Contacts of the helix formed by residues 433 - 454 (chain B) in PDB entry 3S95
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 PRO 433 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLN 3.5 10.3 - - - +
432B TYR* 1.3 97.7 - - + +
434B TRP* 1.3 66.0 + - + +
435B SER* 3.3 13.7 - - - +
436B GLN* 3.1 18.9 + - + +
437B ARG* 3.1 20.7 + - - +
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Residues in contact with TRP 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B SER 4.6 5.8 + - - -
431B GLN 6.2 0.4 - - - -
432B TYR 3.4 4.5 + - - -
433B PRO* 1.3 70.1 - - + +
435B SER* 1.3 61.2 + - - +
437B ARG* 3.2 49.3 + - + +
438B VAL* 2.9 35.3 + - - +
543B ILE* 3.6 14.8 - - + -
572B PRO* 3.4 33.0 - - + -
574B ASN* 3.4 30.8 + - + +
575B CYS* 3.7 13.5 - - + -
576B PRO* 3.4 25.4 - - + -
579B PHE* 3.9 23.8 - + - -
611B LEU* 3.9 16.6 - - + -
640B CL 4.0 1.6 - - + -
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Residues in contact with SER 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B PRO* 4.2 10.9 - - - +
434B TRP* 1.3 78.4 - - - +
436B GLN* 1.3 59.1 + - - +
438B VAL* 3.5 3.1 + - - +
439B SER* 3.0 27.0 + - - -
608B ARG* 4.2 11.1 - - - +
611B LEU* 3.9 26.8 - - - +
612B ALA* 5.1 10.5 - - - -
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Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TYR* 3.7 29.8 - - + +
433B PRO* 3.1 21.0 + - + +
435B SER* 1.3 77.6 + - - +
437B ARG* 1.3 67.9 + - - +
439B SER* 3.2 17.3 + - - -
440B PHE* 2.9 31.2 + - + -
471B ASN 5.1 0.3 - - - +
472B LYS* 3.5 44.8 + - + +
473B ASN* 5.8 0.2 + - - -
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Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B MET* 4.3 11.0 - - + -
429B ASP 3.9 3.4 + - - -
430B SER 3.2 22.0 + - - -
432B TYR* 2.8 49.2 + - + +
433B PRO 3.1 10.3 + - - +
434B TRP* 3.2 42.1 + - + +
436B GLN* 1.3 75.8 - - - +
438B VAL* 1.3 62.6 + - - +
440B PHE* 3.3 13.4 + - - +
441B ALA* 3.2 20.1 + - - +
542B ILE* 3.1 49.2 + - + +
543B ILE 3.6 1.2 + - - -
545B ARG* 3.6 9.7 - - - +
579B PHE* 4.6 1.8 - - + -
640B CL 3.3 23.8 - - - +
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Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B TRP* 2.9 21.2 + - - +
435B SER 3.9 4.3 - - - +
437B ARG* 1.3 76.0 - - - +
439B SER* 1.3 57.3 + - - +
441B ALA* 3.2 2.8 + - - +
442B LYS* 2.9 26.0 + - - +
576B PRO* 4.4 2.0 - - + -
579B PHE* 4.0 23.6 - - + -
604B LEU* 3.4 32.8 - - + +
607B LEU* 3.9 27.8 - - + -
608B ARG* 3.7 17.5 - - + +
611B LEU* 3.9 14.8 - - + -
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Residues in contact with SER 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B SER 3.0 16.0 + - - -
436B GLN* 3.4 25.0 + - - -
438B VAL* 1.3 74.0 - - - +
440B PHE* 1.3 67.6 + - - +
442B LYS* 3.3 3.3 + - - +
443B ASP* 2.9 38.4 + - - +
473B ASN* 4.8 5.2 + - - -
608B ARG* 4.0 22.4 - - - +
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Residues in contact with PHE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LEU* 3.7 23.1 - - + -
