Contacts of the strand formed by residues 326 - 331 (chain B) in PDB entry 5INQ
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 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B THR* 5.0 8.7 + - + +
129B TRP* 5.0 1.9 + - - -
130B ASN 4.2 6.4 + - - -
161B GLN* 4.2 6.8 - - - +
271B GLY 3.4 7.8 - - - +
272B ASP* 3.6 22.3 + - - +
306B THR* 2.6 35.8 + - + +
324B ARG* 4.0 12.5 + - - +
325B PHE* 1.3 78.3 - - - +
327B ARG* 1.3 63.6 + - - +
359B HIS* 2.8 30.2 + - - +
360B TRP 4.6 7.2 - - - +
362B LEU* 3.6 22.7 - - + +
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Residues in contact with ARG 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B THR* 5.1 0.6 - - - +
269B PHE* 4.0 5.7 - - - +
270B ALA* 3.5 2.4 - - - -
271B GLY 3.1 31.2 + - - +
273B THR* 3.8 27.4 + - + +
275B LEU* 3.5 28.6 + - - -
277B ASP* 2.9 30.9 + - - +
280B VAL* 3.7 25.5 - - - +
292B ASP* 4.0 4.6 + - - +
295B GLU* 5.7 0.2 + - - -
324B ARG* 2.8 68.7 + - - +
325B PHE 3.7 0.8 + - - -
326B ASP* 1.3 80.2 - - - +
328B ILE* 1.3 65.3 + - - +
329B PHE* 4.1 16.0 - - + -
362B LEU* 4.7 1.3 - - - +
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 3.8 42.2 - - + -
128B THR* 4.6 4.5 - - + -
268B ILE* 4.3 8.1 - - + -
269B PHE 3.3 9.2 - - - +
270B ALA* 4.0 5.8 - - + -
292B ASP* 3.3 9.9 + - - -
293B ALA* 3.0 46.4 + - + -
294B TRP 5.6 0.2 - - - +
327B ARG* 1.3 79.5 - - - +
329B PHE* 1.3 68.3 + - - +
330B PHE* 5.0 3.4 - - + -
342B LEU* 3.7 30.7 - - + -
362B LEU* 4.1 14.6 - - + +
364B CYS* 3.9 6.5 - - + -
366B LEU* 5.6 3.1 - - + -
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LEU* 3.8 23.8 - - + -
254B VAL* 5.0 2.2 - - + -
255B LEU* 4.6 11.0 - - + -
258B MET* 3.7 18.7 - - + +
268B ILE* 3.5 2.1 - - - +
269B PHE* 2.8 65.5 + + + +
273B THR* 4.5 2.9 - - + -
275B LEU* 4.3 17.3 - - + -
280B VAL* 5.7 2.7 - - + -
286B LEU* 4.2 24.5 - - + -
290B VAL* 4.0 7.4 - - + -
291B PHE 3.2 5.4 - - - +
292B ASP* 3.8 26.0 - - + -
327B ARG* 4.1 20.4 - - + -
328B ILE* 1.3 80.2 - - - +
330B PHE* 1.3 63.0 + - - +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B MET* 3.9 5.6 - - - -
267B VAL 3.2 10.5 - - - +
268B ILE* 4.3 5.6 - - + -
289B ASN 3.8 0.5 - - - +
290B VAL* 3.4 3.6 - - - -
291B PHE* 2.8 68.6 + + + -
292B ASP 4.4 0.2 - - - -
293B ALA* 3.9 23.1 - - + -
296B PHE* 4.0 15.0 - + + -
328B ILE* 5.0 2.7 - - + -
329B PHE* 1.3 78.4 - - - +
331B ARG* 1.3 63.0 + - - +
332B ALA* 4.6 5.4 - - + -
337B LEU* 3.7 46.7 - - + -
339B PRO* 3.6 33.9 - - + -
366B LEU* 5.0 2.5 - - + -
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B MET* 3.0 31.3 + - + +
259B GLN* 3.6 15.4 + - - -
261B ALA* 2.9 23.8 + - - +
262B PRO 2.6 31.1 + - - -
263B ASP* 3.7 14.9 + - - +
265B THR 2.9 17.8 + - - -
266B THR* 3.8 1.7 - - - +
267B VAL* 2.9 47.3 + - + +
289B ASN* 3.2 44.6 - - + +
290B VAL* 4.3 9.2 - - + -
330B PHE* 1.3 74.9 - - - +
332B ALA* 1.3 67.7 + - - +
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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