Contacts of the helix formed by residues 417 - 434 (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 417 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ILE* 3.7 21.3 - - - +
409C GLU* 4.8 3.5 + - - +
415C LYS 5.6 0.2 + - - -
416C PHE* 1.3 75.8 - - - +
418C ILE* 1.3 66.1 + - - +
419C LYS* 3.1 22.1 + - - +
420C SER* 2.8 26.2 + - - -
421C ASP 3.2 5.9 + - - -
480C PRO* 5.2 1.9 - - - +
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Residues in contact with ILE 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C MET* 4.2 6.3 - - + -
354C LEU* 4.7 0.4 - - + -
355C GLU* 3.8 43.7 - - + +
359C PHE 3.6 21.5 - - - +
360C ILE* 3.7 9.0 - - + +
417C SER* 1.3 75.5 - - - +
419C LYS* 1.3 73.6 + - + +
421C ASP* 3.2 25.1 + - - +
422C VAL* 3.0 25.2 + - + +
486C PHE* 3.8 25.1 - - + -
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Residues in contact with LYS 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLU* 5.3 0.8 + - - +
417C SER* 3.1 12.1 + - - +
418C ILE* 1.3 85.6 - - + +
420C SER* 1.3 59.7 + - - +
422C VAL* 3.4 5.9 + - + +
423C TRP 3.1 17.2 + - - -
480C PRO* 3.4 45.1 - - + +
481C SER* 4.6 8.3 - - - +
483C ARG* 2.9 45.5 + - + +
484C PRO 3.3 20.2 + - - +
485C SER* 3.6 12.3 - - - +
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Residues in contact with SER 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ILE* 5.2 0.2 - - - +
405C TRP 4.9 1.2 - - - +
407C ALA* 3.6 19.1 + - - +
409C GLU* 3.7 6.7 + - - -
410C SER* 3.3 23.5 + - - -
415C LYS 4.4 0.9 - - - -
416C PHE* 3.4 15.0 - - - +
417C SER* 2.8 34.2 + - - -
419C LYS* 1.3 76.8 - - - +
421C ASP* 1.4 64.4 + - - +
423C TRP* 3.3 5.0 + - - +
424C ALA* 3.1 21.1 + - - +
483C ARG* 3.9 1.0 - - - +
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Residues in contact with ASP 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C MET* 3.8 5.4 - - + +
360C ILE* 3.4 10.5 - - - +
361C HIS* 2.5 35.1 + - - +
362C ARG* 2.9 28.6 + - - -
363C ASP 4.6 0.2 + - - -
364C LEU* 3.8 6.6 + - + +
417C SER 3.2 10.7 + - - +
418C ILE* 3.2 19.3 + - - +
420C SER* 1.4 74.9 + - - +
422C VAL* 1.3 53.7 + - - +
424C ALA* 3.2 8.8 + - - +
425C PHE* 2.8 35.5 + - - +
486C PHE* 3.6 15.1 - - + -
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Residues in contact with VAL 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLU* 5.0 1.1 - - - +
418C ILE 3.0 19.0 + - - +
419C LYS* 3.5 17.7 - - + +
420C SER 3.4 0.2 - - - -
421C ASP* 1.3 76.6 - - - +
423C TRP* 1.3 62.3 + - - +
425C PHE* 3.2 3.2 + - - +
426C GLY 3.0 18.4 + - - -
475C CYS* 3.3 23.6 - - + +
483C ARG* 4.0 8.5 - - + -
484C PRO* 3.4 28.0 - - + +
485C SER* 4.8 0.4 - - - -
486C PHE* 3.5 31.0 - - + +
489C ILE* 3.7 18.8 - - + -
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Residues in contact with TRP 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LYS 5.1 1.2 + - - -
405C TRP 3.8 9.9 + - - -
406C THR 3.8 8.1 + - - -
407C ALA* 3.6 25.1 - - + -
408C PRO* 3.5 35.7 - - + -
419C LYS 3.1 10.6 + - - +
420C SER 3.4 9.0 - - - +
422C VAL* 1.3 74.5 - - - +
424C ALA* 1.3 65.1 + - - +
426C GLY 3.0 12.0 + - - -
427C VAL* 3.2 23.3 + - + +
440C TYR* 4.3 7.0 + - - -
452C LEU* 3.8 28.9 - - + +
457C ARG* 3.7 26.0 - - - -
475C CYS 3.4 14.1 + - - +
476C TRP* 3.3 47.8 + + + -
477C GLN 3.7 7.4 - - - -
483C ARG* 3.7 11.2 - - - +
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Residues in contact with ALA 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C ARG 6.3 0.9 - - - -
363C ASP* 6.0 0.2 - - - -
364C LEU* 3.6 31.8 - - + +
405C TRP* 3.5 26.4 - - + +
420C SER 3.1 12.9 + - - +
421C ASP* 3.2 9.4 + - - +
423C TRP* 1.3 77.3 - - - +
425C PHE* 1.3 57.0 + - - +
427C VAL* 3.0 9.1 + - - +
428C LEU* 2.8 28.1 + - - +
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Residues in contact with PHE 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ALA* 3.9 9.0 - - + -
347C ILE* 3.6 35.0 - - + -
348C SER* 4.0 14.8 - - - -
364C LEU* 3.8 13.2 - - + +
421C ASP 2.8 17.6 + - - +
422C VAL 3.2 8.3 + - - +
424C ALA* 1.3 70.2 - - - +
426C GLY* 1.3 62.8 + - - +
428C LEU* 3.2 10.1 + - + +
429C LEU* 2.8 56.3 + - + +
432C ILE* 6.0 0.4 - - + -
475C CYS* 4.1 13.5 - - - -
486C PHE* 3.7 21.8 - + + -
