Contacts of the strand formed by residues 216 - 223 (chain A) in PDB entry 5E1O
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 HIS 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ASN* 3.2 2.8 - - - -
169A MET 2.9 34.8 + - - +
206A ARG* 3.2 44.7 + - - +
210A LEU* 5.3 2.5 - - - -
212A ASP 5.5 3.7 + - - -
214A ILE 4.1 8.1 - - - -
215A TYR* 1.3 77.4 - - - +
217A VAL* 1.3 59.8 + - - +
218A TYR* 3.9 22.5 + - + -
5D ILE* 5.1 8.8 - - + +
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Residues in contact with VAL 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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136A TRP* 4.0 21.3 - - + +
166A LYS* 4.0 26.9 - - + -
167A ASP 3.3 11.4 - - - +
168A ASN* 3.5 26.0 - - - +
206A ARG* 3.7 2.7 - - - +
207A GLN* 2.8 45.0 + - + +
210A LEU* 3.7 24.9 - - + +
214A ILE* 5.1 2.7 - - + -
215A TYR 3.6 7.6 - - - +
216A HIS* 1.3 75.8 - - - +
218A TYR* 1.3 65.0 + - - +
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Residues in contact with TYR 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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165A ILE 3.7 1.0 - - - +
166A LYS* 3.2 4.7 - - - +
167A ASP 3.0 31.3 + - - +
169A MET* 3.6 24.9 - - + -
187A LEU* 3.8 32.1 - - + +
204A GLU* 4.4 14.4 - - + -
205A GLU* 3.3 6.5 - - - -
206A ARG* 3.6 43.9 + - + -
207A GLN* 4.6 0.4 - - - +
216A HIS* 3.9 20.0 + - + -
217A VAL* 1.3 78.7 - - - +
219A SER* 1.3 62.5 + - - +
220A PHE* 4.2 12.8 - - + -
321A UNX 3.6 23.2 - - - -
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Residues in contact with SER 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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45A SER* 5.8 0.9 - - - -
48A PHE* 3.8 33.4 - - - +
133A TRP* 5.6 0.3 - - - -
164A VAL* 4.9 2.0 - - - -
165A ILE 3.2 7.0 - - - -
166A LYS* 3.2 34.5 + - - +
204A GLU* 3.1 6.9 - - - +
205A GLU* 2.9 39.0 + - - -
207A GLN* 5.4 0.9 + - - +
218A TYR* 1.3 73.8 - - - +
220A PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 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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48A PHE* 3.9 3.8 - - - -
163A ILE 3.6 0.7 - - - +
164A VAL* 3.2 7.1 - - - +
165A ILE* 2.8 49.1 + - + +
169A MET* 3.6 25.8 - - + -
187A LEU* 3.5 25.8 - - + -
190A VAL* 4.0 18.4 - - + -
191A ARG* 4.4 12.8 - - + -
194A ILE* 4.3 8.5 - - + -
201A LEU* 4.2 13.7 - - + -
203A ALA 3.4 3.6 - - - +
204A GLU* 3.4 36.8 - - + -
218A TYR* 4.2 10.5 - - + -
219A SER* 1.3 75.2 - - - +
221A ALA* 1.3 59.4 + - - +
222A LEU* 4.0 17.8 - - + +
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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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48A PHE* 3.7 12.0 - - + -
52A PHE* 3.5 39.0 - - + -
162A ILE* 4.6 4.5 - - + -
163A ILE 3.4 5.4 - - - +
164A VAL* 4.5 6.1 - - + -
201A LEU* 3.7 0.9 - - - -
202A LEU* 2.7 37.4 + - + -
203A ALA 3.0 9.3 + - - +
220A PHE* 1.3 74.1 - - - +
222A LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 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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150A LEU* 4.8 0.4 - - + -
162A ILE* 3.3 6.4 - - - +
163A ILE* 2.7 52.1 + - + +
165A ILE* 3.8 29.4 - - + -
194A ILE* 3.8 27.6 - - + -
199A LEU* 4.0 27.1 - - + -
200A SER 3.3 10.1 - - - +
201A LEU* 3.9 13.5 - - + -
202A LEU* 4.1 2.4 - - - +
220A PHE* 4.0 16.6 - - + +
221A ALA* 1.3 83.9 - - - +
223A ARG* 1.3 68.4 + - - +
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Residues in contact with ARG 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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154A LYS* 4.4 14.6 - - - +
157A LEU* 4.8 7.8 - - + +
161A GLY 3.9 17.5 - - - +
162A ILE* 5.0 0.4 - - + -
198A GLY 4.5 1.0 - - - +
199A LEU* 3.4 24.4 - - - +
200A SER* 2.7 48.9 + - - +
202A LEU* 3.5 37.2 - - + -
222A LEU* 1.3 74.8 - - - +
307A UNX 3.0 29.0 - - - -
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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