Contacts of the strand formed by residues 323 - 327 (chain B) in PDB entry 1QXP
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 GLU 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B THR* 2.4 33.0 + - - +
283B ARG* 3.5 12.1 + - - -
284B MET 2.1 38.3 - - - +
285B ARG* 3.0 19.1 + - - +
291B VAL* 5.2 4.2 - - - +
319B MET* 3.2 42.9 - - + +
320B GLU* 3.4 30.3 + - - +
321B ASP 2.5 8.5 + - - +
322B GLY* 1.4 69.1 - - - -
324B PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR* 4.1 24.9 - + - -
282B ILE 3.9 0.2 - - - +
283B ARG* 3.4 1.6 - - - +
284B MET* 2.8 63.7 + - + +
290B GLU 5.6 0.2 - - - -
291B VAL* 4.4 21.5 - - + -
293B TRP* 3.1 37.9 - + + -
296B PRO* 5.7 2.9 - - + -
319B MET* 5.0 1.5 - - - -
322B GLY 4.6 6.5 - - - -
323B GLU* 1.3 60.8 - - - +
325B TRP* 1.4 56.9 + - - +
326B MET* 3.4 28.3 - - + -
333B ARG* 3.9 16.6 - - - -
334B GLU* 4.8 3.8 - - - -
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Residues in contact with TRP 325 (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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268B ASP* 4.2 3.6 - - + -
269B ALA* 3.8 18.4 - - - -
270B LYS* 3.6 42.8 - - + -
281B LEU* 3.5 44.4 - - + -
282B ILE 3.6 23.1 - - - -
283B ARG* 3.0 44.7 - - + +
293B TRP* 3.0 18.4 + - - -
296B PRO* 3.3 27.5 + - - +
297B TRP* 3.4 2.4 - - + -
304B TRP* 4.3 20.4 - + + -
314B GLN 4.2 18.0 + - - -
315B LEU 4.4 0.6 + - - -
319B MET* 3.5 25.2 - - + +
324B PHE* 1.4 71.6 - - - +
326B MET* 1.3 65.9 + - - +
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Residues in contact with MET 326 (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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281B LEU* 3.3 11.5 - - - +
282B ILE* 2.7 57.7 + - + +
284B MET* 3.8 13.5 - - + -
293B TRP* 3.3 43.5 - - + -
297B TRP* 3.8 6.7 - - - +
324B PHE* 3.4 29.4 - - + -
325B TRP* 1.3 82.0 - - - +
327B SER* 1.4 64.0 + - - +
330B ASP* 3.7 28.7 - - + -
333B ARG* 4.2 14.8 - - + -
334B GLU* 4.5 6.3 - - - +
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Residues in contact with SER 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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279B VAL* 5.7 3.1 - - - +
280B ASN 3.5 6.7 + - - -
281B LEU* 4.1 6.7 - - - -
282B ILE* 4.5 0.2 - - - +
293B TRP* 5.2 0.4 - - - -
297B TRP* 3.6 22.8 + - - -
298B SER* 6.0 1.8 - - - -
326B MET* 1.4 75.3 - - - +
328B PHE* 1.3 66.0 + - - +
329B ARG* 2.7 33.9 + - - +
330B ASP* 3.2 18.2 + - - +
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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