Contacts of the strand formed by residues 332 - 337 (chain B) in PDB entry 4PC0
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 ILE 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B TRP* 3.5 6.6 - - - -
326B SER* 2.9 28.7 + - - -
329B ASN* 3.0 29.8 + - + +
330B GLU 3.3 0.4 - - - -
331B THR* 1.3 82.3 - - - +
333B LEU* 1.3 64.8 + - - +
344B VAL* 3.9 6.5 - - + -
345B TRP 3.4 7.6 - - - +
346B ASP* 3.5 39.5 - - + +
367B LEU* 4.2 4.7 - - + -
382B TRP* 3.7 28.3 - - + -
388B TRP* 3.9 29.4 - - + -
409B TYR* 6.0 0.4 - - + -
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Residues in contact with LEU 333 (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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290B ALA* 4.1 16.6 - - + -
298B VAL* 4.2 11.2 - - + -
313B PHE* 4.0 20.9 - - + -
323B VAL* 4.1 23.6 - - + -
324B GLN 3.4 13.9 - - - +
325B TRP* 3.7 35.4 - - + +
326B SER 4.2 1.3 - - - +
331B THR 4.2 7.6 - - - +
332B ILE* 1.3 75.4 - - - +
334B ALA* 1.3 63.0 + - - +
344B VAL* 3.5 5.2 - - - +
345B TRP* 2.8 52.1 + - + +
347B LEU* 4.3 2.0 - - + -
382B TRP* 4.1 3.6 - - - -
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 3.3 6.4 - - - +
324B GLN 2.8 31.4 + - - -
333B LEU* 1.3 76.4 - - - +
335B SER* 1.3 62.1 + - - +
342B LEU* 3.9 11.7 - - + -
343B ASN 3.2 13.0 - - - +
344B VAL* 4.3 3.4 - - + -
345B TRP* 4.3 3.1 - - - -
380B PHE* 3.4 22.0 - - + -
382B TRP* 3.6 21.1 - - + +
390B ILE* 4.9 0.7 - - + -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B VAL* 3.8 23.2 - - - +
316B HIS* 2.8 28.9 + - - -
320B ILE* 4.2 4.3 - - - -
322B GLN 3.3 12.1 - - - -
323B VAL* 4.6 2.2 - - - -
334B ALA* 1.3 76.8 - - - +
336B SER* 1.3 64.5 + - - +
342B LEU* 3.5 3.3 - - - +
343B ASN 2.9 29.1 + - - -
345B TRP* 2.8 19.4 + - - -
380B PHE* 4.0 3.8 - - - -
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B HIS* 4.4 4.7 - - - -
320B ILE* 3.3 7.4 - - - +
321B PHE* 2.8 20.8 + - - -
322B GLN* 3.0 20.6 + - - +
335B SER* 1.3 77.7 - - - +
337B GLY* 1.3 60.1 + - - +
341B ARG 4.3 5.8 - - - -
342B LEU* 4.2 7.2 - - - -
377B ILE* 3.7 31.4 + - - +
379B ASP* 5.0 0.5 - - - -
380B PHE* 3.2 27.4 + - - -
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Residues in contact with GLY 337 (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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316B HIS* 5.1 2.2 + - - -
319B GLU 3.3 12.3 - - - -
320B ILE* 5.5 0.2 - - - -
321B PHE* 3.7 13.9 - - - -
336B SER* 1.3 78.5 - - - +
338B THR* 1.3 62.9 + - - -
339B ASP 3.1 10.5 + - - +
341B ARG 4.6 1.6 + - - -
376B LYS* 3.6 2.0 - - - +
377B ILE* 3.1 36.0 + - - +
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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
------------------------------------------------------------
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