Contacts of the strand formed by residues 216 - 220 (chain A) in PDB entry 4ER5
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 TYR 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A VAL* 4.0 8.7 - - + -
171A LEU* 3.4 23.3 - - + -
174A ALA* 4.1 12.1 - - + -
181A HIS* 3.5 4.5 + - - -
182A HIS* 3.0 22.9 - - + +
199A ASP* 2.5 51.1 + - + -
202A PHE* 3.4 21.9 - + - -
203A ARG* 3.7 7.1 - - + +
213A HIS* 3.7 22.7 - + - -
214A ALA 3.7 11.7 - - - -
215A GLU* 1.3 76.6 - - - +
217A THR* 1.3 75.1 + - - +
218A LEU* 4.4 9.9 - - + -
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Residues in contact with THR 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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181A HIS* 2.8 28.6 + - - -
182A HIS 2.8 7.9 + - - -
183A TYR* 3.3 15.9 - - + +
184A GLY 3.1 23.9 + - - +
216A TYR* 1.3 74.8 + - - +
218A LEU* 1.3 69.8 + - - +
219A GLU* 3.4 30.0 + - + +
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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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164A SER* 4.9 3.6 - - - +
166A VAL 3.9 10.3 - - - +
167A GLY* 3.9 15.0 - - - +
170A VAL* 3.9 38.8 - - + -
171A LEU* 5.0 4.9 - - + -
184A GLY* 3.7 6.5 - - - -
195A ALA* 3.5 46.4 - - + +
198A MET* 4.8 1.8 - - + -
199A ASP* 4.5 15.4 - - + +
216A TYR* 4.4 15.0 - - + -
217A THR* 1.3 76.2 - - - +
219A GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 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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183A TYR* 3.3 16.1 - - - -
184A GLY 2.8 15.9 + - - +
185A VAL* 3.5 3.7 - - + -
186A GLU* 3.0 27.2 + - - +
192A ALA* 5.7 1.3 - - - +
217A THR* 3.4 24.3 - - + +
218A LEU* 1.3 72.8 - - - +
220A ARG* 1.3 65.2 + - - +
228A TRP* 4.1 7.7 + - + -
231A ARG* 2.9 44.4 + - - -
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Residues in contact with ARG 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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186A GLU 3.3 14.8 - - - -
187A LYS* 3.0 25.7 + - - +
188A ALA* 4.9 0.2 - - - +
189A ASP* 2.6 40.5 + - - +
192A ALA* 3.7 23.9 - - + +
219A GLU* 1.3 78.4 - - - +
221A GLY* 1.3 59.3 + - - +
228A TRP* 5.7 0.2 + - - -
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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