 64.1 + - - +
225A LYS* 3.0 2.6 + - - +
226A LEU* 3.0 30.1 + - - +
242A PHE* 3.7 29.4 - - + -
249A MET* 3.4 30.1 - - + -
252A LEU* 4.0 9.2 - - + -
253A TYR* 3.6 4.9 - - - +
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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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151A GLY* 3.4 26.7 - - - +
153A THR* 4.0 18.2 - - + +
219A VAL* 3.2 32.7 + - + +
222A PRO* 1.3 78.9 - - + +
224A ASN* 1.3 57.0 - - - +
226A LEU 3.4 0.3 + - - -
227A LEU* 2.9 51.5 + - + +
236A ILE* 3.6 17.6 - - + +
237A PRO 4.2 5.8 - - - +
239A PRO* 3.7 27.6 - - + -
242A PHE* 4.2 17.0 - - + -
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Residues in contact with ASN 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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148A ARG* 2.6 28.9 + - - +
149A ALA 4.2 2.2 + - - -
151A GLY* 4.3 6.3 - - - +
220A SER 2.9 22.6 + - - +
221A LEU* 4.1 1.6 - - - +
223A ILE* 1.3 75.5 - - - +
225A LYS* 1.3 60.6 + - - +
227A LEU* 3.5 16.0 - - - +
228A ASP* 2.9 47.8 + - - +
294A LEU* 3.2 29.3 - - + +
381A PRO* 3.4 21.8 - - - +
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Residues in contact with LYS 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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221A LEU 2.9 18.2 + - - +
222A PRO* 3.5 4.3 - - + +
224A ASN* 1.3 77.4 - - - +
226A LEU* 1.3 64.7 + - + +
228A ASP* 3.7 6.9 + - - +
229A ALA* 3.6 16.5 + - - +
252A LEU* 3.7 23.0 - - + +
253A TYR* 3.4 54.5 - - + +
254A PRO* 5.4 0.8 - - - +
277A ASP* 5.5 1.6 + - - -
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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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222A PRO 3.0 16.4 + - - +
225A LYS* 1.3 76.8 - - + +
227A LEU* 1.3 63.7 + - - +
229A ALA* 3.0 14.4 + - + +
231A VAL* 3.1 38.8 + - + +
236A ILE* 3.6 25.8 - - + -
237A PRO* 4.3 9.2 - - + -
242A PHE* 3.8 33.0 - - + -
248A LEU* 6.3 0.7 - - + -
252A LEU* 3.6 28.7 - - + -
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Residues in contact with LEU 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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104A LEU* 4.4 16.6 - - + +
148A ARG* 4.3 35.5 + - + +
151A GLY* 5.7 0.7 - - - -
152A ILE 6.0 0.2 - - - +
153A THR* 4.6 8.1 - - + -
223A ILE* 2.9 41.4 + - + +
224A ASN* 3.5 21.3 - - - +
226A LEU* 1.3 76.1 - - - +
228A ASP* 1.3 65.9 + - - +
229A ALA 3.2 0.2 - - - -
230A GLY* 3.3 14.0 + - - -
231A VAL 4.3 2.8 + - - +
232A ALA* 4.6 3.5 + - - +
233A ALA* 4.0 24.5 - - + +
236A ILE* 3.4 19.3 - - + +
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Residues in contact with ASP 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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148A ARG* 4.2 10.0 + - - +
224A ASN* 2.9 33.0 + - - +
225A LYS* 4.1 6.9 - - - +
227A LEU* 1.3 78.1 - - - +
229A ALA* 1.3 59.3 + - - +
230A GLY 3.4 0.2 - - - -
286A ASN* 3.3 19.7 + - - +
288A VAL* 3.6 34.2 - - + +
289A THR* 3.0 30.6 - - - +
293A TRP* 5.6 1.4 - - - -
382A TYR* 5.8 0.2 - - - -
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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