Contacts of the strand formed by residues 338 - 345 (chain B) in PDB entry 3C0M
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 ASN 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B ARG* 3.3 35.8 + - - +
320B GLY 3.4 9.2 - - - +
321B PHE* 3.5 5.0 - - - +
336B ARG 4.0 0.2 - - - +
337B PRO* 1.3 69.4 - - - +
339B TRP* 1.3 67.3 + - - +
340B ASN* 4.2 1.6 + - - +
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Residues in contact with TRP 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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125B TYR* 3.6 22.7 - - + +
319B SER* 3.3 5.2 - - - -
320B GLY 2.6 34.0 + - - +
322B LEU* 3.9 22.4 - - + -
329B TRP* 3.3 64.5 - + - -
331B THR* 5.6 0.2 - - - -
333B PRO* 4.6 8.3 - - + -
337B PRO* 3.2 38.0 + - + -
338B ASN* 1.3 76.1 - - - +
340B ASN* 1.3 83.3 + - - +
341B HIS* 4.4 1.4 + - + +
371B TRP* 4.2 12.6 - + - -
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Residues in contact with ASN 340 (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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317B THR* 4.2 12.2 - - - +
318B LEU 3.7 3.8 - - - -
319B SER* 3.1 21.8 + - - -
338B ASN 4.2 1.5 + - - +
339B TRP* 1.3 85.1 + - - +
341B HIS* 1.3 67.1 + - - +
342B THR* 5.6 0.8 + - - -
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Residues in contact with HIS 341 (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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125B TYR* 3.7 13.0 - - - +
316B LEU 3.8 0.9 - - - +
317B THR* 3.1 3.6 - - - +
318B LEU* 2.8 40.9 + - + +
329B TRP* 4.1 10.9 - + - -
339B TRP* 4.4 2.8 + - + -
340B ASN* 1.3 79.6 + - - +
342B THR* 1.3 89.6 + - - +
343B PHE* 3.6 17.1 - + + -
352B ALA* 3.2 32.9 + - + -
370B TRP* 4.4 15.9 - + - -
371B TRP* 3.4 37.0 + + + -
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Residues in contact with THR 342 (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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315B ASP* 3.7 22.7 - - + +
316B LEU 3.2 9.6 - - - +
317B THR* 2.5 25.2 + - - +
340B ASN* 5.6 0.7 + - - -
341B HIS* 1.3 95.3 + - - +
343B PHE* 1.3 72.1 + - - +
344B VAL* 4.7 4.5 - - + +
353B SER* 3.4 15.0 - - - -
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Residues in contact with PHE 343 (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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119B LEU* 4.3 11.2 - - + -
123B LEU* 3.8 23.6 - - + -
315B ASP* 3.5 1.9 - - - -
316B LEU* 2.6 44.0 + - + +
318B LEU* 3.9 21.5 - - + -
341B HIS* 3.6 23.3 - + - -
342B THR* 1.3 77.3 - - - +
344B VAL* 1.3 60.9 + - - +
345B ILE* 3.5 17.0 + - + -
352B ALA 4.3 4.5 - - - -
353B SER 3.8 12.3 - - - +
355B ILE* 3.7 29.4 - - + -
358B GLN* 4.4 5.8 - - - -
371B TRP* 3.5 29.4 - + - -
373B TRP* 4.3 10.5 - + - -
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Residues in contact with VAL 344 (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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313B SER* 6.1 1.1 - - - -
314B TYR 4.0 4.3 - - - +
315B ASP* 3.7 22.2 - - - +
342B THR* 5.0 3.4 - - + -
343B PHE* 1.3 71.9 - - - +
345B ILE* 1.3 63.8 + - - +
346B GLY* 3.3 12.1 + - - +
347B PRO* 3.5 24.4 - - + +
349B LYS* 3.7 32.1 - - + +
353B SER* 2.9 40.1 + - - +
354B SER* 5.3 1.4 - - - -
355B ILE 5.7 0.7 + - - -
393B LEU* 5.8 0.5 - - - +
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Residues in contact with ILE 345 (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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312B VAL 4.6 1.4 - - - +
313B SER* 3.4 5.1 - - - -
314B TYR* 2.8 75.0 + - + +
316B LEU* 4.0 21.3 - - + -
343B PHE* 4.3 15.7 - - + -
344B VAL* 1.3 75.3 - - - +
346B GLY* 1.3 59.4 + - - +
355B ILE* 4.5 9.0 - - + -
392B VAL* 4.1 20.2 - - + +
393B LEU* 4.0 30.1 - - + +
394B ARG 5.4 4.9 - - - +
396B VAL* 6.4 0.4 - - + -
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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