Contacts of the strand formed by residues 323 - 328 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A ARG* 2.9 30.6 + - - +
269A VAL* 3.7 29.8 - - + -
316A TYR* 4.0 2.9 + - + -
321A ILE 2.8 20.8 + - - -
322A PRO* 1.3 70.7 - - - +
324A VAL* 1.3 72.4 - - - +
325A PHE* 4.1 17.3 - - + -
345A TYR* 3.4 38.6 - - - +
346A PRO* 3.6 6.4 - - - +
391A PHE* 4.1 0.7 - - - -
393B LEU* 3.7 7.0 - - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ARG 3.0 7.5 + - - +
268A VAL* 3.3 7.7 - - + +
269A VAL 3.0 22.3 + - - -
323A THR* 1.3 77.1 - - - +
325A PHE* 1.3 67.8 + - - +
326A VAL* 4.5 2.5 - - + -
346A PRO* 3.9 17.3 - - + +
348A ILE* 3.8 30.5 - - + -
387A ALA* 4.3 13.2 - - + +
390A ILE* 4.0 27.1 - - + -
391A PHE* 3.6 26.7 - - + -
393B LEU* 4.1 4.7 - - + -
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A VAL* 3.3 27.1 - - + +
271A LEU* 4.1 11.9 - - + -
313A LYS* 4.0 15.9 - - + -
316A TYR* 3.8 35.4 - + + -
317A GLU* 4.8 1.3 - - + -
323A THR* 4.1 7.0 - - + -
324A VAL* 1.3 74.0 - - - +
326A VAL* 1.3 62.5 + - - +
327A ALA* 4.1 0.4 - - + -
339A MET* 3.6 33.0 - - + -
343A THR* 4.0 28.3 - - + -
345A TYR* 4.1 18.8 - + + -
346A PRO 3.2 14.8 + - - +
347A VAL* 3.4 13.9 - - + -
348A ILE 2.9 24.6 + - - -
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A VAL* 3.7 23.1 - - + -
269A VAL 2.9 7.5 + - - -
270A VAL* 3.3 13.7 - - + +
271A LEU* 2.9 27.2 + - - +
284A ILE* 3.9 31.6 - - + -
324A VAL* 4.5 3.1 - - + -
325A PHE* 1.3 77.3 - - - +
327A ALA* 1.3 59.9 + - - +
328A VAL* 3.8 3.5 + - + -
348A ILE* 3.2 27.4 - - + +
350A CYS* 4.0 15.9 - - + -
383A SER* 4.1 13.5 - - - +
384A ALA* 6.3 0.2 - - - -
387A ALA* 5.2 0.7 - - + -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 3.5 8.3 - - + -
325A PHE* 4.1 1.4 + - + -
326A VAL* 1.3 70.3 - - - +
328A VAL* 1.3 60.1 + - - +
329A ALA 3.9 1.7 + - - -
333A ASN* 4.8 2.4 + - - +
335A LEU* 4.1 13.7 - - + +
336A GLY* 3.6 36.6 - - - +
339A MET* 5.5 2.5 - - + -
347A VAL* 4.4 6.7 - - + -
348A ILE 2.7 12.8 + - - +
349A SER* 3.4 6.2 - - - +
350A CYS 2.9 30.3 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A VAL* 3.9 8.5 - - + -
271A LEU 2.8 12.6 + - - +
272A MET* 3.3 2.7 - - + +
273A GLY 3.1 24.3 + - - -
277A ASP* 4.0 20.0 - - + +
280A HIS* 3.6 20.6 - - + -
281A CYS* 3.8 25.1 - - - -
284A ILE* 3.9 26.2 - - + -
326A VAL* 4.4 3.4 - - + -
327A ALA* 1.3 74.0 - - - +
329A ALA* 1.3 59.5 + - - +
335A LEU* 4.2 0.8 - - - +
350A CYS 3.5 18.4 - - - +
352A PRO* 4.0 6.7 - - + -
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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