Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 1EF1
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 GLU 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A SER* 2.9 27.9 + - - -
208A ILE 3.5 11.7 - - - +
209A LYS* 3.7 27.3 + - - +
213A GLY 3.5 2.4 + - - +
214A SER* 1.3 70.8 - - - +
216A LEU* 1.3 78.6 + - - +
217A TRP* 5.6 2.6 - - - -
230A GLN* 3.4 47.1 + - - +
272A PRO* 5.9 1.2 - - - +
217B TRP* 6.0 3.3 - - + -
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Residues in contact with LEU 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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207A SER* 3.6 6.1 - - - -
208A ILE* 2.8 37.8 + - + +
210A ASN* 4.1 17.9 - - + +
214A SER* 3.7 12.1 - - - +
215A GLU* 1.3 95.2 - - - +
217A TRP* 1.3 71.9 + - - +
227A ILE* 4.2 7.6 - - + -
228A TYR 3.6 13.5 - - - +
229A GLU* 4.6 1.3 - - + -
230A GLN* 4.4 8.1 - - - +
574C PHE* 3.5 36.1 - - + -
577C MSE 4.1 36.8 - - + +
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Residues in contact with TRP 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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205A TYR* 4.1 21.1 - - + -
206A PHE* 3.3 27.8 - - - -
207A SER* 3.7 24.5 - - - -
208A ILE* 4.3 3.8 - - - -
215A GLU* 5.6 1.8 - - - -
216A LEU* 1.3 80.3 - - - +
218A LEU* 1.3 60.4 + - - +
227A ILE* 3.4 7.8 - - - +
228A TYR* 2.8 47.6 + - + -
229A GLU 3.4 23.8 - - - -
230A GLN* 2.8 34.2 + - + +
233A ARG* 3.6 30.8 - - + +
215B GLU* 5.3 5.2 - - + -
217B TRP* 6.5 1.3 - + - -
230B GLN* 3.5 27.6 - - + -
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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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204A ASN 3.5 1.2 - - - +
205A TYR* 3.3 3.8 - - - -
206A PHE* 2.8 35.4 + - + +
208A ILE* 3.7 24.1 - - + +
217A TRP* 1.3 73.6 - - - +
219A GLY* 1.3 68.6 + - - +
220A VAL* 4.1 9.6 - - + -
225A LEU* 4.4 17.7 - - + -
226A ASN 3.4 16.2 - - - +
227A ILE* 3.6 16.4 - - + -
228A TYR* 4.6 1.3 - - - -
267A PHE* 4.9 2.0 - - + -
269A PHE* 3.7 31.6 - - + -
280A ILE* 3.8 30.5 - - + -
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Residues in contact with GLY 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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203A VAL* 3.8 18.4 - - - -
204A ASN 3.3 6.3 - - - -
205A TYR* 4.5 0.9 - - - -
218A LEU* 1.3 75.4 - - - +
220A VAL* 1.3 61.1 + - - -
221A ASP 4.2 0.2 - - - -
224A GLY 4.1 0.3 - - - +
225A LEU* 3.5 8.5 - - - +
226A ASN* 2.8 35.8 + - - +
228A TYR* 3.8 14.5 - - - -
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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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204A ASN* 2.8 47.2 + - + +
206A PHE* 3.6 29.4 - - + -
218A LEU* 4.1 10.5 - - + -
219A GLY* 1.3 73.5 - - - -
221A ASP* 1.3 64.1 + - - +
224A GLY 3.9 2.7 - - - -
225A LEU* 3.8 25.1 - - + -
242A TRP* 4.3 5.4 - - + -
280A ILE* 4.2 10.3 - - + -
283A LEU* 4.0 26.5 - - + +
284A CYS* 4.0 14.1 - - - +
287A ASN* 4.2 5.2 - - - +
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Residues in contact with ASP 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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201A TYR 5.0 1.7 - - - +
202A GLY 3.1 26.7 - - - +
203A VAL* 3.8 18.1 - - + +
204A ASN* 4.6 1.1 - - - +
220A VAL* 1.3 74.8 - - - +
222A ALA* 1.3 67.2 + - - +
223A LEU* 3.1 25.4 + - - +
224A GLY 3.2 17.3 + - - +
226A ASN* 4.0 18.6 + - - -
242A TRP* 3.3 20.4 - - - -
287A ASN* 3.5 11.7 - - - +
555C LYS* 5.3 6.9 + - - -
559C LEU* 5.9 1.6 - - - +
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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