424B ILE* 4.2 9.6 - - + -
428B MET* 3.9 15.9 - - + -
432B TYR* 3.4 38.6 - + - -
436B GLN* 2.9 28.0 + - + -
437B ARG* 3.4 13.9 - - - +
439B SER* 1.3 76.2 - - - +
441B ALA* 1.3 63.8 + - - +
443B ASP* 3.3 2.3 + - - +
444B ILE* 3.2 30.1 + - + +
468B VAL* 4.0 16.8 - - + -
472B LYS* 3.4 23.6 - - + -
474B VAL* 3.4 25.5 - - + +
542B ILE* 4.4 12.3 - - + -
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ARG 3.2 8.6 + - - +
438B VAL 3.2 8.8 + - - +
440B PHE* 1.3 79.4 - - - +
442B LYS* 1.3 63.0 + - - +
444B ILE* 3.3 2.4 + - - -
445B ALA* 2.9 20.4 + - - +
535B PHE* 3.5 15.2 - - + -
539B LEU* 3.5 30.5 - - + -
542B ILE* 4.5 5.8 - - + +
579B PHE* 4.3 4.7 - - + -
604B LEU* 3.8 18.6 - - + -
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GOL 3.9 12.8 + - - -
395B ASN* 5.2 1.2 + - - -
438B VAL 2.9 16.3 + - - +
439B SER* 3.6 8.5 - - - +
441B ALA* 1.3 75.3 - - - +
443B ASP* 1.3 70.0 + - - +
445B ALA* 3.1 4.1 + - - +
446B SER* 2.8 34.1 + - - -
601B GLU* 3.0 39.2 + - + +
604B LEU* 3.9 18.5 - - + +
605B GLU* 3.6 44.6 - - - +
608B ARG* 5.2 2.9 - - - +
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Residues in contact with ASP 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ASN* 3.3 34.4 + - - +
439B SER* 2.9 26.8 + - - +
440B PHE 3.6 4.3 - - - +
442B LYS* 1.3 87.2 + - - +
444B ILE* 1.3 63.4 + - - +
446B SER* 3.2 3.1 + - - -
447B GLY 3.0 19.4 + - - -
472B LYS 4.3 1.4 - - - +
473B ASN* 3.2 20.9 - - - +
474B VAL* 3.0 33.6 + - + +
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Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B LEU* 3.8 23.6 - - + -
440B PHE 3.2 18.4 + - - +
441B ALA* 3.8 8.1 - - - +
443B ASP* 1.3 75.5 - - - +
445B ALA* 1.3 57.8 + - - +
447B GLY* 3.3 1.4 + - - -
448B MET* 2.9 45.9 + - + +
461B LEU* 4.2 11.9 - - + -
466B CYS* 3.7 19.5 - - - -
474B VAL* 3.7 22.4 - - + -
476B VAL* 4.2 15.2 - - + +
535B PHE* 3.7 22.9 - - + -
538B VAL* 4.3 12.1 - - + -
542B ILE* 5.0 0.9 - - + -
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B ALA 2.9 14.4 + - - +
442B LYS 3.5 7.9 - - - +
444B ILE* 1.3 76.2 - - - +
446B SER* 1.3 58.1 + - - +
449B ALA* 2.8 32.6 + - - +
535B PHE* 4.0 3.2 - - + -
597B PHE* 3.6 24.5 - - + +
600B LEU* 4.1 2.9 - - + -
601B GLU* 3.8 26.9 - - - +
604B LEU* 4.1 11.4 - - + -
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Residues in contact with SER 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B HIS* 3.3 19.6 + - - -
395B ASN* 3.4 16.0 + - - -
442B LYS* 2.8 25.0 + - - -
443B ASP* 3.2 5.1 + - - -
445B ALA* 1.3 74.4 - - - +
447B GLY* 1.3 61.2 + - - +
449B ALA* 3.4 2.4 + - - +
450B TYR* 3.1 22.9 + - - +
601B GLU* 2.6 35.1 + - - +
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Residues in contact with GLY 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B HIS* 4.0 8.7 - - - -
395B ASN* 3.6 28.4 - - - +
396B VAL* 3.8 6.0 - - - +
443B ASP 3.0 11.5 + - - -
444B ILE 3.8 2.5 - - - -
446B SER* 1.3 74.5 - - - +
