Contacts of the helix formed by residues 345 - 362 (chain V) in PDB entry 1I84
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 345 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343V GLY 3.0 8.5 + - - -
344V PHE* 1.3 77.2 - - - +
346V GLU* 1.3 97.2 + - + +
347V GLU* 3.6 20.4 - - + +
348V GLU* 2.7 46.7 + - - +
349V GLN* 3.1 4.7 + - - +
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Residues in contact with GLU 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 THR* 6.0 0.4 - - - -
344V PHE 3.5 1.0 + - - -
345V THR* 1.3 90.7 - - + +
347V GLU* 1.3 67.5 + - + +
349V GLN* 3.5 26.2 + - - +
350V THR* 3.8 9.7 + - - +
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Residues in contact with GLU 347 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345V THR* 3.6 19.0 - - + +
346V GLU* 1.3 76.0 - - + +
348V GLU* 1.3 75.1 + - - +
349V GLN 2.4 18.1 + - - -
350V THR* 2.5 34.3 + - + +
351V SER* 2.7 11.5 + - - +
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Residues in contact with GLU 348 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343V GLY 4.5 0.3 - - - +
344V PHE* 3.2 18.2 - - + -
345V THR* 2.7 54.1 + - - +
347V GLU* 1.3 82.4 + - - +
349V GLN* 1.3 57.1 + - - +
351V SER* 3.7 9.0 + - - -
352V ILE* 2.8 23.0 - - - +
441V TRP* 4.1 15.8 - - + -
445V ARG* 2.9 45.0 + - - +
620V PHE* 5.3 1.1 - - + -
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Residues in contact with GLN 349 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336V LEU* 3.1 32.0 - - + +
339V MET* 3.6 29.1 - - + +
340V THR* 3.5 19.3 - - - +
344V PHE* 2.8 36.5 + - + +
345V THR 3.3 10.2 + - - +
346V GLU* 3.6 17.6 + - - +
347V GLU 2.4 12.7 + - - -
348V GLU* 1.3 70.6 - - - +
350V THR* 1.3 68.8 + - + +
351V SER 2.8 1.6 - - - -
352V ILE* 2.6 23.7 + - - +
353V LEU* 3.0 19.8 + - + +
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Residues in contact with THR 350 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301V MET* 6.3 4.0 - - + -
305V LEU* 4.5 7.2 - - - +
346V GLU 3.8 13.5 - - - +
347V GLU* 2.5 34.0 + - + +
349V GLN* 1.3 72.7 - - + +
351V SER* 1.3 67.2 + - - +
353V LEU* 3.1 18.1 + - + +
354V ARG* 3.1 24.1 + - - +
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Residues in contact with SER 351 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347V GLU* 2.7 20.1 + - - +
348V GLU* 3.7 8.2 - - - -
349V GLN 2.6 3.6 + - - -
350V THR* 1.3 71.4 + - - +
352V ILE* 1.3 54.6 + - - -
353V LEU 2.5 16.7 + - - -
354V ARG* 2.8 38.5 + - - +
355V VAL* 3.1 4.9 + - - +
620V PHE* 3.5 31.2 - - - -
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Residues in contact with ILE 352 (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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234V PHE* 4.4 12.2 - - + -
339V MET* 4.7 5.8 - - + -
344V PHE* 3.7 21.5 - - + -
348V GLU 2.8 24.7 - - - +
349V GLN* 2.6 14.7 + - - +
351V SER* 1.3 71.1 - - - +
353V LEU* 1.3 57.6 + - + +
355V VAL* 4.3 2.9 - - - -
356V VAL* 2.8 21.3 + - - +
438V LEU* 3.6 25.0 - - + +
441V TRP* 3.4 24.2 - - + -
442V ILE* 3.2 28.9 - - + -
620V PHE* 3.6 15.5 - - + -
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Residues in contact with LEU 353 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289V ILE* 4.5 12.8 - - + -
293V LEU* 3.3 40.5 - - + +
301V MET* 4.9 9.4 - - - -
305V LEU* 3.7 13.0 - - + -
332V PHE* 3.6 21.5 - - + -
336V LEU* 4.9 13.2 - - + -
339V MET* 5.0 6.5 - - + -
349V GLN* 3.0 26.0 + - + +
350V THR* 3.2 18.6 - - + +
351V SER 2.5 9.7 + - - -
352V ILE* 1.3 76.8 - - + +
354V ARG* 1.3 57.5 + - - +
355V VAL 3.2 1.3 - - - -
356V VAL* 2.7 32.0 + - - +
357V SER* 3.1 5.7 + - - -
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Residues in contact with ARG 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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304V ASP* 4.1 17.6 + - - +
305V LEU* 3.6 27.6 - - + +
350V THR* 3.1 11.5 + - - -
351V SER* 2.8 43.1 + - - +
353V LEU* 1.3 72.2 - - - +
355V VAL* 1.3 61.9 + - + +
356V VAL 2.7 9.0 + - - -
357V SER* 2.6 24.7 + - - +
358V SER* 2.7 19.1 + - - -
389V HIS* 5.5 8.1 + - - -
390V LEU* 4.3 31.6 - - + +
618V ASP* 4.0 21.4 + - - -
620V PHE* 5.7 0.4 - - - -
