Contacts of the helix formed by residues 217 - 231 (chain A) in PDB entry 1EBF
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 GLY 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ASP 3.5 9.3 + - - -
215A LEU 3.2 6.0 - - - -
216A ASN* 1.3 79.5 + - - +
218A LEU* 1.3 59.0 + - - +
219A ASP* 3.2 2.9 - - - -
220A VAL* 3.2 8.3 + - - +
221A ALA* 2.7 30.7 + - - +
243A VAL* 4.0 9.6 - - - +
244A GLN 5.0 0.2 - - - -
287A PHE* 4.4 22.9 - - - -
300A VAL* 4.5 0.6 - - - +
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Residues in contact with LEU 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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213A ASP 5.8 0.2 - - - +
216A ASN* 2.7 30.0 + - - +
217A GLY* 1.3 70.4 - - - +
219A ASP* 1.3 56.5 + - - +
221A ALA* 3.2 7.0 + - + +
222A ARG* 2.8 62.2 + - + +
238A PRO* 4.3 21.8 - - + +
239A THR* 4.8 12.8 - - + -
243A VAL* 5.3 0.9 - - - -
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 3.0 32.0 + - - +
173A PHE 4.5 4.5 - - - +
174A SER* 4.6 11.7 + - - +
213A ASP 4.8 12.0 + - - +
214A ASP* 5.4 9.2 - - - +
216A ASN* 4.2 1.6 + - - -
217A GLY* 3.2 1.3 - - - -
218A LEU* 1.3 79.7 - - - +
220A VAL* 1.3 64.0 + - + +
222A ARG* 3.3 15.4 + - - +
223A LYS* 3.3 33.4 + - - +
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Residues in contact with VAL 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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173A PHE* 4.2 22.8 - - + +
174A SER* 3.5 35.7 - - - +
177A LEU* 4.0 16.2 - - + -
217A GLY* 3.2 8.5 + - - +
219A ASP* 1.3 79.2 - - + +
221A ALA* 1.3 59.6 + - - +
223A LYS* 3.4 8.7 + - - +
224A VAL* 2.8 27.0 + - - +
287A PHE* 4.1 8.1 - - + +
288A ILE 4.4 3.6 - - - +
289A GLY* 4.3 7.9 - - - +
300A VAL* 3.5 25.8 - - + -
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Residues in contact with ALA 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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217A GLY 2.7 17.7 + - - +
218A LEU* 3.5 9.6 - - + +
220A VAL* 1.3 76.2 - - - +
222A ARG* 1.3 61.5 + - - +
224A VAL* 3.0 20.6 - - - +
225A THR* 2.8 20.3 + - - -
238A PRO* 3.6 25.1 - - + +
241A PHE* 3.6 2.1 - - + -
243A VAL* 3.8 21.8 - - + -
300A VAL* 3.9 2.2 - - - -
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 4.1 25.9 - - + +
118A LYS* 3.8 43.4 + - - +
121A SER* 3.1 46.2 + - - +
122A SER* 5.4 2.8 - - - -
218A LEU* 2.8 58.3 + - + +
219A ASP* 3.3 6.2 + - - +
221A ALA* 1.3 76.6 - - - +
223A LYS* 1.3 61.4 + - - +
225A THR* 3.3 5.8 + - - -
226A ILE* 3.2 29.6 + - - +
238A PRO* 4.4 13.3 - - + +
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Residues in contact with LYS 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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117A LYS* 3.6 11.0 - - + +
145A THR 3.4 28.0 - - - +
146A VAL* 4.1 13.8 - - + +
147A GLY 4.7 7.7 - - - +
173A PHE* 3.0 47.1 + - + +
174A SER* 5.1 0.4 - - - +
219A ASP* 3.3 38.1 + - - +
220A VAL* 3.7 7.0 - - - +
221A ALA 3.3 0.2 - - - -
222A ARG* 1.3 75.8 - - - +
224A VAL* 1.3 58.9 + - - +
226A ILE* 3.4 9.9 + - - +
227A VAL* 3.0 33.9 + - - +
319A ASN* 4.8 1.8 - - - +
338A GLY 4.8 8.3 + - - -
2109A NAD 5.2 11.3 - - - -
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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
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173A PHE* 5.4 5.1 - - + -
220A VAL* 2.8 22.4 + - + +
221A ALA* 3.0 23.1 - - - +
223A LYS* 1.3 71.4 - - - +
225A THR* 1.3 56.6 + - - +
226A ILE 3.1 0.2 - - - -
227A VAL* 4.3 6.7 - - - +
228A GLY* 2.7 30.3 + - - -
241A PHE* 3.7 3.6 - - + -
289A GLY* 4.6 10.3 - - - -
290A LYS 3.9 14.8 - - - +
291A VAL* 4.1 7.9 - - + -
298A VAL* 3.2 30.0 - - + +
299A SER 4.4 4.0 - - - +
