Contacts of the strand formed by residues 214 - 221 (chain A) in PDB entry 5H2U
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 VAL 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A LEU* 3.2 4.6 - - - -
210A TRP* 2.8 63.3 + - + +
213A ARG* 1.3 79.6 - - + +
215A GLN* 1.3 71.9 - - - +
216A VAL* 3.4 4.3 + - + +
251A TYR* 3.8 26.0 - - + +
265A GLU* 4.8 10.8 - - + +
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Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A GLU* 4.2 7.2 - - - +
208A GLY 3.6 7.2 - - - +
209A LEU* 4.2 15.0 - - + -
213A ARG 3.4 6.1 + - - +
214A VAL* 1.3 76.9 - - - +
216A VAL* 1.3 63.9 + - - +
265A GLU* 3.7 6.2 - - - +
266A LEU* 3.2 42.7 + - + +
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Residues in contact with VAL 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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191A PHE* 4.6 3.1 - - + -
207A GLU 3.7 0.9 - - - -
208A GLY 2.7 49.5 + - - +
209A LEU 3.6 11.2 - - - +
210A TRP* 4.0 4.0 - - + +
214A VAL* 3.7 13.0 - - + +
215A GLN* 1.3 80.5 - - - +
217A ALA* 1.3 57.3 + - - +
218A ILE* 3.8 21.5 - - + -
251A TYR* 3.8 31.9 - - + -
263A ILE* 3.5 8.3 - - + -
264A THR 3.2 15.0 - - - +
265A GLU* 4.6 1.3 - - - -
266A LEU* 3.7 13.8 - - - +
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Residues in contact with ALA 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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197A LEU* 4.9 0.4 - - + -
205A VAL* 4.7 2.0 - - + -
206A PHE 3.3 8.1 - - - +
216A VAL* 1.3 74.0 - - - +
218A ILE* 1.3 60.8 + - - +
263A ILE* 3.3 6.9 - - - +
264A THR* 2.8 32.3 + - - +
265A GLU 4.2 1.1 - - - +
266A LEU* 3.9 6.3 - - + +
501A 1N1 3.1 57.8 - - + +
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Residues in contact with ILE 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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191A PHE* 4.2 13.9 - - + -
192A THR 3.7 22.9 - - - +
193A LEU* 3.8 18.4 - - + -
204A GLU 3.6 1.4 - - - +
205A VAL* 3.4 2.9 - - - -
206A PHE* 2.8 47.4 + - + +
207A GLU 5.2 0.2 - - - -
208A GLY* 4.1 4.7 - - - -
216A VAL* 3.8 20.2 - - + -
217A ALA* 1.3 79.4 - - - +
219A LYS* 1.3 61.0 + - - +
220A VAL* 3.8 6.4 + - + -
261A TYR* 3.6 38.4 - - + -
262A ILE 3.7 2.2 - - - -
263A ILE* 3.7 15.3 - - + -
501A 1N1 4.0 1.6 - - - -
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Residues in contact with LYS 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A PHE* 3.4 55.4 - - + -
204A GLU 3.3 3.4 - - - +
205A VAL* 4.1 8.5 - - + +
218A ILE* 1.3 70.9 - - - +
220A VAL* 1.3 61.7 + - - +
221A ILE* 3.9 8.2 + - + +
260A VAL 3.4 1.6 - - - +
261A TYR* 3.3 6.9 - - - -
262A ILE* 2.9 41.0 + - + +
317A ASN* 5.1 3.2 - - - +
330A ASP* 2.8 28.8 + - - -
333A LEU* 3.6 14.1 - - + -
501A 1N1 3.1 52.2 + - + +
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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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193A LEU* 4.2 8.7 - - + -
203A GLY* 3.5 6.6 - - - -
204A GLU* 2.9 39.8 + - - +
206A PHE* 3.6 32.8 - - + -
218A ILE* 4.1 6.3 - - + +
219A LYS* 1.3 74.7 - - - +
221A ILE* 1.3 58.8 + - - +
222A SER 4.2 1.1 + - - +
259A PRO* 3.5 34.8 - - + -
260A VAL 3.4 2.9 - - - -
261A TYR* 3.8 22.2 - - + -
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Residues in contact with ILE 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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202A PHE* 3.2 28.9 - - + +
219A LYS* 4.2 14.1 - - + +
220A VAL* 1.3 75.2 - - - +
222A SER* 1.3 71.6 + - - +
223A ARG 3.5 0.2 + - - -
225A ASN* 4.4 4.3 - - + -
226A LEU* 3.7 28.9 - - + +
259A PRO* 4.0 1.6 - - - -
260A VAL* 2.8 40.4 + - + +
262A ILE* 3.5 31.2 - - + -
333A LEU* 4.2 17.7 - - + -
336A LEU* 5.2 0.2 - - + -
337A ILE* 4.3 20.4 - - + -
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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