Contacts of the strand formed by residues 327 - 332 (chain B) in PDB entry 3EI1
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 VAL 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B THR* 2.7 33.0 + - - +
297B SER* 3.9 3.8 - - - -
298B SER 3.1 14.6 + - - +
301B ALA 4.2 10.1 - - - -
302B THR 4.3 0.2 - - - +
303B VAL* 3.6 23.8 - - + -
323B HIS* 3.5 41.1 - - + +
325B LYS 3.9 0.9 - - - +
326B PRO* 1.3 76.1 - - - +
328B ASN* 1.3 55.6 + - - +
329B ALA 3.2 26.2 - - - +
342B THR* 4.2 4.3 - - + +
343B THR 3.3 17.5 - - - +
344B ASP* 4.9 1.1 - - - -
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Residues in contact with ASN 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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282B THR* 3.4 23.7 + - - +
283B HIS* 4.2 0.9 - - - +
326B PRO 4.1 0.2 + - - -
327B VAL* 1.3 74.2 - - - +
329B ALA* 1.3 56.0 + - - +
343B THR* 2.7 13.9 + - - +
344B ASP 3.8 11.1 + - - -
345B GLN* 2.9 41.9 + - - +
368B HIS 5.3 3.4 + - - -
370B GLN* 5.0 2.6 - - - +
376B PRO* 3.7 22.2 - - - +
377B ILE 3.2 28.3 + - - +
378B LYS* 3.1 32.5 + - + +
10G C 4.7 0.2 + - - -
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B HIS* 4.0 6.3 - - + +
297B SER* 3.6 8.9 + - - -
327B VAL* 3.2 19.6 + - - +
328B ASN* 1.3 81.7 - - + +
330B ALA* 1.3 63.2 + - - +
331B TYR* 3.7 33.7 - - + +
341B LEU 4.0 2.0 - - - +
342B THR* 3.6 1.9 - - - -
343B THR* 3.5 18.8 + - - +
378B LYS* 3.8 16.8 - - + -
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B HIS* 3.3 25.2 + - + -
285B GLU* 3.7 7.6 - - - +
295B ALA* 4.4 7.6 - - + +
297B SER* 3.9 10.5 + - - +
303B VAL* 3.9 29.6 - - + -
329B ALA* 1.3 78.6 - - - +
331B TYR* 1.3 61.4 + - - +
340B LEU* 3.8 19.2 - - + +
341B LEU 3.1 7.6 - - - +
342B THR* 4.4 2.0 - - - +
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B HIS* 3.5 27.3 + + - -
285B GLU* 3.5 16.2 - - - +
329B ALA* 3.7 18.6 - - + +
330B ALA* 1.3 73.7 - - - +
332B PHE* 1.3 61.3 + - - +
340B LEU* 3.3 5.4 - - - +
341B LEU* 2.7 41.0 + - + +
378B LYS* 3.6 26.5 - - + +
379B ALA 3.2 28.0 - - - -
380B THR* 3.7 24.5 - - + +
381B TRP* 2.9 25.0 + + + +
433B LYS* 4.8 11.4 + - - -
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Residues in contact with PHE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 2.8 34.8 + - + +
287B ASN* 3.3 48.9 - - + -
288B PRO* 4.6 6.3 - - + -
293B LEU* 4.0 13.7 - - + -
295B ALA* 3.8 30.5 - - + -
305B LEU* 4.2 7.4 - - + -
331B TYR* 1.3 73.3 - - - +
333B ASN* 1.3 64.8 + - - +
334B PRO* 3.4 4.5 - - - +
337B SER* 3.7 19.5 - - - +
339B LYS 3.3 13.9 - - - -
340B LEU* 3.7 14.6 - - + -
357B TRP* 3.7 26.2 - + - -
381B TRP* 3.4 8.1 - - - -
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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