Contacts of the helix formed by residues 421 - 438 (chain C) in PDB entry 3OS8
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 MET 421 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C KN0 3.7 34.3 - - + -
342C MET* 3.9 28.3 - - + +
343C MET* 3.2 40.2 - - + -
346C LEU* 4.3 4.7 - - + -
415C GLY 4.4 0.2 - - - -
418C VAL* 3.8 23.1 - - + -
419C GLU 2.9 3.5 + - - +
420C GLY* 1.3 77.0 - - - +
422C VAL* 1.3 54.7 + - - +
423C GLU 3.2 3.4 - - - -
424C ILE* 3.0 11.4 + - + +
425C PHE* 2.6 40.4 + - + +
524C HIS* 3.5 23.3 - - + +
528C MET* 5.5 2.0 - - + -
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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
----------------------------------------------------------
531B LYS* 3.2 29.4 - - + +
412C ARG* 4.2 31.6 - - + +
415C GLY 3.5 23.7 + - - +
416C LYS* 4.2 10.5 - - + -
418C VAL 3.7 0.4 - - - +
419C GLU 3.0 21.5 - - - +
420C GLY* 3.4 1.7 - - - -
421C MET* 1.3 72.3 - - - +
423C GLU* 1.3 59.0 + - + +
425C PHE* 3.3 5.6 - - + +
426C ASP* 2.9 34.1 + - - +
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Residues in contact with GLU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C GLY 4.4 6.4 + - - +
421C MET 3.2 0.6 - - - -
422C VAL* 1.3 81.7 - - + +
424C ILE* 1.3 59.9 + - + +
426C ASP* 3.2 9.3 + - - +
427C MET* 3.0 37.5 + - + +
520C LYS* 4.9 13.4 + - - -
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Residues in contact with ILE 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C KN0 3.3 48.2 - - + -
388C MET* 4.1 12.3 - - + -
420C GLY 4.5 11.4 - - - +
421C MET* 3.0 7.8 + - - +
423C GLU* 1.3 74.5 - - + +
425C PHE* 1.3 60.4 + - - +
427C MET* 3.2 25.6 + - + +
428C LEU* 2.9 38.2 + - + +
517C MET* 4.7 2.2 - - + +
520C LYS* 3.8 14.6 - - + +
521C GLY* 3.7 19.7 - - - +
524C HIS* 4.2 8.7 - - + -
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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
----------------------------------------------------------
1C KN0 5.7 2.6 - + - -
342C MET* 4.8 3.4 - - + -
402C LEU* 3.5 34.1 - - + -
404C PHE* 4.0 17.3 - + - -
410C LEU* 3.7 27.1 - - + -
411C ASP 3.5 32.3 - - - -
412C ARG* 3.9 9.9 - - + -
415C GLY* 3.8 22.0 - - - +
418C VAL* 4.9 4.9 - - + -
421C MET* 2.6 23.7 + - + +
422C VAL* 3.3 12.1 - - + +
424C ILE* 1.3 72.4 - - - +
426C ASP* 1.3 58.6 + - - +
428C LEU* 3.2 7.9 + - + +
429C LEU* 2.9 45.8 + - + +
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Residues in contact with ASP 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 5.4 13.0 - - + +
412C ARG* 2.8 52.3 + - - +
422C VAL 2.9 17.9 + - - +
423C GLU* 3.5 12.1 - - - +
425C PHE* 1.3 77.5 - - - +
427C MET* 1.3 57.7 + - + +
429C LEU* 3.2 11.6 + - - +
430C ALA* 2.8 30.0 + - - +
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Residues in contact with MET 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A THR* 3.8 22.0 - - + -
423C GLU* 3.0 19.0 + - + +
424C ILE* 3.2 39.9 + - + +
426C ASP* 1.3 76.1 - - + +
428C LEU* 1.3 61.1 + - - +
430C ALA* 3.2 5.3 + - - +
431C THR* 2.9 28.4 + - - -
513C HIS* 3.5 12.6 + - - +
516C HIS* 3.8 27.1 - - - -
517C MET* 3.6 26.5 - - + -
520C LYS* 4.0 19.5 - - + -
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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
----------------------------------------------------------
1C KN0 3.4 32.5 - - + -
388C MET* 4.1 24.7 - - + +
391C LEU* 3.9 17.0 - - + -
392C VAL* 3.8 21.8 - - + +
402C LEU* 3.9 23.6 - - + -
424C ILE* 2.9 25.0 + - + +
425C PHE* 3.4 7.0 - - - +
427C MET* 1.3 76.7 - - - +
429C LEU* 1.3 61.9 + - - +
431C THR* 3.1 4.8 + - - -
432C SER* 3.0 23.0 + - - -
517C MET* 3.6 22.4 - - + -
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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
----------------------------------------------------------
400C GLY* 3.5 22.7 - - - +
401C LYS 3.5 42.2 - - - +
402C LEU* 4.1 12.7 - - + +
412C ARG* 4.4 12.6 - - + -
425C PHE* 2.9 32.7 + - + +
426C ASP* 3.5 19.3 - - - +
428C LEU* 1.3 75.1 - - - +
430C ALA* 1.3 64.0 + - - +
432C SER* 3.3 7.2 + - - -
433C SER* 3.0 24.3 + - - -
436C ARG* 5.1 2.6 + - - +
