Contacts of the helix formed by residues 421 - 438 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D KN0 3.7 33.4 - - + -
342D MET* 3.9 13.9 - - + +
343D MET* 3.2 38.6 - - + -
346D LEU* 4.3 4.9 - - + -
415D GLY 4.4 0.4 - - - +
418D VAL* 3.2 44.3 + - + +
420D GLY* 1.3 76.8 - - - +
422D VAL* 1.3 54.6 + - - +
423D GLU 3.2 3.4 - - - -
424D ILE* 3.0 11.7 + - + -
425D PHE* 2.6 41.8 + - + +
524D HIS* 3.5 24.0 - - + -
528D MET* 5.5 1.3 - - + -
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Residues in contact with VAL 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LYS* 3.2 33.0 - - + +
532A ASN* 6.4 0.7 - - + -
412D ARG* 4.2 31.0 - - + +
415D GLY 3.5 25.2 + - - +
416D LYS* 4.1 12.3 - - + -
418D VAL 3.6 2.0 - - - +
419D GLU 3.3 14.6 - - - +
420D GLY 3.4 1.1 - - - -
421D MET* 1.3 71.8 - - - +
423D GLU* 1.3 59.0 + - + +
425D PHE* 3.3 5.6 - - + +
426D ASP* 2.9 33.7 + - - +
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Residues in contact with GLU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D GLY 4.4 6.4 + - - +
421D MET 3.2 0.6 - - - -
422D VAL* 1.3 80.5 - - + +
424D ILE* 1.3 59.9 + - + +
426D ASP* 3.3 9.3 + - - +
427D MET* 3.0 37.3 + - + +
520D LYS* 4.9 13.7 + - - -
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Residues in contact with ILE 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D KN0 3.5 45.3 - - + -
388D MET* 4.1 12.6 - - + -
420D GLY 4.5 11.2 - - - +
421D MET* 3.0 8.5 + - - +
423D GLU* 1.3 74.3 - - + +
425D PHE* 1.3 66.4 + - - +
427D MET* 3.3 24.8 + - + +
428D LEU* 2.9 33.9 + - + +
517D MET* 4.7 2.2 - - + +
520D LYS* 3.8 15.0 - - + +
521D GLY* 3.7 21.1 - - - +
524D HIS* 4.2 8.7 - - + -
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Residues in contact with PHE 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D KN0 5.8 2.4 - + - -
342D MET* 4.8 3.6 - - + -
402D LEU* 3.5 36.1 - - + +
404D PHE* 4.0 16.4 - + - -
410D LEU* 3.7 27.4 - - + -
411D ASP 3.5 32.1 - - - -
412D ARG* 3.9 9.4 - - + -
415D GLY* 3.8 21.5 - - - +
418D VAL* 5.3 3.1 - - + -
421D MET* 2.6 25.3 + - + +
422D VAL* 3.3 11.7 - - + +
424D ILE* 1.3 72.9 - - - +
426D ASP* 1.3 58.0 + - - +
428D LEU* 3.2 6.7 + - + +
429D LEU* 2.9 46.1 + - + +
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Residues in contact with ASP 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B LEU* 5.6 1.8 - - + +
412D ARG* 2.8 51.6 + - - +
422D VAL 2.9 17.9 + - - +
423D GLU* 3.5 12.8 - - - +
424D ILE 3.2 0.2 - - - -
425D PHE* 1.3 77.8 - - - +
427D MET* 1.3 57.4 + - + +
429D LEU* 3.3 11.7 + - - +
430D ALA* 2.9 29.7 + - - +
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Residues in contact with MET 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B THR* 3.8 22.9 - - + -
423D GLU* 3.0 18.7 + - + +
424D ILE* 3.3 39.5 + - + +
426D ASP* 1.3 75.1 - - + +
428D LEU* 1.3 61.2 + - - +
430D ALA* 3.2 5.3 + - - +
431D THR* 2.9 28.9 + - - -
513D HIS* 3.5 13.5 + - - +
516D HIS* 3.8 27.1 - - - -
517D MET* 3.6 26.7 - - + -
520D LYS* 4.0 19.5 - - + -
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Residues in contact with LEU 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D KN0 3.6 31.2 - - + -
388D MET* 4.2 24.5 - - + +
391D LEU* 3.9 16.8 - - + -
392D VAL* 3.8 22.3 - - + +
402D LEU* 3.9 24.4 - - + +
424D ILE* 2.9 25.3 + - + +
425D PHE* 3.4 7.0 - - + +
427D MET* 1.3 76.6 - - - +
429D LEU* 1.3 62.3 + - - +
431D THR* 3.1 4.4 + - - -
432D SER* 3.0 23.2 + - - -
517D MET* 3.7 22.4 - - + -
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Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400D GLY* 3.5 21.1 - - - +
401D LYS 3.5 42.4 - - - +
402D LEU* 4.1 11.9 - - + +
412D ARG* 4.4 12.3 - - + -
425D PHE* 2.9 34.2 + - + +
426D ASP* 3.5 19.7 - - - +
428D LEU* 1.3 75.6 - - - +
430D ALA* 1.3 64.3 + - - +
432D SER* 3.3 7.3 + - - -
433D SER* 3.0 24.5 + - - -
436D ARG* 5.1 2.6 + - - +
