Contacts of the helix formed by residues 220 - 234 (chain A) in PDB entry 5EN4
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 GLN 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ILE* 3.7 6.3 - - - +
188A TRP* 5.8 0.4 - - + -
217A ARG* 3.8 20.4 - - - +
218A MET 4.9 1.3 - - - +
219A GLY* 1.3 77.7 - - - +
221A PRO* 1.3 75.0 - - + +
222A ALA* 4.0 14.9 - - + +
223A GLU* 2.9 41.7 + - + +
224A VAL* 3.4 5.5 + - - +
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Residues in contact with PRO 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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20A GLY* 3.6 33.4 - - - +
21A ILE* 4.0 9.3 - - + +
24A GLY* 4.0 16.1 - - - -
187A ILE* 3.9 11.9 - - + -
188A TRP* 3.5 24.5 - - + +
189A THR* 4.3 1.6 - - + -
220A GLN* 1.3 85.1 - - + +
222A ALA* 1.3 56.6 + - - +
224A VAL* 3.1 5.8 + - + +
225A GLY* 2.9 24.9 + - - -
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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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24A GLY* 4.6 9.3 - - - -
28A ALA* 5.2 1.9 - - - +
220A GLN* 3.1 15.0 + - + +
221A PRO* 1.3 78.6 - - - +
223A GLU* 1.3 58.7 + - + +
225A GLY* 3.3 2.9 + - - +
226A ALA* 2.9 27.5 + - - +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ILE* 6.2 0.4 - - + -
217A ARG* 2.7 39.7 + - - -
219A GLY* 3.5 4.2 - - - -
220A GLN* 2.9 47.9 + - + +
222A ALA* 1.3 76.7 - - + +
224A VAL* 1.3 65.3 + - - +
226A ALA* 3.4 7.3 + - - +
227A ALA* 3.3 19.9 + - - +
245A VAL* 4.7 15.1 - - + +
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.7 31.6 - - + -
25A ILE* 4.3 9.0 - - + -
139A ILE* 4.5 4.3 - - + -
182A ILE* 4.1 23.7 - - + +
184A PRO* 4.5 9.2 - - + -
187A ILE* 4.0 32.5 - - + -
220A GLN 3.4 6.3 + - - +
221A PRO 3.1 6.8 + - - +
223A GLU* 1.3 76.1 - - + +
225A GLY* 1.3 63.8 + - - +
227A ALA* 3.2 7.1 + - - +
228A ALA* 3.0 21.5 + - - +
245A VAL* 4.4 12.3 - - + -
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Residues in contact with GLY 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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24A GLY 4.0 1.3 - - - -
25A ILE* 3.9 21.4 - - - +
28A ALA* 3.6 19.4 - - - +
221A PRO 2.9 13.4 + - - -
222A ALA 3.3 3.8 + - - -
223A GLU 3.2 0.4 - - - -
224A VAL* 1.3 77.0 - - - +
226A ALA* 1.3 60.7 + - - +
228A ALA* 3.2 3.6 + - - +
229A VAL* 3.0 27.0 + - - +
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Residues in contact with ALA 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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6A ARG* 5.2 4.2 + - - +
28A ALA* 4.2 3.9 - - - +
222A ALA 2.9 16.4 + - - +
223A GLU* 3.8 7.4 - - - +
225A GLY* 1.3 76.0 - - - +
227A ALA* 1.3 61.7 + - - +
229A VAL* 3.4 7.0 + - - +
230A PHE* 3.0 22.7 + - - +
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Residues in contact with ALA 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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182A ILE* 4.1 9.9 - - + -
223A GLU 3.3 10.2 + - - +
224A VAL 3.2 9.9 + - - +
226A ALA* 1.3 79.9 - - - +
228A ALA* 1.3 61.7 + - - +
230A PHE* 3.4 8.2 + - - +
231A LEU* 3.0 27.0 + - - +
243A LEU* 3.9 22.6 - - + +
245A VAL* 4.2 16.4 - - + -
