Contacts of the strand formed by residues 216 - 225 (chain A) in PDB entry 4H5T
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 ILE 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A THR 3.5 2.3 - - - +
212A ILE* 3.3 4.9 - - - -
213A GLU* 2.7 69.6 + - + +
214A ASP 3.1 3.2 - - - +
215A GLY* 1.3 76.2 - - - +
217A PHE* 1.3 70.6 + - - +
218A GLU* 5.4 0.6 - - - +
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Residues in contact with PHE 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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177A THR* 3.6 31.6 - - + +
180A ALA* 3.7 15.7 - - + -
181A ILE* 4.1 10.8 - - + -
186A ASP* 3.2 33.2 - - + -
210A LEU* 3.7 34.8 - - + -
211A THR 3.7 0.7 - - - -
212A ILE* 3.2 41.7 - - + -
215A GLY 4.0 11.0 + - - -
216A ILE* 1.3 84.1 - - - +
218A GLU* 1.3 60.5 + - - +
219A VAL* 4.3 1.2 - - - +
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Residues in contact with GLU 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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210A LEU* 3.3 5.2 - - - -
211A THR* 2.7 47.7 + - + +
216A ILE 5.4 0.4 - - - +
217A PHE* 1.3 75.8 - - - +
219A VAL* 1.3 70.8 + - - +
220A LYS* 3.2 34.2 + - + +
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Residues in contact with VAL 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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148A ALA* 4.3 13.7 - - + +
174A ASN* 3.9 24.2 - - + +
177A THR* 5.3 1.6 - - - +
209A ILE 3.6 6.3 - - - +
210A LEU* 3.9 18.2 - - + -
217A PHE 5.8 0.9 - - - +
218A GLU* 1.3 75.6 - - - +
220A LYS* 1.3 59.6 + - - +
221A SER* 4.1 5.8 - - - +
222A THR* 3.5 32.8 - - + -
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Residues in contact with LYS 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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192A GLU* 4.9 2.9 + - - -
194A ASN* 3.8 8.9 - - - +
209A ILE* 2.9 15.6 + - + +
210A LEU 4.4 0.9 - - - -
211A THR* 2.7 51.0 + - - +
218A GLU* 3.2 28.9 - - - +
219A VAL* 1.3 73.4 - - - +
221A SER* 1.3 62.4 + - - +
323A ASP 4.2 8.7 - - - +
324A ALA* 3.8 31.8 + - + +
326A LEU* 4.7 7.5 - - - +
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Residues in contact with SER 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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207A VAL 4.7 0.2 - - - -
209A ILE* 3.1 31.4 + - - +
219A VAL* 3.5 3.0 - - - +
220A LYS* 1.3 78.1 - - - +
222A THR* 1.3 69.5 + - - +
320A ALA* 2.6 36.0 + - - +
323A ASP* 3.7 22.4 - - - -
324A ALA* 3.4 10.6 - - - +
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Residues in contact with THR 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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148A ALA* 4.2 15.0 - - + +
149A TYR* 4.8 18.4 - - + +
206A ASP* 6.5 0.7 - - - -
207A VAL 3.2 7.9 - - - -
208A SER* 3.7 18.4 - - - +
219A VAL* 3.5 23.1 - - + -
221A SER* 1.3 82.2 - - - +
223A ALA* 1.3 62.9 + - - +
320A ALA* 4.8 1.3 - - - -
323A ASP* 5.1 5.4 - - - +
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Residues in contact with ALA 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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205A PHE 3.9 0.2 - - - +
206A ASP* 3.6 6.8 - - - +
207A VAL* 2.8 28.4 + - + +
222A THR* 1.3 75.4 - - - +
224A GLY* 1.3 59.9 + - - +
316A PRO* 3.1 33.4 - - + +
319A LYS* 4.4 10.8 - - + -
320A ALA* 3.7 16.1 - - + +
323A ASP* 5.6 0.2 - - - +
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Residues in contact with GLY 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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205A PHE* 3.1 15.5 - - - -
206A ASP* 4.5 0.4 - - - -
207A VAL 4.5 0.4 - - - -
223A ALA* 1.3 80.2 - - - +
225A ASP* 1.3 64.2 + - - +
316A PRO* 3.5 24.6 - - - +
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Residues in contact with ASP 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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205A PHE* 3.0 36.6 + - + -
206A ASP* 5.9 0.7 - - - -
224A GLY* 1.3 75.5 - - - +
226A THR* 1.3 64.3 + - - +
227A HIS* 2.9 32.9 + - - +
228A LEU* 3.6 30.8 + - + +
316A PRO* 5.5 2.0 - - + -
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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