Contacts of the strand formed by residues 335 - 339 (chain B) in PDB entry 4PGF
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 ARG 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASN* 3.6 12.9 + - - +
291B LYS 3.9 1.2 - - - +
292B ASP* 2.6 44.3 + - - +
293B ASP* 2.5 40.2 + - - +
294B ALA 3.5 2.9 + - - -
327B ARG* 3.4 42.1 - - + +
328B TYR 3.1 17.3 - - - +
329B ARG* 3.8 25.0 - - + +
333B GLY 4.1 9.4 + - - -
334B ARG* 1.3 76.7 - - - +
336B ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B PHE* 4.2 20.6 - - + +
290B MET* 3.7 36.8 - - + +
291B LYS 4.3 1.6 - - - +
294B ALA* 3.7 13.9 - - + +
296B VAL* 4.0 23.1 - - + -
311B LEU* 4.7 11.4 - - + -
326B ASP 3.7 0.5 - - - +
327B ARG* 3.4 1.7 - - - -
328B TYR* 2.8 45.3 + - + +
330B LEU* 4.0 23.3 - - + -
334B ARG* 6.0 0.9 - - + -
335B ARG* 1.3 81.6 - - - +
337B ILE* 1.3 70.3 + - - +
338B LEU* 3.8 2.9 + - + +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 4.5 22.0 - - + -
207B THR* 4.2 15.0 - - + -
293B ASP* 3.7 39.0 - - + +
294B ALA 2.9 14.3 + - - +
295B ILE* 3.4 17.0 - - + +
296B VAL* 2.9 28.6 + - - +
321B ILE* 6.0 0.4 - - + -
325B VAL* 4.3 10.8 - - + -
326B ASP 3.3 9.6 - - - +
327B ARG* 3.9 16.4 - - + +
336B ILE* 1.3 73.9 - - - +
338B LEU* 1.3 60.5 + - - +
339B LEU* 4.1 20.0 - - + -
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL* 3.6 27.6 - - + +
306B ILE* 4.2 20.4 - - + -
308B VAL* 3.5 37.7 - - + -
311B LEU* 4.0 17.3 - - + -
324B GLN 4.6 0.2 - - - -
325B VAL* 3.7 0.2 - - - -
326B ASP* 2.9 36.2 + - + +
328B TYR* 4.0 22.4 - - + +
336B ILE* 3.8 3.4 + - + -
337B ILE* 1.3 73.8 - - - +
339B LEU* 1.3 80.1 - - - +
341B GLU* 4.1 11.2 + - - -
342B GLY 4.3 4.0 - - - +
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Residues in contact with LEU 339 (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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203B ILE* 4.2 15.0 - - + -
206B ALA* 3.7 30.1 - - + -
207B THR* 3.9 16.2 - - + -
295B ILE* 4.3 15.7 - - + -
296B VAL 3.2 11.7 + - - +
297B CYS* 4.0 22.4 - - + +
324B GLN 3.5 7.9 - - - +
325B VAL* 4.1 5.8 - - + -
337B ILE* 4.1 8.5 - - + -
338B LEU* 1.3 81.7 - - - +
340B ALA* 1.3 58.4 + - - +
341B GLU 2.8 17.0 + - - -
342B GLY* 2.9 14.2 + - - -
343B ARG 4.4 0.9 - - - +
345B VAL* 3.7 26.7 - - + -
349B CYS* 4.3 1.3 - - - -
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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
------------------------------------------------------------
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