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Residues in contact with VAL 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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351V SER 3.1 7.2 + - - +
352V ILE 4.3 5.4 - - - +
354V ARG* 1.3 81.4 - - + +
356V VAL* 1.3 56.9 + - - +
358V SER* 3.1 21.1 + - - -
359V VAL* 3.2 15.2 - - + +
390V LEU 5.8 2.2 - - - +
434V LYS* 4.3 29.4 - - + +
438V LEU* 4.1 21.3 - - + +
620V PHE* 3.3 38.6 - - + -
621V VAL* 5.1 10.3 - - + -
624V LEU* 4.5 10.1 - - + -
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Residues in contact with VAL 356 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234V PHE* 5.3 1.8 - - + -
289V ILE* 4.4 21.1 - - + -
290V PHE* 3.2 39.5 - - + -
293V LEU* 3.8 13.9 - - + -
352V ILE 2.8 30.5 - - - +
353V LEU* 2.7 19.6 + - + +
355V VAL* 1.3 77.0 - - - +
357V SER* 1.3 65.5 + - - +
358V SER 3.0 0.9 - - - -
359V VAL* 2.8 16.8 + - - +
360V LEU* 3.1 16.7 + - + +
435V PHE* 5.5 3.6 - - + -
438V LEU* 4.7 8.3 - - + -
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Residues in contact with SER 357 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293V LEU* 4.6 1.4 - - - +
305V LEU* 3.1 43.1 + - - +
306V LEU 4.7 3.1 - - - -
307V LEU* 3.5 20.4 - - - -
313V TYR* 4.7 4.6 - - - -
353V LEU 3.1 1.8 + - - -
354V ARG* 2.6 16.6 + - - -
356V VAL* 1.3 75.6 - - - +
358V SER* 1.3 52.6 + - - +
360V LEU* 2.7 33.6 + - - +
361V GLN* 2.8 15.0 + - - +
390V LEU* 4.3 3.8 - - - +
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Residues in contact with SER 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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354V ARG 2.7 15.5 + - - -
355V VAL* 3.1 13.4 + - - -
357V SER* 1.3 78.2 - - - +
359V VAL* 1.3 66.3 + - - +
360V LEU 2.6 11.8 + - - -
361V GLN* 3.0 10.9 + - - +
362V LEU* 3.1 20.7 + - - +
387V VAL* 4.5 5.1 - - - +
390V LEU* 3.6 30.4 - - - +
391V MET* 5.3 3.1 - - - -
434V LYS* 3.3 26.2 + - - +
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Residues in contact with VAL 359 (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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277V ALA* 5.1 7.4 - - + +
290V PHE* 3.7 26.0 - - + -
315V PHE* 3.1 24.0 - - + -
355V VAL* 3.2 16.1 + - + +
356V VAL* 2.8 15.7 + - - +
358V SER* 1.3 79.7 + - - +
360V LEU* 1.3 55.8 + - - +
362V LEU* 4.7 1.1 - - - -
431V ALA* 4.0 34.5 - - + +
434V LYS* 4.0 18.2 - - + -
435V PHE* 4.1 21.3 - - + +
438V LEU* 6.5 0.4 - - + -
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Residues in contact with LEU 360 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290V PHE* 3.3 36.8 - - + +
293V LEU* 6.2 1.8 - - + -
294V ILE* 4.4 10.8 - - + -
307V LEU* 6.1 1.1 - - + -
313V TYR* 3.4 35.7 - - + +
314V THR 5.2 0.3 + - - -
315V PHE* 3.4 14.1 - - + +
316V LEU* 3.6 34.8 - - + -
356V VAL* 3.1 26.4 + - + +
357V SER* 2.7 15.6 + - - +
358V SER 2.6 4.9 + - - -
359V VAL* 1.3 75.6 - - - +
361V GLN* 1.3 57.0 + - - +
362V LEU 3.2 1.6 - - - -
363V GLY* 2.9 21.4 + - - -
364V ASN* 3.7 6.8 - - - +
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Residues in contact with GLN 361 (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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305V LEU 5.1 0.3 - - - +
306V LEU* 3.6 22.5 - - - +
308V GLU* 3.6 11.7 + - - +
313V TYR* 4.4 7.0 - - + -
357V SER* 2.8 17.2 + - - +
358V SER* 3.8 4.9 - - - +
360V LEU* 1.3 67.2 - - - +
362V LEU* 1.3 53.3 + - - +
363V GLY 2.4 18.7 + - - -
364V ASN* 2.4 57.1 + - - +
365V ILE 3.6 2.6 + - - -
382V THR* 5.7 0.4 + - - -
383V ALA* 4.0 14.9 + - - +
386V LYS* 3.6 35.2 - - + +
387V VAL* 3.2 23.8 - - + +
390V LEU* 4.8 3.5 - - + +
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Residues in contact with LEU 362 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315V PHE* 4.0 5.0 - - + -
358V SER* 3.1 18.4 + - - +
359V VAL* 5.4 0.2 - - - -
360V LEU 3.2 0.2 - - - -
361V GLN* 1.3 75.7 - - - +
363V GLY* 1.3 57.9 + - - +
364V ASN 3.5 0.2 - - - -
365V ILE* 4.0 10.4 - - + +
387V VAL* 3.2 37.3 - - + +
391V MET* 3.7 24.0 - - + -
398V PHE* 4.9 0.4 - - + -
427V ILE* 2.8 68.7 - - + +
430V LEU* 3.6 16.8 - - + -
431V ALA* 3.6 22.2 - - + -
434V LYS* 5.2 2.0 - - + -
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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