Contacts of the strand formed by residues 247 - 256 (chain A) in PDB entry 3VI4
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 ASP 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A VAL* 3.3 8.5 - - - +
238A GLY 2.8 35.8 + - - +
239A GLU* 2.7 15.9 - - - +
240A PHE* 3.4 5.3 + - - +
241A SER* 3.1 18.7 + - - -
246A GLU* 1.3 71.9 - - - +
248A PHE* 1.3 64.7 + - - +
264A ILE* 4.2 13.5 - - + -
265A LEU 3.3 6.7 - - - +
266A ASN* 3.3 10.6 - - - +
267A GLY 3.0 20.9 + - - +
273A LEU* 3.8 2.2 - - + +
2001A CA 2.3 30.3 - - - -
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Residues in contact with PHE 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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173A THR* 4.2 9.4 - - + -
177A ARG* 4.9 6.3 - - - -
179A VAL* 3.7 37.0 - - + -
192A ILE* 4.4 6.7 - - + -
194A SER* 4.0 21.8 - - - -
217A LEU* 4.8 3.4 - - + -
235A VAL* 5.9 2.0 - - + -
236A ALA 3.7 2.9 - - - +
237A VAL* 4.0 4.7 - - + -
246A GLU 3.9 12.3 - - - -
247A ASP* 1.3 75.9 - - - +
249A VAL* 1.3 64.5 + - - +
250A ALA* 4.0 1.3 + - + -
263A THR 3.5 1.0 - - - +
264A ILE* 3.0 7.0 - - - -
265A LEU* 2.7 55.3 + - + +
266A ASN 4.6 0.4 - - - -
267A GLY* 3.7 27.6 - - - -
270A ILE* 3.9 35.4 - - + -
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 3.1 10.7 - - - +
236A ALA* 2.6 49.7 + - + +
240A PHE* 3.7 29.4 - - + -
247A ASP 5.2 0.4 - - - +
248A PHE* 1.3 74.8 - - - +
250A ALA* 1.3 61.8 + - - +
262A VAL* 3.6 22.4 - - + -
263A THR 3.4 2.5 - - - -
264A ILE* 4.0 15.7 - - + -
289A VAL* 3.7 23.6 - - + -
291A ALA* 4.6 3.6 - - + -
302A LEU* 3.8 16.2 - - + -
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 3.7 25.4 - - + -
231A LEU* 3.6 25.1 - - + -
234A SER 3.5 4.3 - - - +
235A VAL* 4.2 1.1 - - + -
248A PHE* 4.0 1.3 + - + +
249A VAL* 1.3 75.5 - - - +
251A GLY* 1.3 63.4 + - - +
252A VAL* 3.4 4.2 - - - +
262A VAL* 3.5 6.3 - - - -
263A THR* 2.9 39.7 + - - +
265A LEU* 4.9 5.6 - - + -
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Residues in contact with GLY 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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230A TYR 3.4 2.8 - - - +
232A GLY 2.8 31.5 + - - -
233A TYR 3.4 1.7 + - - -
234A SER* 2.9 20.6 + - - -
249A VAL 4.3 0.2 - - - -
250A ALA* 1.3 71.6 - - - +
252A VAL* 1.3 59.3 + - - +
253A PRO* 3.7 6.3 - - - -
261A TYR 4.3 1.1 - - - -
262A VAL* 4.8 1.1 - - - -
286A GLY* 3.4 28.0 - - - -
289A VAL* 4.5 5.7 - - - +
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Residues in contact with VAL 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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229A SER* 3.5 28.0 - - - +
230A TYR 3.9 0.4 - - - -
231A LEU* 3.6 22.4 - - + -
250A ALA 3.4 10.8 - - - +
251A GLY* 1.3 78.2 - - - +
253A PRO* 1.3 66.0 - - - +
254A LYS 3.3 1.1 - - - -
255A GLY* 3.2 9.4 + - - -
261A TYR* 2.9 66.2 + - + +
263A THR* 3.5 19.1 - - - +
286A GLY* 4.4 1.2 + - - -
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Residues in contact with PRO 253 (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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229A SER 3.7 1.8 - - - +
230A TYR* 3.3 20.9 - - + +
233A TYR* 3.5 17.9 - - + -
252A VAL* 1.3 86.6 - - - +
254A LYS* 1.3 60.9 + - + +
255A GLY 3.4 0.9 - - - -
258A THR 3.7 11.8 - - - +
260A GLY* 3.6 13.4 - - - -
284A TYR* 3.2 50.8 - - + -
285A PHE 3.2 18.2 + - - +
286A GLY 3.7 14.8 - - - +
264B PHE* 5.2 1.9 - - - -
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Residues in contact with LYS 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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228A ASP* 3.3 32.2 + - - +
229A SER* 3.2 11.4 + - - +
230A TYR* 3.4 37.8 + - + -
253A PRO* 1.3 78.7 - - - +
255A GLY* 1.3 62.2 + - - +
256A ASN 3.7 1.6 - - - -
257A LEU* 4.5 0.7 + - - -
258A THR* 3.4 27.7 + - + +
284A TYR* 4.9 2.5 - - + +
228B PRO* 3.9 24.4 - - - +
262B PHE 4.7 5.8 - - - -
263B HIS* 4.1 2.6 + - - -
264B PHE* 3.7 31.4 - - + -
267B ASP* 3.3 35.9 + - - +
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Residues in contact with GLY 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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226A TYR* 5.7 3.5 - - - -
229A SER* 3.5 25.1 + - - -
252A VAL 3.2 10.9 + - - -
253A PRO 3.4 1.4 - - - -
254A LYS* 1.3 79.6 - - - +
256A ASN* 1.3 58.4 + - - +
257A LEU 3.6 3.7 + - - -
259A TYR 3.6 1.8 + - - -
261A TYR* 3.6 23.8 - - - -
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Residues in contact with ASN 256 (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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255A GLY* 1.3 69.9 - - - +
257A LEU* 1.3 73.9 + - - +
258A THR 3.2 0.2 - - - -
259A TYR* 3.0 34.9 + - + +
260A GLY 4.5 3.8 - - - +
261A TYR* 4.1 13.8 - - + -
277A SER* 4.5 8.8 + - - +
2007A NAG 1.4 70.5 + - + +
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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