Contacts of the strand formed by residues 247 - 255 (chain A) in PDB entry 3HVK
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ILE* 3.8 19.0 - - + +
216A VAL* 3.4 16.1 - - - +
238A SER* 4.0 13.9 - - - +
239A SER 3.5 9.0 - - - +
240A TYR* 3.9 22.2 - - + +
246A VAL* 1.3 78.0 - - - +
248A ASP* 1.3 71.8 + - - +
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Residues in contact with ASP 248 (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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89A LYS* 2.8 28.5 + - + +
213A ASN* 3.1 20.5 + - - -
215A ILE* 3.1 20.0 + - - +
216A VAL* 2.9 35.9 + - + +
238A SER* 3.8 2.3 + - - -
239A SER* 2.8 29.3 + - - +
240A TYR 3.9 2.9 - - - -
241A LEU* 3.5 20.1 - - - +
246A VAL 3.4 1.4 + - - -
247A VAL* 1.3 81.1 - - - +
249A GLY* 1.3 68.6 + - - +
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Residues in contact with GLY 249 (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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89A LYS* 4.6 2.2 - - - +
213A ASN 3.4 9.9 + - - -
214A VAL* 3.2 26.0 + - - -
215A ILE* 3.7 3.6 - - - +
236A HIS* 4.0 12.1 - - - -
237A TYR 3.2 12.8 - - - -
239A SER* 4.0 4.7 - - - -
248A ASP* 1.3 83.5 + - - +
250A LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 250 (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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85A VAL* 4.7 2.0 - - + -
89A LYS* 3.8 31.6 - - + +
92A ILE* 3.6 30.1 - - + -
93A MET* 3.9 13.9 - - + +
182A PHE* 4.7 8.3 - - + -
210A LEU* 4.1 19.1 - - + -
211A ALA 3.3 5.8 - - - +
212A ASP* 3.4 39.5 - - + +
214A VAL* 4.2 3.1 - - - -
236A HIS* 3.5 4.3 + - - -
237A TYR* 2.9 41.3 + - + +
249A GLY* 1.3 73.4 - - - -
251A GLU* 1.3 58.6 + - - +
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Residues in contact with GLU 251 (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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209A LEU 3.6 1.4 - - - +
210A LEU* 3.4 6.2 - - - +
211A ALA* 2.9 37.3 + - + +
214A VAL* 3.9 19.1 - - + +
222A PHE* 4.9 2.6 - - + -
223A LEU* 3.6 14.1 - - + +
226A VAL* 4.6 9.4 - - + -
227A ARG* 2.9 43.0 + - - +
234A CYS* 3.4 22.6 - - + +
235A THR 3.6 12.8 - - - +
236A HIS* 2.9 18.4 + - - +
250A LEU* 1.3 72.8 - - - +
252A LYS* 1.3 66.7 + - - +
253A ALA* 4.1 2.0 + - + +
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Residues in contact with LYS 252 (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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96A VAL* 4.6 8.7 - - + +
99A GLU* 4.5 7.7 + - - -
100A TYR* 2.9 42.7 + - + +
208A VAL* 3.8 21.3 - - + -
209A LEU 3.2 4.5 - - - +
210A LEU* 4.1 7.8 - - + +
233A GLU 3.7 0.8 - - - +
234A CYS* 3.1 5.9 - - - +
235A THR* 2.9 46.9 + - - +
237A TYR* 3.1 39.2 + - + +
250A LEU 4.2 0.6 - - - -
251A GLU* 1.3 74.6 - - - +
253A ALA* 1.3 62.0 + - - +
254A ILE* 4.1 15.4 - - + +
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Residues in contact with ALA 253 (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 THR 3.8 0.2 - - - +
209A LEU* 2.8 44.3 + - + +
222A PHE* 5.0 4.0 - - + -
226A VAL* 4.1 16.6 - - + -
232A PHE* 3.8 20.2 - - + -
233A GLU 3.5 5.2 - - - -
234A CYS* 3.9 15.9 - - - -
251A GLU* 4.0 2.2 - - + +
252A LYS* 1.3 74.7 - - - +
254A ILE* 1.3 63.2 + - - +
255A TYR 3.8 1.8 + - - -
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Residues in contact with ILE 254 (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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100A TYR* 3.3 32.3 - - + +
206A GLY* 3.8 32.1 - - - +
207A THR 3.4 3.1 - - - +
208A VAL* 4.4 7.2 - - + -
232A PHE* 3.3 3.8 - - - -
233A GLU* 2.8 42.7 + - + +
252A LYS* 4.1 22.0 - - + +
253A ALA* 1.3 73.0 - - - +
255A TYR* 1.3 63.5 + - - +
256A GLN* 3.1 18.3 + - - +
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Residues in contact with TYR 255 (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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198A GLU* 3.4 35.7 + - + +
203A LEU* 3.6 34.1 - - + -
204A ARG* 3.4 22.9 - - - +
205A LYS 3.7 0.2 - - - -
206A GLY* 2.8 31.2 + - - -
207A THR* 2.9 21.1 + - + +
209A LEU* 5.7 0.7 - - + -
231A SER* 3.4 22.7 - - - -
232A PHE* 3.8 26.2 - + + -
253A ALA 3.8 2.6 + - - -
254A ILE* 1.3 71.1 - - - +
256A GLN* 1.3 61.3 + - - +
257A GLY* 3.4 33.4 - - - -
258A PRO* 3.4 21.6 - - + +
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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