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Residues in contact with ALA 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B TYR* 2.9 36.6 - - + +
462B LEU* 4.0 17.5 - - + +
426D ASP 2.9 16.5 + - - +
427D MET* 3.2 7.4 + - - +
429D LEU* 1.3 76.9 - - - +
431D THR* 1.3 58.2 + - - +
433D SER* 3.5 7.2 + - - -
434D ARG* 3.1 25.8 + - - +
437D MET* 5.6 0.7 - - - +
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Residues in contact with THR 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B TYR* 5.6 2.2 - - + -
392D VAL* 3.8 22.9 - - + -
427D MET 2.9 14.7 + - - -
428D LEU 3.1 7.4 + - - -
430D ALA* 1.3 75.0 - - - +
432D SER* 1.3 65.8 + - - +
434D ARG* 3.1 7.8 + - + +
435D PHE* 2.9 27.2 + - + -
510D ILE* 3.9 28.0 - - + -
513D HIS* 2.9 24.3 - - + -
514D ILE* 4.6 3.6 - - + -
517D MET* 3.4 11.7 - - + +
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Residues in contact with SER 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D VAL* 3.5 23.5 - - - +
395D SER* 3.2 19.5 + - - -
396D MET* 3.2 25.3 - - - +
401D LYS 5.6 0.2 - - - -
402D LEU* 5.3 1.6 - - - -
428D LEU 3.0 11.5 + - - -
429D LEU* 3.6 12.3 - - - -
431D THR* 1.3 77.2 - - - +
433D SER* 1.3 57.6 + - - +
435D PHE* 3.2 6.0 + - - +
436D ARG* 3.0 33.5 + - - +
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Residues in contact with SER 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D LEU 3.0 17.8 + - - -
430D ALA* 3.7 8.1 - - - -
432D SER* 1.3 74.5 - - - +
434D ARG* 1.3 61.3 + - - +
436D ARG* 3.3 28.7 + - - +
437D MET* 3.0 42.6 + - - +
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Residues in contact with ARG 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B TYR* 4.1 16.0 + - + -
476B HIS* 3.5 46.2 + - - +
430D ALA 3.1 13.9 + - - +
431D THR* 3.1 13.0 + - + +
433D SER* 1.3 73.4 - - - +
435D PHE* 1.3 65.6 + - + +
437D MET* 3.0 38.6 - - + +
438D MET* 3.0 47.4 + - - +
506D GLN* 3.7 37.4 + - - +
510D ILE* 3.7 28.6 - - + +
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Residues in contact with PHE 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D ILE* 4.1 29.8 - - + -
392D VAL* 3.4 26.2 - - + -
393D TRP* 4.3 13.5 - - + -
396D MET* 3.6 20.9 - - + +
431D THR* 2.9 20.3 + - + -
432D SER 3.3 9.6 - - - +
434D ARG* 1.3 75.6 - - - +
436D ARG* 1.3 63.0 + - - +
438D MET* 3.3 4.3 + - - -
439D ASN 3.1 2.9 + - - -
440D LEU* 3.1 61.7 + - + -
445D PHE* 4.7 0.9 - + - -
448D LEU* 4.7 7.9 - - + -
507D LEU* 6.0 0.9 - - + -
510D ILE* 3.9 37.0 - - + -
514D ILE* 4.9 0.2 - - + -
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Residues in contact with ARG 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D SER 4.0 1.8 + - - -
396D MET* 2.6 41.9 + - + +
397D GLU* 5.4 1.6 - - - +
398D HIS 4.2 0.6 + - - -
399D PRO* 3.4 48.1 - - - +
400D GLY 4.6 1.6 - - - +
429D LEU* 5.1 2.2 + - - +
432D SER* 3.0 28.0 + - - +
433D SER* 3.4 38.9 + - - +
435D PHE* 1.3 77.6 - - - +
437D MET* 1.3 61.2 + - - +
439D ASN* 3.1 21.7 + - - +
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Residues in contact with MET 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B LEU* 5.7 5.6 - - + -
472B LYS* 5.3 15.7 - - + +
476B HIS* 5.1 7.0 - - - +
430D ALA 5.6 0.7 - - - +
433D SER* 3.0 33.6 + - - +
434D ARG* 3.0 58.6 - - + +
436D ARG* 1.3 76.0 - - - +
438D MET* 1.3 59.4 + - - +
439D ASN* 3.3 6.7 + - - +
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Residues in contact with MET 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D ARG* 3.0 56.0 + - - +
435D PHE* 3.8 7.2 - - - +
436D ARG 3.1 0.2 - - - -
437D MET* 1.3 76.7 - - - +
439D ASN* 1.3 69.1 + - - +
440D LEU* 4.2 4.7 - - + +
503D ARG* 2.8 41.0 + - + +
506D GLN* 3.4 32.8 - - + +
507D LEU* 3.6 29.4 - - + +
510D ILE* 3.6 20.6 - - - -
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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