Contacts of the helix formed by residues 528 - 545 (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 GLU 528 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GOL 4.0 23.8 + - - +
452B HIS* 3.2 45.5 - - + +
457B ILE* 3.6 16.5 - - + +
485B MET* 4.0 28.1 - - + +
527B ASP* 1.3 86.6 - - - +
529B LYS* 1.3 81.9 + - + +
530B VAL 3.1 1.1 - - - -
531B ASP* 3.0 20.0 + - - +
532B VAL 4.0 0.5 + - - -
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Residues in contact with LYS 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ASP* 2.9 20.5 + - - +
528B GLU* 1.3 94.4 - - + +
530B VAL* 1.3 63.9 + - - +
531B ASP 3.1 0.4 - - - -
532B VAL* 3.1 31.1 + - + +
533B PHE 3.2 4.3 + - - -
591B PRO* 3.1 41.0 + - + +
592B GLU* 3.8 12.3 + - - +
594B ARG* 2.7 47.5 + - + +
596B SER* 4.3 18.2 - - - +
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Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ILE* 3.7 20.9 - - + -
459B ARG* 4.7 1.6 - - + -
517B ALA* 3.7 23.1 + - + +
519B GLU* 3.5 18.6 + - + +
520B MET* 3.8 24.5 - - + -
526B TYR* 3.5 29.2 - - + -
527B ASP 3.3 18.6 - - - +
528B GLU 3.1 1.0 - - - -
529B LYS* 1.3 77.0 - - - +
531B ASP* 1.3 68.8 - - - +
533B PHE* 3.3 6.8 + - - +
534B SER* 3.2 23.7 + - - -
594B ARG* 3.9 0.9 - - - +
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Residues in contact with ASP 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B MET* 3.3 13.4 - - + +
452B HIS* 2.8 26.5 + - - +
457B ILE* 3.4 9.9 - - - +
458B HIS* 2.9 24.9 + - - +
459B ARG* 2.9 28.8 + - - -
460B ASP 4.6 0.3 + - - -
461B LEU* 3.8 7.5 - - + +
528B GLU 3.0 9.5 + - - +
530B VAL* 1.3 79.9 - - - +
532B VAL* 1.3 59.9 + - - +
534B SER* 3.4 9.4 + - - -
535B PHE* 3.0 21.8 + - - +
597B PHE* 3.5 16.5 - - + -
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Residues in contact with VAL 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B HIS* 4.7 1.8 - - + -
528B GLU 4.5 1.3 - - - +
529B LYS* 3.1 24.7 + - + +
531B ASP* 1.3 74.4 - - - +
533B PHE* 1.3 61.7 + - - +
535B PHE* 3.2 2.1 + - - +
536B GLY 2.9 24.1 + - - -
586B CYS* 3.6 27.1 - - + +
594B ARG* 3.8 18.8 - - + -
595B PRO* 3.3 27.8 - - + +
596B SER* 4.7 0.9 - - - -
597B PHE* 3.6 34.5 - - + +
600B LEU* 4.0 5.2 - - + -
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Residues in contact with PHE 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B TRP 3.8 5.8 - - - -
516B MET 3.6 10.5 - - - -
517B ALA* 3.6 15.7 - - + -
518B PRO* 3.5 22.2 - - + -
529B LYS 3.2 6.3 + - - -
530B VAL 3.5 8.5 - - - +
532B VAL* 1.3 75.9 - - - +
534B SER* 1.3 64.6 + - - +
536B GLY* 3.0 11.8 + - - -
537B ILE* 3.1 30.7 + - + +
555B ARG* 3.5 19.5 - - - -
559B PHE 3.5 22.2 - - - -
560B GLY* 4.5 5.6 - - - -
586B CYS 3.4 8.8 + - - -
587B CYS* 3.4 40.3 - - + -
588B ASP 4.7 0.2 - - - -
594B ARG* 3.8 22.2 - - - +
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Residues in contact with SER 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ARG* 5.5 3.5 + - - -
460B ASP* 5.8 0.2 - - - -
461B LEU* 3.4 32.8 + - - +
515B TRP* 2.7 29.6 + - - -
516B MET* 4.5 2.9 - - - -
517B ALA 4.6 0.3 + - - -
530B VAL 3.2 12.2 + - - -
531B ASP* 3.5 11.8 + - - -
532B VAL 3.3 0.2 - - - -
533B PHE* 1.3 77.8 - - - +
535B PHE* 1.3 62.6 + - - +
537B ILE* 3.1 7.0 + - - +
538B VAL* 3.1 25.6 + - - +
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Residues in contact with PHE 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ALA* 3.5 29.8 - - - -
444B ILE* 3.7 31.9 - - + -
