Contacts of the strand formed by residues 323 - 328 (chain B) in PDB entry 6YB9
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 THR 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A LEU* 3.6 12.3 - - - +
267B ARG* 2.9 31.8 + - - +
269B VAL* 3.7 30.7 - - + -
316B TYR* 4.4 2.7 - - + -
321B ILE 2.7 20.1 + - - -
322B PRO* 1.3 70.0 - - - +
324B VAL* 1.3 71.6 + - - +
325B PHE* 4.2 16.8 - - + -
345B TYR* 3.4 39.4 - - - +
346B PRO* 3.7 1.7 - - - +
391B PHE* 4.1 0.9 - - - -
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 4.1 4.7 - - + -
267B ARG 3.0 5.9 + - - -
268B VAL* 3.3 7.8 - - + +
269B VAL 3.0 22.3 + - - -
323B THR* 1.3 76.6 - - - +
325B PHE* 1.3 70.8 + - - +
326B VAL* 4.6 2.5 - - + -
346B PRO* 3.9 17.7 - - + +
348B ILE* 3.8 25.4 - - + -
387B ALA* 4.3 13.5 - - + +
390B ILE* 4.0 27.6 - - + -
391B PHE* 3.6 28.9 - - + -
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 3.3 33.0 - - + +
271B LEU* 4.1 11.7 - - + -
313B LYS* 4.0 16.6 - - + -
316B TYR* 3.9 33.2 - + + -
317B GLU* 4.8 1.8 - - + -
323B THR* 4.2 6.3 - - + -
324B VAL* 1.3 74.6 - - - +
326B VAL* 1.3 62.7 + - - +
327B ALA 4.1 0.4 - - - -
339B MET* 3.6 32.8 - - + -
343B THR* 3.9 28.5 - - + -
345B TYR* 4.1 19.7 - + + -
346B PRO 3.3 14.0 + - - +
347B VAL* 3.4 14.2 - - + -
348B ILE 3.0 23.4 + - - -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 3.8 22.2 - - + -
269B VAL 2.8 11.0 + - - +
270B VAL* 3.3 11.3 - - + +
271B LEU* 2.9 33.1 + - - +
284B ILE* 3.9 24.0 - - + -
324B VAL* 4.6 3.6 - - + -
325B PHE* 1.3 78.5 - - - +
327B ALA* 1.3 56.8 - - - +
328B VAL* 3.8 3.1 + - + -
348B ILE* 3.2 26.0 - - + +
350B CYS* 3.9 24.5 - - + -
383B SER* 4.1 13.0 - - - +
387B ALA* 5.3 1.3 - - + -
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.6 7.6 - - + -
325B PHE 4.1 0.8 - - - -
326B VAL* 1.3 70.9 - - - +
328B VAL* 1.3 59.2 + - - +
329B ALA* 3.9 2.1 + - - -
333B ASN* 4.8 3.2 + - - +
335B LEU* 4.1 12.8 - - + -
336B GLY* 3.5 36.6 - - - +
339B MET* 5.6 2.5 - - + -
347B VAL* 4.4 7.6 - - + +
348B ILE 2.7 12.8 + - - +
349B SER* 3.4 6.2 - - - +
350B CYS 2.9 30.8 + - - -
351B PRO 4.4 0.2 - - - -
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.9 8.1 - - + -
271B LEU 2.8 14.0 + - - +
272B MET* 3.3 3.0 - - + +
273B GLY 3.1 24.3 + - - -
277B ASP* 4.0 20.7 - - + +
280B HIS* 3.7 20.4 - - + -
281B CYS* 3.8 25.6 - - - -
284B ILE* 3.9 26.2 - - + -
326B VAL* 4.4 3.6 - - + -
327B ALA* 1.3 72.7 - - - +
329B ALA* 1.3 58.4 + - - +
335B LEU* 4.2 1.0 - - - +
350B CYS 3.5 19.1 - - - +
352B PRO* 4.0 7.0 - - + -
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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
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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