Contacts of the helix formed by residues 336 - 357 (chain C) in PDB entry 3MSS
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 SER 336 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B MS7 5.7 9.0 - - - -
332C ARG 4.0 6.3 - - - -
333C GLN* 4.1 13.9 - - - -
334C GLU 3.0 4.0 + - - -
335C VAL* 1.3 77.3 - - - +
337C ALA* 1.3 66.6 + - - +
338C VAL* 3.7 11.8 + - - +
339C VAL* 2.9 24.1 + - - +
340C LEU* 3.0 11.6 + - - +
435C TYR* 4.1 5.2 - - - -
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C SER* 1.3 74.8 - - - +
338C VAL* 1.3 58.4 + - + +
340C LEU* 3.2 10.8 + - + +
341C LEU 2.9 24.1 + - - -
435C TYR* 4.5 1.8 + - - -
463C GLY 5.6 5.4 - - - +
465C PRO* 6.0 0.9 - - + -
516C MS7 3.2 36.4 - - + +
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Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C SER* 3.2 8.2 + - - +
337C ALA* 1.3 75.8 - - + +
339C VAL* 1.3 62.2 + - + +
341C LEU* 3.4 8.1 + - + +
342C TYR* 2.9 26.5 + - - +
497C PHE* 4.2 19.9 - - + -
516C MS7 4.0 23.1 - - + -
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C GLU 3.5 21.5 - - - +
335C VAL* 4.0 16.2 - - + -
336C SER* 2.9 19.9 + - - +
338C VAL* 1.3 76.4 - - + +
340C LEU* 1.3 61.4 + - - +
342C TYR* 3.1 9.3 + - + +
343C MET* 2.8 37.0 + - - +
375C HIS* 3.5 48.0 - - + +
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Residues in contact with LEU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C LEU* 3.9 7.6 - - + -
335C VAL* 3.8 17.7 - - + -
336C SER 3.0 15.3 + - - +
337C ALA* 3.2 11.4 + - - +
339C VAL* 1.3 76.5 - - - +
341C LEU* 1.3 62.1 + - - +
343C MET* 3.1 26.5 + - + +
344C ALA* 3.0 24.3 + - - +
432C ILE* 3.6 36.2 - - + +
433C ALA* 4.5 4.5 - - - +
435C TYR* 3.9 28.5 - - + +
516C MS7 4.0 25.8 - - + -
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Residues in contact with LEU 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ALA 2.9 13.3 + - - +
338C VAL* 3.6 11.2 - - + +
340C LEU* 1.3 75.6 - - - +
342C TYR* 1.3 57.9 + - - +
344C ALA* 3.2 1.6 + - - +
345C THR* 2.8 39.0 + - - +
493C PHE* 3.6 33.7 - - + +
496C MET* 4.0 20.2 - - + +
497C PHE* 3.7 34.8 - - + +
516C MS7 3.6 48.3 - - + +
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Residues in contact with TYR 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C VAL 2.9 17.4 + - - +
339C VAL* 3.1 12.1 + - + +
341C LEU* 1.3 71.7 - - - +
343C MET* 1.3 63.3 + - - +
345C THR* 3.3 4.8 + - + -
346C GLN* 3.0 63.7 + - + -
374C ASN 3.6 16.4 + - - -
375C HIS* 3.5 25.3 + - + -
376C LEU* 4.8 6.4 - - - +
497C PHE* 3.5 40.1 - + + -
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Residues in contact with MET 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LEU* 4.0 21.5 - - + -
326C TYR* 4.8 9.6 - - - -
327C LEU* 3.8 16.6 - - + -
335C VAL* 4.5 6.3 - - - -
339C VAL* 2.8 33.3 + - + +
340C LEU* 3.1 35.2 + - + +
342C TYR* 1.3 73.9 - - - +
344C ALA* 1.3 62.5 + - - +
346C GLN* 3.3 8.9 + - - +
347C ILE* 3.1 31.3 + - + +
371C VAL* 5.7 0.9 - - - -
375C HIS* 4.4 9.6 - - + +
377C VAL* 3.6 22.2 - - + +
