Contacts of the helix formed by residues 213 - 227 (chain A) in PDB entry 4OE4
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 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 4.1 2.7 - - - -
153A LYS* 3.4 21.8 - - - -
160A ILE* 4.9 7.0 - - + -
161A ASP* 3.2 24.9 - - + +
165A GLU* 3.9 24.5 - - - -
210A PRO* 4.4 7.8 - - - +
211A PHE 4.6 0.9 - - - -
212A ASN* 1.3 109.5 + - - +
214A THR* 1.3 66.2 + - - +
215A ALA* 4.7 1.1 - - + -
216A ILE* 3.1 39.6 + - + +
217A ALA* 3.5 7.3 + - - +
243A ASN* 5.4 0.5 + - - -
346A PHE* 4.9 3.1 - + - -
349A GLN 4.4 1.6 - - - -
350A LYS* 3.9 37.7 - - + -
351A CYS* 5.7 2.7 - - - -
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Residues in contact with THR 214 (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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143A MET* 4.0 25.4 - - + -
147A THR* 3.0 19.4 + - - +
151A GLN* 3.2 12.6 + - - +
161A ASP* 2.9 6.0 + - - -
162A CYS* 3.8 17.7 - - + -
166A LEU* 4.0 12.1 - - + +
213A PHE* 1.3 71.2 - - - +
215A ALA* 1.3 62.5 + - - +
217A ALA* 3.1 14.7 + - - +
218A ALA* 3.2 10.9 + - - +
242A SER* 3.0 26.3 + - - +
243A ASN* 4.4 10.8 - - - +
246A LEU* 4.5 4.6 - - + +
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Residues in contact with ALA 215 (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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161A ASP* 2.8 33.1 + - - +
165A GLU* 3.8 16.2 - - + +
166A LEU* 3.5 29.8 - - - +
169A PHE* 3.4 17.3 - - + -
213A PHE* 4.7 1.1 - - + -
214A THR* 1.3 78.6 - - - +
216A ILE* 1.3 56.7 + - + +
218A ALA* 3.2 1.6 + - - +
219A ASN 2.9 23.0 + - - -
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Residues in contact with ILE 216 (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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165A GLU* 5.7 2.0 - - - +
169A PHE* 4.6 10.1 - - + -
210A PRO* 3.7 23.3 - - + -
212A ASN* 4.0 9.6 - - - +
213A PHE* 3.1 40.1 + - + +
215A ALA* 1.3 76.5 - - + +
217A ALA* 1.3 60.1 + - - +
219A ASN* 3.3 11.2 + - - +
220A LEU* 2.9 30.7 + - + +
286A THR* 3.8 28.9 - - + +
351A CYS* 4.6 15.0 - - - -
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Residues in contact with ALA 217 (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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209A SER* 3.8 19.6 - - - +
210A PRO* 4.9 2.0 - - - +
213A PHE 3.5 4.6 + - - +
214A THR 3.1 11.0 + - - +
216A ILE* 1.3 78.0 - - - +
218A ALA* 1.3 63.5 + - - +
220A LEU* 3.2 1.8 + - - +
221A ILE* 3.2 28.6 + - - +
233A TRP* 3.8 13.5 - - + -
243A ASN* 3.3 31.9 - - - +
246A LEU* 4.3 5.2 - - + -
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Residues in contact with ALA 218 (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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166A LEU* 3.7 32.3 - - + +
169A PHE* 5.4 0.7 - - + -
170A PHE* 3.3 36.4 - - + -
214A THR 3.2 3.8 + - - +
215A ALA 3.5 8.1 - - - +
216A ILE 3.2 0.2 - - - -
217A ALA* 1.3 79.5 - - - +
219A ASN* 1.3 56.3 + - - +
221A ILE* 3.5 3.1 - - - +
222A GLY* 2.8 24.9 + - - -
246A LEU* 3.7 13.6 - - + +
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Residues in contact with ASN 219 (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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169A PHE* 3.9 26.3 - - + -
170A PHE* 5.1 0.2 - - - -
173A TYR* 2.4 44.6 + - - -
215A ALA 2.9 13.4 + - - +
216A ILE* 3.3 14.7 + - - +
218A ALA* 1.3 76.6 - - - +
220A LEU* 1.3 77.1 + - - +
223A ALA* 3.1 27.0 + - - +
284A HIS* 3.9 7.1 + - - -
286A THR* 5.4 1.6 + - - -
548A ILE* 5.0 1.8 - - - +
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Residues in contact with LEU 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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207A ALA* 4.0 16.3 - - + +
208A VAL 3.5 26.5 - - - +
209A SER* 3.5 22.9 - - - -
