Contacts of the strand formed by residues 327 - 333 (chain L) in PDB entry 6C23
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 ALA 327 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305L HIS* 5.0 1.6 - - - -
322L LYS* 4.1 10.7 - - - -
323L SER 4.1 5.5 + - - -
325L GLU* 3.1 15.8 - - + +
326L ASN* 1.3 79.4 - - - +
328L ILE* 1.3 63.9 - - - +
329L VAL* 3.9 8.3 + - + +
355L ARG* 3.7 20.0 - - + +
356L PHE 3.6 4.7 - - - -
357L ASP* 3.1 24.2 - - - +
358L TYR* 3.1 12.3 + - - -
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Residues in contact with ILE 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320L LEU* 4.6 13.9 - - + -
321L SER 3.9 11.4 - - - +
322L LYS* 3.9 14.8 - - + +
327L ALA* 1.3 76.6 - - - +
329L VAL* 1.3 77.0 + - - +
355L ARG* 3.5 8.0 - - - +
356L PHE* 2.8 48.5 + - + +
358L TYR* 3.6 11.4 - - + -
368L PHE* 4.3 23.8 - - + -
377L LEU* 3.8 26.2 - - + -
378L ALA 4.8 0.4 - - - +
379L LEU* 4.1 9.4 - - + -
389L TRP* 4.1 15.7 - - + -
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Residues in contact with VAL 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304L ILE* 4.4 10.3 - - + +
305L HIS* 4.1 16.4 - - + +
320L LEU* 3.2 5.3 - - - +
321L SER* 2.9 43.2 + - - +
327L ALA* 4.3 6.5 - - + +
328L ILE* 1.3 86.0 - - - +
330L CYS* 1.3 79.1 + - - +
331L TRP* 4.1 13.2 - - + -
352L ILE* 4.3 14.6 - - + -
354L GLY 3.7 9.6 - - - +
355L ARG* 4.9 11.2 - - + +
356L PHE* 5.6 0.9 - - - -
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Residues in contact with CYS 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 4.8 7.2 - - + -
315L LEU* 4.5 4.9 - - - -
318L LEU* 3.7 38.4 - - - -
319L ILE 3.4 4.0 - - - -
320L LEU* 3.4 22.2 - - + -
329L VAL* 1.3 85.8 - - - +
331L TRP* 1.3 66.5 + - - +
352L ILE* 4.0 0.3 - - - -
353L LEU* 3.5 19.4 + - - -
354L GLY* 3.1 29.9 + - - +
356L PHE* 5.3 8.2 - - + -
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Residues in contact with TRP 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252L MET* 4.0 14.1 - - + -
260L LEU* 3.5 25.5 - - + +
262L LEU* 6.2 0.4 - - + -
299L PHE* 4.2 13.7 - + - -
301L THR* 4.1 17.0 - - + -
304L ILE* 3.5 28.3 - - + -
318L LEU* 3.5 5.2 - - - +
319L ILE* 2.8 83.6 + - + +
321L SER* 3.4 22.4 + - - -
329L VAL* 4.1 7.0 - - + -
330L CYS* 1.3 80.7 - - - +
332L LYS* 1.3 101.6 + - - +
333L PRO* 3.7 14.6 - - + -
350L VAL* 5.1 2.9 - - + -
351L THR 3.1 17.3 - - - +
352L ILE* 4.3 1.3 - - - -
353L LEU* 3.3 8.1 - - - -
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Residues in contact with LYS 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C MET* 4.3 16.7 - - + +
317L ASP 4.3 9.9 - - - +
318L LEU* 3.8 19.5 - - + -
319L ILE* 5.2 0.7 - - - -
331L TRP* 1.3 87.8 - - - +
333L PRO* 1.3 71.5 - - + +
335L LYS 3.4 17.5 - - - +
336L MET* 3.7 22.5 + - - -
337L GLU* 4.0 2.4 - - - +
338L ASP* 3.8 22.0 + - - -
340L ILE* 5.6 2.0 - - + -
350L VAL* 3.5 0.3 - - - -
351L THR* 2.8 56.5 + - + -
353L LEU* 4.2 7.6 - - + -
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Residues in contact with PRO 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262L LEU* 5.3 4.0 - - + -
299L PHE* 3.9 33.0 - - + -
317L ASP 5.4 0.7 - - - +
319L ILE* 5.3 4.9 - - + -
331L TRP* 3.8 12.6 - - + -
332L LYS* 1.3 92.4 - - + +
334L GLY* 1.3 60.1 + - - +
335L LYS 3.8 1.9 - - - +
338L ASP* 2.9 24.1 - - - +
340L ILE* 3.4 33.0 - - + -
343L ILE* 3.9 18.9 - - + +
349L ASN 3.9 3.8 - - - +
350L VAL* 4.3 0.9 - - - -
351L THR* 4.1 0.2 - - - -
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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