432C ILE* 3.8 13.2 - - + -
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Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C LEU 3.0 16.3 + - - +
341C LEU 3.6 4.0 - - - +
343C MET* 1.3 74.1 - - - +
345C THR* 1.3 65.5 + - - +
347C ILE* 3.4 5.0 + - - +
348C SER* 3.0 25.1 + - - -
425C PHE* 3.9 5.1 - - - -
429C LEU* 3.6 30.5 - - + -
432C ILE* 4.3 10.7 - - + +
493C PHE* 4.1 15.5 - - + -
516C MS7 4.3 6.5 - - + -
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Residues in contact with THR 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C LEU* 2.8 29.0 + - - +
342C TYR* 3.6 8.7 - - + -
344C ALA* 1.3 77.3 - - - +
346C GLN* 1.3 63.4 + - + +
348C SER* 2.9 21.0 + - - -
349C SER* 3.0 8.5 + - - -
490C HIS* 3.6 24.2 + - + +
493C PHE* 3.4 18.9 + - + +
494C GLU* 4.2 18.2 - - + +
497C PHE* 4.0 18.0 - - + +
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Residues in contact with GLN 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ASN* 3.1 40.5 + - - +
342C TYR* 3.0 58.8 + - + +
343C MET* 3.7 8.7 - - - +
345C THR* 1.3 77.2 - - + +
347C ILE* 1.3 64.2 + - - +
349C SER* 3.2 14.0 + - - -
350C ALA 3.2 10.0 + - - -
375C HIS 3.0 23.4 + - - -
376C LEU* 3.5 11.3 - - - +
377C VAL* 2.9 28.6 + - + +
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Residues in contact with ILE 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ASN* 5.4 0.2 - - - -
323C LEU* 3.9 20.6 - - + -
343C MET 3.1 19.2 + - - +
344C ALA* 3.9 4.3 - - - +
346C GLN* 1.3 78.4 - - - +
348C SER* 1.3 61.5 + - - +
350C ALA* 3.3 3.6 + - - +
351C MET* 3.0 26.4 + - + +
364C LEU* 4.4 1.1 - - + -
369C CYS* 4.1 2.9 - - - -
377C VAL* 3.9 18.2 - - + -
379C VAL* 3.8 26.5 - - + -
425C PHE* 3.6 24.0 - - + -
428C LEU* 3.9 19.5 - - + -
432C ILE* 3.8 26.2 - - + -
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Residues in contact with SER 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ALA 3.0 15.0 + - - -
345C THR* 2.9 21.1 + - - -
347C ILE* 1.3 77.9 - - - +
349C SER* 1.3 55.9 + - - +
351C MET* 4.0 6.0 - - - +
352C GLU* 2.9 28.8 + - - +
425C PHE* 4.0 10.7 - - - -
486C PHE* 4.3 4.9 - - - +
489C ILE* 3.9 21.3 - - - -
490C HIS* 3.3 31.3 + - - +
493C PHE* 3.9 3.3 - - - -
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Residues in contact with SER 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C HIS* 3.1 28.9 + - - -
297C ASN* 4.1 5.2 + - - -
345C THR 3.0 13.8 + - - -
346C GLN* 3.4 11.9 - - - -
347C ILE 3.1 0.4 - - - -
348C SER* 1.3 74.7 + - - +
350C ALA* 1.3 64.3 + - - +
352C GLU* 3.4 6.1 + - - +
353C TYR 3.1 17.7 + - - -
490C HIS* 3.8 25.9 + - - -
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Residues in contact with ALA 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C HIS* 3.6 12.4 - - - -
297C ASN* 3.4 34.1 - - + +
298C LEU* 4.0 11.5 - - + +
346C GLN 3.2 3.2 + - - +
347C ILE 3.5 8.1 - - - +
349C SER* 1.3 79.0 - - - +
351C MET* 1.3 59.7 + - + +
353C TYR* 3.3 5.5 + - - +
354C LEU* 3.0 29.3 + - - +
379C VAL* 3.8 15.0 - - + -