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Residues in contact with ALA 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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25A ILE* 4.2 17.9 - - + -
29A PHE* 4.0 18.6 - - + -
87A VAL* 5.2 0.7 - - + -
137A ILE* 3.4 20.7 - - + +
182A ILE* 3.7 17.0 - - + +
224A VAL 3.0 13.3 + - - +
225A GLY 3.2 8.3 + - - +
227A ALA* 1.3 76.2 - - - +
229A VAL* 1.3 61.8 + - - +
231A LEU* 3.3 1.1 + - - -
232A ALA* 3.0 21.0 + - - +
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Residues in contact with VAL 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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6A ARG* 3.9 26.9 - - + +
7A TYR* 5.4 0.9 - - + -
28A ALA* 3.8 33.7 - - + +
29A PHE* 4.0 24.9 - - + +
32A SER* 3.5 22.4 - - - +
225A GLY 3.0 16.3 + - - +
226A ALA* 3.8 6.5 - - - +
227A ALA 3.3 0.2 - - - -
228A ALA* 1.3 75.5 - - - +
230A PHE* 1.3 62.6 + - - +
232A ALA* 3.9 0.2 - - - +
233A SER* 2.7 35.9 + - - +
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Residues in contact with PHE 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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6A ARG* 4.1 12.5 - - - +
226A ALA 3.0 13.1 + - - +
227A ALA* 3.5 12.3 - - - +
228A ALA 3.3 0.2 - - - -
229A VAL* 1.3 77.8 - - - +
231A LEU* 1.3 77.8 + - + +
233A SER* 4.3 0.9 - - - -
234A GLU* 2.9 53.2 + - + -
235A ALA* 3.1 27.9 + - + -
238A CYS* 5.1 7.6 - - - -
241A ILE* 5.8 1.8 - - + -
243A LEU* 4.6 13.0 - - + -
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Residues in contact with LEU 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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135A ASN* 4.1 1.8 - - - +
137A ILE* 4.0 16.6 - - + -
178A ARG* 2.8 29.8 + - - -
180A ASN* 4.1 28.5 - - + +
181A CYS 4.5 4.7 - - - +
182A ILE* 3.6 32.3 - - + -
227A ALA 3.0 18.4 + - - +
228A ALA 3.3 4.5 + - - +
230A PHE* 1.3 85.7 - - + +
232A ALA* 1.3 59.8 + - - +
235A ALA* 3.8 18.2 + - + +
238A CYS* 4.8 0.4 - - + -
241A ILE* 4.1 24.9 - - + -
243A LEU* 4.2 12.1 - - + -
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Residues in contact with ALA 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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7A TYR* 3.6 25.3 - - + +
29A PHE* 3.7 27.6 - - + -
85A CYS* 4.1 3.8 - - - -
135A ASN* 3.5 20.7 + - - +
137A ILE* 4.1 0.8 - - + +
178A ARG* 3.1 17.3 + - - -
228A ALA 3.0 16.3 + - - +
229A VAL 3.9 1.1 - - - +
231A LEU* 1.3 79.0 - - - +
233A SER* 1.3 59.8 + - - +
236A ASN* 4.8 1.2 - - - +
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Residues in contact with SER 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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6A ARG* 3.5 38.2 + - - +
7A TYR* 3.6 19.3 - - - -
229A VAL* 2.7 25.4 + - - +
232A ALA* 1.3 78.1 - - - +
234A GLU* 1.3 74.3 + - - +
235A ALA 3.9 0.4 - - - -
236A ASN* 4.1 13.4 + - - +
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Residues in contact with GLU 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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6A ARG* 2.5 37.4 + - + +
230A PHE* 2.9 28.4 + - + +
233A SER* 1.3 89.2 - - - +
235A ALA* 1.3 58.5 + - - +
236A ASN* 3.4 16.9 + - - +
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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