Contacts of the strand formed by residues 217 - 224 (chain A) in PDB entry 2EX4
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ASN* 3.1 6.9 - - - -
170A MET* 2.7 39.0 + - + +
172A GLN* 4.4 22.3 + - + -
207A ARG* 3.4 39.9 + - - +
211A LEU* 5.2 2.7 - - - -
213A ASP 5.8 1.8 - - - -
215A ILE 4.6 5.8 - - - -
216A TYR* 1.3 72.5 - - - +
218A VAL* 1.3 57.4 + - - +
219A TYR* 4.3 21.1 + - + -
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Residues in contact with VAL 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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137A TRP* 4.3 19.1 - - + -
167A LYS* 3.9 28.7 - - + -
168A ASP 3.2 11.9 - - - +
169A ASN* 4.0 14.1 - - - +
207A ARG* 3.5 6.3 - - - +
208A GLN* 2.8 50.4 + - + +
211A LEU* 3.3 25.4 - - + +
215A ILE* 5.7 1.3 - - + -
216A TYR 3.9 6.1 - - - +
217A HIS* 1.3 77.9 - - - +
219A TYR* 1.3 67.2 + - - +
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Residues in contact with TYR 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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166A ILE 3.6 1.7 - - - +
167A LYS* 3.4 4.2 - - - -
168A ASP 3.0 29.7 + - - +
170A MET* 3.5 19.7 - - + -
188A LEU* 3.4 38.9 - - + +
192A ARG* 5.2 0.4 - - - -
205A GLU* 4.1 22.4 - - + -
206A GLU 3.4 5.2 - - - -
207A ARG* 3.6 47.6 - - + +
217A HIS* 4.3 17.6 + - + -
218A VAL* 1.3 78.8 - - - +
220A SER* 1.3 61.5 + - - +
221A PHE* 3.6 24.7 - - + -
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Residues in contact with SER 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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45A SER* 5.8 0.9 - - - -
48A PHE* 3.8 34.9 - - - +
134A TRP* 5.9 0.4 - - - -
165A VAL* 4.7 2.7 - - - -
166A ILE 3.2 6.7 - - - -
167A LYS* 3.2 32.7 + - - +
204A ALA 3.8 0.3 - - - +
205A GLU* 3.3 6.2 - - - +
206A GLU* 2.8 41.2 + - - -
208A GLN* 5.7 0.9 - - - +
219A TYR* 1.3 72.4 - - - +
221A PHE* 1.3 62.6 + - - +
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Residues in contact with PHE 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* 4.3 3.4 - - - -
164A ILE 3.5 1.6 - - - +
165A VAL* 3.3 4.4 - - - +
166A ILE* 2.8 54.8 + - + +
170A MET* 3.8 22.9 - - + -
188A LEU* 3.9 15.0 - - + -
191A VAL* 4.1 13.9 - - + -
192A ARG* 4.4 12.3 - - + -
195A ILE* 4.2 12.8 - - + -
202A LEU* 3.8 26.0 - - + -
204A ALA 3.3 5.8 - - - -
205A GLU* 3.6 30.1 - - + -
219A TYR* 3.6 29.4 - - + -
220A SER* 1.3 73.2 - - - +
222A ALA* 1.3 58.9 + - - +
223A LEU* 3.9 11.4 - - + +
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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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48A PHE* 3.8 14.4 - - + -
52A PHE* 3.4 39.9 - - + -
163A ILE* 4.2 11.9 - - + -
164A ILE 3.4 4.3 - - - -
165A VAL* 4.3 2.2 - - + -
202A LEU* 3.7 0.2 - - - -
203A LEU* 2.7 33.8 + - + -
204A ALA 2.9 11.2 + - - +
221A PHE* 1.3 72.2 - - - +
223A LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 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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151A LEU* 4.7 0.4 - - + -
163A ILE* 3.2 4.4 - - - +
164A ILE* 2.8 53.5 + - + +
166A ILE* 3.9 29.2 - - + -
195A ILE* 3.6 33.7 - - + -
200A LEU* 3.9 30.1 - - + -
201A SER 3.2 13.7 - - - +
202A LEU* 3.7 19.1 - - + -
203A LEU* 3.7 5.1 - - - +
221A PHE* 3.9 6.3 - - + +
222A ALA* 1.3 84.9 - - - +
224A ARG* 1.3 65.2 - - - +
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Residues in contact with ARG 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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52A PHE* 4.6 6.3 - - - -
61A THR* 4.0 4.4 + - - +
155A LYS* 4.5 18.1 + - - -
158A LEU* 4.0 11.2 - - + -
161A ASN* 3.1 37.9 + - - +
162A GLY 3.0 24.9 + - - +
163A ILE* 3.3 14.6 - - - +
199A GLY 4.8 0.7 - - - +
200A LEU* 3.4 23.1 - - - +
201A SER* 2.8 39.9 + - - -
203A LEU* 3.8 29.9 - - + +
223A LEU* 1.3 78.3 - - - +
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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