448B MET* 1.3 58.8 + - - +
450B TYR* 3.3 4.9 + - - +
451B LEU* 2.9 30.7 + - - +
476B VAL* 4.8 2.2 - - - -
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Residues in contact with MET 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ILE* 2.9 25.8 + - + +
447B GLY* 1.3 74.4 - - - +
449B ALA* 1.3 64.8 + - - +
451B LEU* 3.2 23.1 + - + +
452B HIS* 2.9 34.3 + - + +
458B HIS* 3.8 12.1 - - + -
461B LEU* 3.9 27.6 - - + -
476B VAL* 4.1 16.6 - - + -
531B ASP* 3.3 42.2 - - + +
597B PHE* 3.5 26.7 - - + -
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Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GOL 4.9 0.9 + - - -
445B ALA 2.8 22.4 + - - +
446B SER 3.7 5.2 - - - +
448B MET* 1.3 71.4 - - - +
450B TYR* 1.3 62.0 + - - +
452B HIS* 3.4 4.8 + - - +
453B SER* 2.9 24.8 + - - -
597B PHE* 3.4 28.7 - - + +
598B VAL* 3.9 17.2 - - + +
601B GLU* 4.0 13.2 - - - +
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Residues in contact with TYR 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B CYS 4.2 0.9 + - - -
391B LEU* 3.6 20.2 - - + -
392B GLU* 2.9 40.2 + - - +
393B HIS* 3.5 44.0 - + + -
396B VAL* 3.9 11.7 - - + -
446B SER 3.1 8.9 + - - +
447B GLY 3.4 6.5 - - - +
448B MET 3.2 0.2 - - - -
449B ALA* 1.3 77.9 - - - +
451B LEU* 1.3 65.4 + - + +
453B SER* 2.7 28.1 + - - -
454B MET* 3.1 42.4 + - + +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B LEU* 3.8 27.4 - - + -
396B VAL* 4.2 10.8 - - + -
447B GLY 2.9 17.7 + - - +
448B MET* 3.2 35.2 + - + +
450B TYR* 1.3 75.9 - - + +
452B HIS* 1.3 58.8 + - + +
454B MET* 3.0 20.9 + - - +
455B ASN 3.3 0.2 + - - -
456B ILE* 3.1 36.4 + - + +
458B HIS* 4.1 12.3 - - + -
476B VAL* 4.3 5.2 - - + -
479B PHE* 3.4 36.1 - - + -
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Residues in contact with HIS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GOL 3.4 23.3 + - - +
448B MET* 2.9 23.5 + - + +
449B ALA* 3.9 5.4 - - - +
451B LEU* 1.3 75.5 - - - +
453B SER* 1.3 57.8 + - - +
455B ASN* 3.0 24.7 + - - +
456B ILE 3.2 21.1 - - - +
457B ILE* 4.5 0.2 - - - -
485B MET* 4.1 6.1 - - + +
528B GLU* 3.2 49.6 + - + +
531B ASP* 2.8 25.2 + - - +
532B VAL* 4.7 2.7 - - + +
596B SER* 6.2 0.2 - - - -
597B PHE* 3.4 33.4 + + + +
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Residues in contact with SER 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GOL 3.7 12.5 + - - -
449B ALA 2.9 15.2 + - - -
450B TYR* 2.7 29.6 + - - -
452B HIS* 1.3 76.9 - - - +
454B MET* 1.3 62.8 + - - +
455B ASN* 3.2 9.2 + - - +
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Residues in contact with MET 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B CYS* 3.8 27.4 - - + +
391B LEU* 4.3 7.2 - - + -
450B TYR* 3.1 46.9 + - + +
451B LEU 3.0 10.3 + - - +
453B SER* 1.3 79.2 - - - +
455B ASN* 1.3 69.9 + - - +
456B ILE* 3.3 20.8 + - + +
484B LEU* 4.4 5.5 - - - +
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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