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Residues in contact with ALA 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TYR* 2.8 36.6 - - + +
460A THR* 5.2 0.2 - - - -
462A LEU* 4.9 11.4 - - + -
472A LYS* 6.6 0.4 - - - -
426C ASP 2.8 16.1 + - - +
427C MET* 3.5 7.0 - - - +
428C LEU 3.2 0.4 - - - -
429C LEU* 1.3 76.4 - - - +
431C THR* 1.3 58.0 + - - +
433C SER* 3.4 7.2 + - - -
434C ARG* 3.1 26.0 + - - +
437C MET* 5.6 0.5 - - - +
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Residues in contact with THR 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TYR* 5.6 2.5 - - + -
392C VAL* 3.8 23.3 - - + -
427C MET 2.9 15.1 + - - -
428C LEU 3.1 7.4 + - - -
430C ALA* 1.3 75.4 - - - +
432C SER* 1.3 65.4 + - - +
434C ARG* 3.1 8.2 + - + +
435C PHE* 2.9 27.0 + - + -
510C ILE* 3.9 27.6 - - + -
513C HIS* 2.9 23.7 - - + -
514C ILE* 4.6 3.6 - - + -
517C MET* 3.4 11.7 - - + +
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Residues in contact with SER 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C VAL* 3.5 23.7 - - - +
395C SER* 3.3 19.0 + - - -
396C MET* 3.2 25.3 - - - +
401C LYS 5.7 0.2 - - - -
402C LEU* 5.3 1.6 - - - -
428C LEU 3.0 12.1 + - - -
429C LEU* 3.6 12.3 - - - -
431C THR* 1.3 76.8 - - - +
433C SER* 1.3 57.9 + - - +
435C PHE* 3.2 5.9 + - - +
436C ARG* 3.0 33.3 + - - +
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Residues in contact with SER 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C LEU 3.0 17.3 + - - -
430C ALA* 3.7 7.4 - - - -
432C SER* 1.3 76.2 - - - +
434C ARG* 1.3 59.4 + - - +
436C ARG* 3.4 28.6 + - - +
437C MET* 3.0 42.1 + - - +
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Residues in contact with ARG 434 (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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459A TYR* 4.1 19.0 + - + -
476A HIS* 3.4 46.7 + - - +
430C ALA 3.1 13.7 + - - +
431C THR* 3.1 13.4 + - + +
433C SER* 1.3 73.4 - - - +
435C PHE* 1.3 65.7 + - + +
437C MET* 3.0 38.6 - - + +
438C MET* 3.0 47.7 + - - +
506C GLN* 3.7 37.0 + - - +
510C ILE* 3.7 25.7 - - + +
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Residues in contact with PHE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ILE* 4.1 30.1 - - + -
392C VAL* 3.5 26.2 - - + -
393C TRP* 4.4 16.4 - - - -
396C MET* 3.6 16.6 - - + +
431C THR* 2.9 20.7 + - + -
432C SER 3.3 9.6 - - - +
434C ARG* 1.3 75.8 - - - +
436C ARG* 1.3 63.3 + - - +
438C MET* 3.3 4.5 + - - -
439C ASN* 3.1 3.3 + - - -
440C LEU* 3.0 61.3 + - + -
445C PHE* 4.7 2.5 - + - -
448C LEU* 4.7 7.6 - - + -
507C LEU* 5.9 0.9 - - + -
510C ILE* 3.9 38.1 - - + -
514C ILE* 4.9 0.2 - - + -
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Residues in contact with ARG 436 (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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395C SER 4.0 1.8 + - - -
396C MET* 2.6 42.0 + - + +
397C GLU* 5.4 1.8 - - - +
398C HIS 4.2 0.6 + - - -
399C PRO* 3.4 47.5 - - - +
400C GLY 4.6 1.8 - - - +
429C LEU* 5.1 2.6 + - - +
432C SER* 3.0 27.6 + - - +
433C SER* 3.4 38.5 + - - +
435C PHE* 1.3 77.6 - - - +
437C MET* 1.3 61.8 + - - +
439C ASN* 3.1 21.7 + - - +
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Residues in contact with MET 437 (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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469A LEU* 5.5 6.7 - - + -
472A LYS* 5.1 19.3 - - + +
476A HIS* 5.1 6.7 - - - -
430C ALA 5.6 0.4 - - - +
433C SER* 3.0 33.1 + - - +
434C ARG* 3.0 58.6 - - + +
436C ARG* 1.3 76.2 - - - +
438C MET* 1.3 59.6 + - - +
439C ASN* 3.3 6.2 + - - +
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Residues in contact with MET 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C ARG* 3.0 56.1 + - - +
435C PHE* 3.8 7.4 - - - +
436C ARG 3.1 0.2 - - - -
437C MET* 1.3 76.6 - - - +
439C ASN* 1.3 69.2 + - - +
440C LEU* 4.2 4.9 - - + +
503C ARG* 2.8 41.6 + - + +
506C GLN* 3.4 32.3 - - + +
507C LEU* 3.6 28.9 - - + -
510C ILE* 3.6 20.9 - - - -
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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