Contacts of the helix formed by residues 345 - 358 (chain V) in PDB entry 5IY8
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 GLY 345 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320V GLN* 3.9 11.8 + - - -
343V GLY 4.0 0.2 - - - -
344V ALA* 1.3 76.2 - - - +
346V LYS* 1.4 62.9 + - - +
347V SER* 3.3 6.5 - - - -
348V LEU* 3.3 16.0 + - - +
349V VAL* 3.2 23.0 + - - +
377V GLN* 5.4 2.9 - - - -
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Residues in contact with LYS 346 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340V LEU* 3.9 40.2 - - + +
341V PRO 4.3 6.4 + - - +
342V CYS* 3.8 28.3 - - - +
343V GLY 5.9 0.6 - - - +
345V GLY* 1.4 73.8 - - - +
347V SER* 1.3 63.3 + - - +
349V VAL* 3.2 12.9 + - - +
350V GLY* 3.2 9.0 + - - -
374V TRP* 5.1 1.0 - - - -
441V ASP* 2.7 34.8 + - - +
442V GLU* 3.1 29.4 + - - +
466V LEU* 3.9 32.5 - - + +
467V THR* 4.0 6.7 - - - +
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Residues in contact with SER 347 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345V GLY* 4.7 2.4 - - - -
346V LYS* 1.3 80.5 - - - +
348V LEU* 1.4 61.2 + - - +
350V GLY* 3.1 16.8 + - - -
351V VAL* 3.2 17.5 + - - +
373V GLN* 4.9 6.5 + - - +
374V TRP* 4.3 36.1 - - - +
377V GLN* 3.1 34.3 + - - +
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Residues in contact with LEU 348 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314V ALA* 4.3 10.8 - - + -
315V VAL 3.8 22.9 - - - +
316V LEU* 3.9 25.4 - - + -
320V GLN* 4.9 4.7 - - - +
345V GLY* 3.3 12.5 + - - +
347V SER* 1.4 78.2 + - - +
349V VAL* 1.4 63.7 - - - +
351V VAL* 3.3 7.6 - - + +
352V THR* 2.8 34.4 + - + -
377V GLN* 3.6 31.2 - - + +
381V TRP* 3.8 28.0 - - + -
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Residues in contact with VAL 349 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316V LEU* 3.9 20.6 - - + -
320V GLN* 4.1 20.0 - - + +
323V SER* 6.5 0.4 - - - -
324V LEU* 4.2 14.5 - - + +
338V ILE* 4.8 15.7 - - + -
340V LEU* 4.5 9.9 - - + -
345V GLY 3.2 12.1 + - - +
346V LYS* 3.2 10.9 + - - +
348V LEU* 1.4 74.9 - - - +
350V GLY* 1.3 58.4 + - - +
352V THR* 3.1 6.6 + - - -
353V ALA* 2.9 31.1 + - + +
464V LEU* 5.1 3.1 - - + -
466V LEU* 3.6 27.4 - - + -
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Residues in contact with GLY 350 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346V LYS 3.2 6.7 + - - -
347V SER 3.1 8.1 + - - -
349V VAL* 1.3 75.7 - - - +
351V VAL* 1.4 55.5 + - - +
353V ALA* 3.2 6.2 + - - +
354V ALA* 3.0 29.2 + - - +
374V TRP* 4.0 19.3 - - - -
404V SER* 5.0 0.7 - - - -
439V ILE* 4.4 6.9 - - - +
466V LEU* 3.7 19.8 - - - +
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Residues in contact with VAL 351 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347V SER 3.2 8.5 + - - +
348V LEU* 3.3 23.1 - - - +
350V GLY* 1.4 71.5 - - - +
352V THR* 1.3 60.2 + - - +
354V ALA* 3.5 1.9 + - - +
355V CYS* 2.9 36.2 + - - -
374V TRP* 4.4 10.2 - - + +
377V GLN* 4.0 12.1 - - + -
378V PHE* 3.5 45.1 - - + +