489C ILE* 3.6 22.9 - - + -
493C PHE* 3.6 19.5 - + - -
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Residues in contact with GLY 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C VAL 3.0 7.5 + - - -
423C TRP 3.0 9.9 + - - -
425C PHE* 1.3 78.3 - - - +
427C VAL* 1.3 61.0 + - - +
429C LEU* 3.3 8.4 + - - +
430C TRP* 3.2 16.3 + - - +
472C MET* 4.0 6.8 - - - +
475C CYS* 3.8 18.4 - - - -
476C TRP* 3.3 24.6 - - - -
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Residues in contact with VAL 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LYS 3.7 23.8 - - - +
405C TRP* 3.4 33.2 - - + +
423C TRP* 3.2 22.8 + - + +
424C ALA* 3.0 7.9 + - - +
426C GLY* 1.3 75.7 - - - +
428C LEU* 1.3 64.3 + - - +
430C TRP* 3.1 5.7 + - - +
431C GLU* 3.0 21.0 + - + +
439C PRO* 3.9 20.2 - - + -
440C TYR* 4.9 2.9 - - - +
458C MET* 4.4 5.4 - - + -
476C TRP* 3.6 22.2 - - + +
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Residues in contact with LEU 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LEU* 4.3 4.9 - - + -
347C ILE* 3.9 23.3 - - + -
364C LEU* 3.8 33.2 - - + -
365C ALA* 4.1 8.3 - - - -
366C ALA* 3.5 33.7 - - + +
369C CYS* 4.1 7.4 - - - -
405C TRP* 4.5 0.6 - - - +
424C ALA 2.8 16.8 + - - +
425C PHE* 3.5 11.7 - - + +
427C VAL* 1.3 74.0 - - - +
429C LEU* 1.3 62.1 + - - +
431C GLU* 3.1 12.7 + - - +
432C ILE* 3.0 39.2 + - + +
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ALA* 3.6 31.0 - - + -
425C PHE* 2.8 39.5 + - + +
426C GLY* 3.5 9.6 - - - +
428C LEU* 1.3 74.4 - - - +
430C TRP* 1.3 57.8 + - - +
432C ILE* 3.3 8.4 + - + +
433C ALA* 2.9 29.1 + - - +
468C VAL* 4.3 8.1 - - + +
471C LEU* 4.5 3.6 - - + -
472C MET* 3.8 37.5 - - + +
475C CYS* 5.3 0.9 - - - -
493C PHE* 3.6 26.0 - - + -
516C MS7 4.2 13.9 - - + -
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Residues in contact with TRP 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C GLY 3.2 8.9 + - - +
427C VAL 3.1 10.4 + - - +
429C LEU* 1.3 77.6 - - - +
431C GLU* 1.3 67.5 + - + +
433C ALA* 3.2 1.9 + - - +
434C THR* 3.0 47.5 + - + +
437C MET* 3.6 35.9 - - + -
438C SER 3.4 26.5 - - - -
439C PRO* 3.6 10.8 - - + -
441C PRO* 4.3 9.2 - - + -
458C MET* 3.6 45.4 - - + +
459C GLU* 3.0 39.4 + - - -
461C PRO* 3.5 18.4 - - + +
472C MET* 3.7 20.3 - - - +
476C TRP* 4.0 2.5 - + + -
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Residues in contact with GLU 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C LEU* 3.7 16.3 - - - +
327C LEU* 4.0 1.7 - - - +
366C ALA* 2.9 42.9 + - + +
367C ARG* 4.6 1.2 + - - -
405C TRP* 2.9 43.7 + - + +
427C VAL* 3.0 18.0 + - + +
428C LEU* 3.1 14.8 + - - +
430C TRP* 1.3 79.0 - - + +
432C ILE* 1.4 61.3 + - - +
434C THR* 3.2 9.2 + - - -
436C GLY* 2.7 33.4 + - - +
437C MET 4.2 13.9 - - - +
439C PRO* 4.9 3.3 - - + +
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Residues in contact with ILE 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LEU* 4.3 12.6 - - + -
327C LEU* 3.9 11.1 - - + +
340C LEU* 3.6 49.0 - - + +
343C MET* 3.8 10.5 - - + -
344C ALA* 4.3 20.0 - - + +
347C ILE* 3.8 28.7 - - + -
425C PHE* 6.0 0.7 - - + -
428C LEU* 3.0 30.6 + - + +
429C LEU* 3.6 10.1 - - + +
430C TRP 3.3 0.2 - - - -
431C GLU* 1.4 77.5 - - - +
433C ALA* 1.3 62.4 + - - +
435C TYR* 3.1 12.5 + - - -
516C MS7 3.9 10.3 - - + -
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Residues in contact with ALA 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C LEU* 4.5 4.3 - - - +
429C LEU 2.9 17.2 + - - +
430C TRP 3.2 1.5 + - - +
432C ILE* 1.3 77.4 - - - +
434C THR* 1.3 56.4 + - - +
435C TYR* 3.4 10.3 + - - -
461C PRO* 3.8 31.5 - - + +
462C GLU 4.4 8.5 - - - +
463C GLY 6.0 0.2 - - - -
464C CYS* 4.3 7.9 + - + +
472C MET* 4.3 7.9 - - + -
516C MS7 3.6 26.9 - - + -
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Residues in contact with THR 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ARG* 4.8 2.6 + - - -
430C TRP* 3.0 41.4 + - + +
431C GLU* 3.2 6.1 + - - -
432C ILE 3.2 0.2 - - - -
433C ALA* 1.3 75.4 - - - +
435C TYR* 1.3 71.4 + - - +
436C GLY 3.3 0.2 + - - -
437C MET* 2.9 53.6 + - + +
461C PRO* 3.7 27.1 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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