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Residues in contact with MET 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ILE* 3.0 27.0 + - + +
348C SER* 4.0 0.9 - - - +
350C ALA* 1.3 74.3 - - - +
352C GLU* 1.3 60.0 + - - +
354C LEU* 3.8 23.1 - - + +
355C GLU* 2.9 30.0 + - - +
361C HIS* 4.1 11.4 - - + -
364C LEU* 3.8 34.3 - - + -
379C VAL* 4.5 8.5 - - - -
418C ILE* 4.2 6.2 - - + +
421C ASP* 3.8 22.9 - - + +
486C PHE* 3.4 48.5 - - + -
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Residues in contact with GLU 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C SER 2.9 18.6 + - - +
349C SER* 3.6 6.6 + - - +
351C MET* 1.3 73.3 - - - +
353C TYR* 1.3 58.1 + - - +
355C GLU* 3.3 6.3 + - - +
356C LYS* 2.9 34.2 + - + +
486C PHE* 3.5 18.9 - - - +
487C ALA* 3.9 30.3 - - + +
490C HIS* 2.6 38.2 - - - -
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Residues in contact with TYR 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C GLU 3.8 2.1 + - - -
293C ILE* 3.4 21.4 - - + -
294C LYS* 2.7 39.6 + - - +
295C HIS* 3.5 28.9 - + + -
298C LEU* 3.4 25.4 - - + -
349C SER 3.1 6.8 + - - +
350C ALA 3.3 7.9 - - - +
352C GLU* 1.3 78.8 - - - +
354C LEU* 1.3 58.7 + - + +
356C LYS* 3.2 25.8 + - - +
357C LYS* 2.9 70.9 + - + +
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Residues in contact with LEU 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C STI 5.0 7.0 - - - -
293C ILE* 4.0 28.9 - - + -
298C LEU* 3.7 34.3 - - + -
350C ALA 3.0 18.5 + - - +
351C MET* 3.4 36.8 + - + +
353C TYR* 1.3 73.3 - - + +
355C GLU* 1.3 61.4 + - - +
357C LYS* 3.2 3.8 + - - -
358C ASN 3.0 4.2 + - - -
359C PHE* 2.9 51.3 + - + +
360C ILE 5.4 0.4 - - - -
361C HIS* 4.4 22.0 - - + +
418C ILE* 5.0 0.2 - - + -
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Residues in contact with GLU 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C MET 2.9 17.8 + - - +
352C GLU* 3.3 6.2 - - - +
354C LEU* 1.3 77.0 - - - +
356C LYS* 1.3 58.5 + - - +
358C ASN* 3.0 23.9 + - - +
359C PHE 4.4 1.6 - - - -
418C ILE* 3.8 35.8 - - + +
419C LYS* 5.3 0.5 + - - -
422C VAL* 5.0 0.9 - - - +
485C SER* 3.6 13.5 - - - -
486C PHE* 2.8 31.8 + - + +
487C ALA* 3.1 31.4 + - - +
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Residues in contact with LYS 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C GLU* 2.9 21.8 + - + +
353C TYR* 3.5 28.3 - - - +
355C GLU* 1.3 77.0 - - - +
357C LYS* 1.3 66.8 + - - +
358C ASN* 3.4 10.0 + - - -
309D PRO* 5.6 3.6 - - - +
310D PRO* 5.0 20.0 - - - +
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Residues in contact with LYS 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C GLU* 3.6 22.5 + - - +
353C TYR* 2.9 60.9 + - + +
354C LEU* 3.9 0.9 - - - +
355C GLU 3.2 0.4 - - - -
356C LYS* 1.3 86.1 - - + +
358C ASN* 1.3 71.7 + - - +
359C PHE* 3.3 35.2 + - + -
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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
------------------------------------------------------------
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