381V TRP* 4.0 23.6 - - + -
404V SER* 4.1 18.8 - - - -
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Residues in contact with THR 352 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313V THR* 6.4 0.2 - - - -
314V ALA* 5.4 5.4 - - + +
316V LEU* 4.0 15.5 - - + +
324V LEU* 4.0 17.6 - - - +
348V LEU* 2.8 37.6 + - + +
349V VAL* 3.1 17.0 + - - -
351V VAL* 1.3 71.9 - - - +
353V ALA* 1.4 57.8 + - - +
355V CYS* 3.7 6.6 - - + +
356V THR* 2.9 38.6 + - - +
381V TRP* 4.2 22.2 - - + +
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Residues in contact with ALA 353 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324V LEU* 4.4 9.2 - - + +
327V MET* 4.6 6.3 - - + -
349V VAL* 2.9 24.5 + - + +
350V GLY* 3.3 7.2 - - - +
352V THR* 1.4 70.2 + - - +
354V ALA* 1.4 58.7 + - - +
356V THR* 3.1 5.9 + - - -
357V VAL* 3.0 37.5 + - - +
439V ILE* 4.2 6.7 - - + -
464V LEU* 3.5 31.2 - - + -
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Residues in contact with ALA 354 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308V ILE* 4.2 6.9 - - + +
310V LEU* 5.2 1.8 - - + -
350V GLY 3.0 15.4 + - - +
351V VAL 3.8 2.9 - - - +
353V ALA* 1.4 74.3 - - - +
355V CYS* 1.3 56.2 + - - +
358V ARG* 2.9 31.5 + - - -
361V CYS* 4.3 20.2 - - + -
378V PHE* 6.3 0.4 - - + -
404V SER* 3.7 20.6 - - - +
405V VAL* 4.7 7.6 - - + -
437V LEU* 4.2 11.0 - - + +
439V ILE* 4.4 5.6 - - + +
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Residues in contact with CYS 355 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308V ILE* 5.6 0.4 - - - -
309V ASP 4.4 4.0 - - - +
310V LEU* 3.6 35.2 - - + +
312V PRO 5.1 1.3 - - - +
351V VAL 2.9 32.7 + - - +
352V THR* 3.8 6.7 - - + +
354V ALA* 1.3 71.2 - - - +
356V THR* 1.3 58.8 + - + +
358V ARG* 3.6 23.8 + - - +
378V PHE* 4.5 4.7 - - - -
381V TRP* 3.2 43.3 - - + +
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Residues in contact with THR 356 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324V LEU* 3.8 24.8 - - + +
327V MET* 4.8 1.4 - - - +
352V THR* 2.9 24.4 + - - +
353V ALA* 3.1 13.2 + - - -
355V CYS* 1.3 67.1 - - + +
357V VAL* 1.4 76.1 + - - +
358V ARG* 3.2 17.2 + - - +
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Residues in contact with VAL 357 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327V MET* 3.5 29.4 - - + -
353V ALA 3.0 27.4 + - - +
356V THR* 1.4 78.2 + - - +
358V ARG* 1.3 68.1 + - - +
359V LYS* 3.7 15.9 + - + +
437V LEU* 4.1 32.8 - - + -
439V ILE* 5.5 1.3 - - + -
462V CYS* 4.3 20.0 - - + -
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Residues in contact with ARG 358 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307V ASN* 3.3 14.1 + - - +
308V ILE* 3.2 33.9 - - + +
309V ASP* 3.5 27.5 + - - +
311V LYS* 4.9 14.8 - - - +
354V ALA 2.9 15.3 + - - -
355V CYS 3.6 15.6 + - - +
356V THR* 3.6 14.5 + - - +
357V VAL* 1.3 78.4 - - - +
359V LYS* 1.3 67.3 + - - +
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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