Contacts of the strand formed by residues 327 - 331 (chain B) in PDB entry 6E3Y
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
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Residue Dist Surf HB Arom Phob DC
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45B MET* 4.7 5.2 - - + -
286B LEU* 3.7 26.0 - - + -
308B LEU* 5.1 6.3 - - + -
318B LEU* 4.1 13.7 - - + -
319B GLY 3.3 9.6 - - - +
320B VAL* 3.9 7.2 - - + -
326B ALA* 1.3 77.7 - - - +
328B ALA* 1.3 61.3 + - - +
329B THR* 4.3 12.6 - - + -
338B ILE* 4.4 0.9 - - - -
339B TRP* 2.8 49.9 + - + +
50G LEU* 3.7 33.2 - - + -
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Residues in contact with ALA 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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61B MET* 3.7 21.9 - - + +
63B TRP* 3.6 22.8 - - + -
70B LEU* 4.2 3.6 - - + -
318B LEU* 3.7 0.5 - - - -
319B GLY 2.9 31.0 + - - -
326B ALA 4.1 1.0 - - - -
327B VAL* 1.3 71.4 - - - +
329B THR* 1.3 64.2 + - - +
336B LEU* 5.5 5.6 - - + -
337B LYS 3.3 6.3 - - - +
338B ILE* 3.7 19.7 - - + +
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Residues in contact with THR 329 (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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294B CYS* 4.2 16.4 - - + -
308B LEU* 4.9 3.6 - - + -
311B HIS* 2.4 38.9 + - - -
315B VAL* 5.0 1.6 - - - -
317B CYS 3.6 7.9 - - - -
318B LEU* 3.8 28.5 - - + -
327B VAL* 4.3 7.2 - - + -
328B ALA* 1.3 76.9 - - - +
330B GLY* 1.3 59.9 + - - +
336B LEU* 3.5 4.7 - - - -
337B LYS 3.0 25.5 + - - -
339B TRP* 3.3 22.7 + - + +
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Residues in contact with GLY 330 (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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58B ILE* 4.3 3.4 - - - -
315B VAL* 3.5 2.8 - - - +
316B SER* 2.9 25.6 + - - -
317B CYS* 2.9 34.3 + - - +
328B ALA 4.0 1.0 + - - -
329B THR* 1.3 72.8 - - - +
331B SER* 1.3 61.5 + - - -
335B PHE 4.0 1.1 - - - -
336B LEU* 3.7 18.1 - - - +
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Residues in contact with SER 331 (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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58B ILE* 3.2 25.5 + - - +
311B HIS* 3.3 25.1 - - - -
313B ASN 3.1 20.1 + - - -
314B ARG 2.9 14.3 + - - -
315B VAL* 3.7 5.6 - - - +
329B THR 4.1 0.2 + - - -
330B GLY* 1.3 74.1 - - - -
332B TRP* 1.3 71.7 + - - +
333B ASP* 3.2 26.4 + - - +
334B SER 3.8 3.5 + - - -
335B PHE 3.4 7.7 + - - -
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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