210A PRO* 3.9 4.7 - - + -
216A ILE* 2.9 19.5 + - + +
217A ALA* 3.2 4.7 + - - +
219A ASN* 1.3 83.4 - - - +
221A ILE* 1.3 59.2 + - + +
224A PRO* 3.1 12.1 - - - +
284A HIS* 2.9 61.5 + - + +
285A PHE 4.1 0.7 - - - +
286A THR* 3.6 26.5 - - - +
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Residues in contact with ILE 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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128A PHE* 5.4 0.2 - - + -
170A PHE* 5.3 1.8 - - + -
207A ALA* 3.9 9.6 - - + -
217A ALA 3.2 16.5 + - - +
218A ALA* 3.5 5.6 - - - +
220A LEU* 1.3 77.5 - - + +
222A GLY* 1.3 63.2 + - - +
224A PRO* 3.3 5.7 - - - +
225A ALA* 3.2 30.2 + - - +
231A VAL* 4.0 9.3 - - + +
233A TRP* 3.5 64.2 - - + -
246A LEU* 4.1 8.5 - - + -
250A LEU* 3.7 28.7 - - + -
260A ILE* 4.1 15.9 - - + -
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Residues in contact with GLY 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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128A PHE* 3.8 24.5 - - - -
170A PHE* 4.1 7.4 - - - -
173A TYR* 4.9 4.5 - - - -
218A ALA 2.8 19.5 + - - -
221A ILE* 1.3 76.5 - - - +
223A ALA* 1.3 59.3 + - - +
226A LEU* 2.9 35.3 + - - +
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Residues in contact with ALA 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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173A TYR* 3.8 25.8 - - + -
219A ASN* 3.1 15.5 + - - +
222A GLY* 1.3 75.7 - - - +
224A PRO* 1.4 71.2 - - + +
226A LEU* 3.6 2.1 + - - +
227A MET* 3.4 22.2 + - - +
284A HIS* 4.2 8.1 - - + -
548A ILE* 4.2 11.7 - - + -
549A LEU* 3.8 21.4 - - + +
552A PHE* 4.4 5.6 - - + -
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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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205A VAL* 3.9 25.4 - - + -
220A LEU 3.1 29.2 - - - +
221A ILE 3.3 10.5 - - - +
223A ALA* 1.4 94.0 - - + +
225A ALA* 1.3 60.8 + - - +
227A MET 3.2 6.1 + - - -
229A ASN* 3.0 28.4 + - + +
231A VAL* 4.1 10.5 - - + -
284A HIS* 3.8 7.6 - - + +
552A PHE* 3.7 31.4 - - + -
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Residues in contact with ALA 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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116A TRP* 2.8 33.7 + - + +
128A PHE* 3.7 20.6 - - + -
221A ILE 3.2 19.4 + - - +
222A GLY 4.1 0.2 - - - +
223A ALA 3.3 0.4 - - - -
224A PRO* 1.3 78.6 - - - +
226A LEU* 1.3 63.1 + - - +
228A GLY 2.9 4.9 + - - -
229A ASN 3.4 16.6 - - - +
231A VAL* 4.4 2.7 - - + +
259A VAL* 4.5 1.6 - - + -
260A ILE* 4.2 17.5 - - + -
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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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116A TRP* 4.9 0.9 - - - -
121A PHE* 4.3 8.1 - - + -
124A ARG* 2.9 27.6 + - - +
125A SER* 3.7 40.8 - - - +
128A PHE* 4.1 19.7 - - + -
173A TYR* 3.6 46.7 - - + +
174A VAL* 3.7 12.1 - - + +
177A ALA* 4.0 9.6 - - + -
222A GLY 2.9 18.2 + - - +
223A ALA 3.9 4.5 - - - +
224A PRO 3.3 0.2 - - - -
225A ALA* 1.3 77.4 - - - +
227A MET* 1.3 61.0 + - - +
228A GLY 3.1 0.2 - - - -
549A LEU* 4.8 2.0 - - + -
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Residues in contact with MET 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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124A ARG* 3.9 1.7 + - - -
177A ALA* 3.7 23.6 - - + -
180A LEU* 3.9 27.4 - - + -
181A TYR* 3.3 46.9 + - + +
198A TYR* 5.5 0.9 - - + -
200A PRO* 3.5 21.1 - - - +
223A ALA 3.4 15.7 - - - +
224A PRO 3.2 7.1 + - - +
225A ALA 3.1 1.2 - - - -
226A LEU* 1.3 79.4 - - - +
228A GLY* 1.3 59.4 + - - +
229A ASN* 3.4 7.4 - - - +
549A LEU* 4.0 31.2 - - + +
552A PHE* 4.2 2.2 - - + +
553A VAL* 3.5 24.5 - - + +
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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