Contacts of the strand formed by residues 327 - 333 (chain K) in PDB entry 5LS6
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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305K HIS* 4.8 0.5 - - - -
321K SER 4.3 0.2 - - - +
322K LYS* 3.7 18.0 - - - +
323K SER 4.1 4.3 + - - +
325K GLU* 3.3 10.8 - - + +
326K ASN* 1.3 79.4 - - - +
328K ILE* 1.3 66.7 + - - +
329K VAL* 4.1 7.9 + - + +
355K ARG* 4.5 16.2 - - + +
356K PHE 3.2 17.9 - - - +
357K ASP* 4.4 9.9 - - - +
358K TYR* 3.1 14.8 + - - -
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Residues in contact with ILE 328 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320K LEU* 4.0 25.6 - - + -
321K SER 3.6 9.6 - - - +
322K LYS* 3.9 16.8 - - + -
327K ALA* 1.3 73.5 - - - +
329K VAL* 1.3 61.7 + - - +
330K CYS 4.2 0.2 - - - -
355K ARG* 3.5 2.6 - - - -
356K PHE* 2.8 53.3 + - + -
358K TYR* 3.6 8.2 - - + -
368K PHE* 3.7 35.7 - - + -
377K LEU* 4.2 10.3 - - + -
379K LEU* 4.0 16.8 - - + -
389K TRP* 4.2 18.2 - - + -
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Residues in contact with VAL 329 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304K ILE* 4.3 6.5 - - + +
305K HIS* 4.0 20.4 - - + +
319K ILE 3.4 4.3 - - - +
320K LEU* 3.4 3.0 - - - -
321K SER 3.0 31.5 + - - +
325K GLU* 5.3 3.1 - - - +
327K ALA* 4.7 7.6 - - + +
328K ILE* 1.3 75.7 - - - +
330K CYS* 1.3 66.5 + - - +
331K TRP* 3.4 8.5 - - + -
352K ILE* 3.5 44.9 - - + -
354K GLY 3.6 4.5 - - - +
355K ARG* 4.1 26.7 - - + +
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Residues in contact with CYS 330 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J PHE* 3.8 20.2 - - + -
315K LEU* 4.4 5.8 - - + -
318K LEU* 3.6 34.8 - - - -
319K ILE 3.2 11.2 - - - -
320K LEU* 3.6 21.8 - - + +
328K ILE 4.2 1.4 + - - -
329K VAL* 1.3 72.4 - - - +
331K TRP* 1.3 62.6 + - - +
353K LEU* 3.0 25.6 + - - -
354K GLY* 3.3 23.3 + - - +
356K PHE* 4.6 9.0 - - + -
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Residues in contact with TRP 331 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252K MET* 4.1 13.2 - - + -
260K LEU* 3.4 25.8 - - + -
299K PHE* 4.1 10.1 - + - -
301K THR* 4.1 13.2 - - + -
304K ILE* 3.4 38.5 - - + +
318K LEU* 3.8 3.5 - - - +
319K ILE* 2.9 63.0 + - + +
321K SER* 3.0 19.5 + - - -
329K VAL* 3.4 17.5 - - + -
330K CYS* 1.3 72.5 - - - +
332K LYS* 1.3 89.5 + - - +
333K PRO* 3.6 24.7 - - + -
350K VAL* 4.3 3.8 - - + -
351K THR 3.4 8.3 - - - +
352K ILE* 3.4 26.0 - - + -
353K LEU* 4.2 4.9 - - - +
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Residues in contact with LYS 332 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J MET* 4.2 9.9 - - + +
317K ASP 5.4 0.7 - - - +
318K LEU* 3.6 24.2 - - + -
319K ILE* 5.0 0.2 - - - -
331K TRP* 1.3 85.7 - - - +
333K PRO* 1.3 88.4 - - + +
335K LYS 3.7 6.9 + - - +
336K MET* 3.1 38.4 + - + +
337K GLU 3.9 1.4 + - - -
338K ASP 2.5 28.6 + - - +
339K ASP* 4.8 1.2 - - - +
340K ILE* 5.1 4.6 - - - +
350K VAL* 3.5 3.5 - - - -
351K THR* 2.9 50.6 + - - +
353K LEU* 4.5 2.7 - - + -
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Residues in contact with PRO 333 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252K MET* 4.4 8.3 - - + -
262K LEU* 5.3 0.7 - - + -
299K PHE* 3.8 35.4 - - + -
317K ASP 5.2 2.5 - - - +
319K ILE* 4.4 8.5 - - + -
331K TRP* 3.8 20.6 - - + -
332K LYS* 1.3 105.2 - - + +
334K GLY* 1.3 58.7 + - - +
338K ASP 4.0 0.3 - - - +
340K ILE* 3.4 31.5 - - + +
343K ILE* 3.7 17.0 - - + +
349K ASN 4.2 3.4 - - - +
350K VAL* 4.7 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