300A VAL* 3.4 15.7 - - + -
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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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121A SER* 4.1 14.8 - - - -
221A ALA 2.8 19.2 + - - -
222A ARG* 3.3 12.1 - - - -
224A VAL* 1.3 78.0 - - - +
226A ILE* 1.3 56.4 + - - +
228A GLY* 4.0 0.5 - - - -
229A ARG* 3.1 62.8 + - - +
235A VAL* 4.0 18.8 - - + +
238A PRO* 3.4 24.9 - - - +
241A PHE* 3.5 8.2 - - - -
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Residues in contact with ILE 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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117A LYS* 4.2 19.3 - - + +
120A PHE* 3.5 34.5 - - + +
121A SER* 4.4 0.4 - - - -
127A TRP* 3.6 13.5 - - + -
142A HIS* 3.7 26.7 - - + +
145A THR* 3.8 23.3 - - - -
146A VAL* 4.0 13.7 - - + -
222A ARG 3.2 16.8 + - - +
223A LYS* 3.5 10.3 - - - +
224A VAL 3.1 0.4 - - - -
225A THR* 1.3 74.7 - - - +
227A VAL* 1.3 64.4 + - - +
229A ARG 3.3 1.2 + - - -
230A ILE* 3.1 33.9 + - + +
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Residues in contact with VAL 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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146A VAL* 3.9 27.6 - - + -
152A ILE* 5.7 0.7 - - + -
153A ILE* 5.7 0.7 - - + -
156A LEU* 4.3 13.0 - - + -
169A ILE* 3.4 40.4 - - + -
173A PHE* 4.6 11.9 - - + -
223A LYS 3.0 19.4 + - - +
224A VAL* 4.1 5.8 - - - +
226A ILE* 1.3 72.6 - - + +
228A GLY* 1.3 66.8 + - - +
230A ILE* 3.3 10.2 + - + +
231A SER* 2.9 27.0 + - - -
291A VAL* 4.5 6.1 - - + -
321A ILE* 4.6 4.5 - - + -
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Residues in contact with GLY 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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224A VAL 2.7 22.6 + - - -
225A THR 4.0 0.7 - - - -
227A VAL* 1.3 73.6 - - - +
229A ARG* 1.3 58.0 + - - +
231A SER* 3.1 10.0 + - - -
232A GLY 3.2 0.2 + - - -
233A VAL* 2.8 33.6 + - - +
235A VAL* 4.6 1.1 - - - -
291A VAL* 4.0 22.1 - - - +
298A VAL* 4.5 5.2 - - - -
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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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120A PHE 3.2 24.4 + - - -
121A SER* 4.0 0.2 - - - +
122A SER 2.6 31.9 + - - +
123A ASP 3.6 15.1 + - - -
124A LEU* 3.6 19.8 - - + +
127A TRP* 3.7 45.7 + - + +
225A THR* 3.1 34.8 + - - +
226A ILE 3.8 1.3 - - - +
227A VAL 3.3 0.2 - - - -
228A GLY* 1.3 73.0 - - - +
230A ILE* 1.3 65.3 + - - +
232A GLY* 3.1 11.8 + - - -
233A VAL 3.3 16.8 - - - +
234A GLU* 4.8 0.4 - - - -
235A VAL* 2.9 23.2 + - + +
236A GLU 2.9 22.0 + - - -
237A SER* 4.3 0.6 - - - +
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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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127A TRP* 3.8 15.9 - - + -
142A HIS* 4.2 3.8 - - - +
153A ILE* 3.9 38.6 - - + -
156A LEU* 3.8 36.3 - - + -
157A ARG* 4.2 22.4 - - + +
160A ILE* 4.5 17.3 - - + +
226A ILE* 3.1 28.1 + - + +
227A VAL* 3.5 11.7 - - - +
228A GLY 3.2 0.2 - - - -
229A ARG* 1.3 77.7 - - - +
231A SER* 1.3 60.1 + - - +
232A GLY* 3.1 5.2 + - - -
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Residues in contact with SER 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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156A LEU* 5.3 0.2 - - - +
160A ILE* 5.6 1.1 - - - -
166A VAL* 3.4 43.4 + - - +
169A ILE* 3.4 13.5 - - - +
227A VAL* 2.9 15.1 + - - +
228A GLY* 3.1 13.2 + - - -
230A ILE* 1.3 77.0 - - - +
232A GLY* 1.3 59.2 + - - +
233A VAL 4.7 0.2 - - - -
291A VAL* 4.3 4.5 - - - +
293A VAL* 3.7 24.4 - - - +
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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