445B ALA* 4.0 7.6 - - + -
461B LEU* 4.0 8.0 - - + +
531B ASP 3.0 14.1 + - - +
532B VAL 3.3 7.2 - - - +
534B SER* 1.3 75.5 - - - +
536B GLY* 1.3 58.8 + - - +
538B VAL* 3.1 12.8 + - + +
539B LEU* 2.8 60.9 + - + +
586B CYS* 4.0 3.4 - - - -
597B PHE* 3.6 15.7 - + + -
600B LEU* 3.8 31.0 - - + -
604B LEU* 3.7 17.9 - - + -
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Residues in contact with GLY 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL 2.9 10.7 + - - -
533B PHE 3.0 5.3 + - - -
535B PHE* 1.3 76.9 - - - +
537B ILE* 1.3 61.4 + - - +
539B LEU* 3.2 9.6 + - - +
540B CYS* 3.0 25.3 + - - -
583B THR* 3.5 4.1 - - - +
586B CYS* 3.6 23.3 - - - -
587B CYS* 3.6 13.2 - - - -
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Residues in contact with ILE 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B TYR 3.9 13.7 - - - +
515B TRP* 3.4 24.7 - - + -
533B PHE* 3.1 34.5 + - + +
534B SER 3.1 7.6 + - - +
536B GLY* 1.3 73.5 - - - +
538B VAL* 1.3 62.6 + - - +
540B CYS* 3.1 9.8 + - - +
541B GLU* 3.0 20.1 + - - +
548B ALA* 3.6 23.6 - - + -
553B LEU* 3.9 15.3 - - + -
555B ARG* 3.8 28.5 - - - +
561B LEU* 5.4 3.4 - - + -
587B CYS* 4.1 11.2 - - - -
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LEU* 3.8 28.9 - - + -
444B ILE* 4.3 11.7 - - + -
461B LEU* 4.8 6.1 - - + -
462B ASN* 3.8 18.8 - - - +
463B SER* 3.8 4.0 - - - +
466B CYS* 5.5 1.1 - - - -
515B TRP* 3.7 18.6 - - + +
534B SER 3.1 16.5 + - - +
535B PHE* 3.1 15.0 + - + +
537B ILE* 1.3 74.8 - - - +
539B LEU* 1.3 60.1 + - + +
541B GLU* 3.0 16.3 + - - +
542B ILE* 3.0 28.7 + - + +
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Residues in contact with LEU 539 (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* 3.5 32.1 - - + -
535B PHE* 2.8 47.7 + - + +
536B GLY* 3.2 7.4 + - - +
538B VAL* 1.3 73.9 - - + +
540B CYS* 1.3 58.8 + - - +
542B ILE* 3.2 9.8 + - + +
543B ILE* 2.9 35.2 + - + +
579B PHE* 4.0 16.4 - - + -
582B ILE* 4.1 16.4 - - + -
583B THR* 3.2 36.1 - - - +
586B CYS* 4.2 4.3 - - - -
604B LEU* 5.4 0.9 - - + -
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Residues in contact with CYS 540 (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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536B GLY 3.0 19.2 + - - -
537B ILE* 3.1 13.0 + - - +
539B LEU* 1.3 75.9 - - - +
541B GLU* 1.3 57.3 + - - +
543B ILE* 4.7 0.7 - - - -
544B GLY* 2.9 26.9 + - - -
546B VAL* 3.6 9.3 - - - +
553B LEU* 3.7 23.6 - - + -
561B LEU* 3.8 33.2 - - - -
566B PHE* 3.7 14.7 - - + -
583B THR* 3.5 18.4 - - - +
587B CYS* 4.5 3.6 - - - -
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Residues in contact with GLU 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ARG* 4.0 13.7 - - - -
425B ILE* 3.6 17.1 - - + +
463B SER* 2.5 34.9 + - - -
515B TRP* 2.8 37.2 + - - -
537B ILE 3.0 14.1 + - - +
538B VAL* 3.0 14.1 + - - +
540B CYS* 1.3 75.4 - - - +
542B ILE* 1.3 55.8 + - - +
545B ARG* 2.8 34.3 + - - -
546B VAL* 3.3 25.6 + - + +
548B ALA* 3.9 15.3 + - + +
553B LEU* 5.4 0.7 - - + -
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Residues in contact with ILE 542 (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* 4.2 12.8 - - + -
425B ILE* 3.9 22.4 - - + -
428B MET* 4.6 4.4 - - + +
437B ARG* 3.1 68.7 + - + +
440B PHE* 4.4 11.0 - - + -
441B ALA* 4.5 6.3 - - + +
444B ILE* 5.0 0.4 - - + -
535B PHE* 6.4 0.2 - - + -
538B VAL* 3.0 32.4 + - + +
539B LEU* 3.2 20.6 + - + +
541B GLU* 1.3 75.8 - - - +
543B ILE* 1.3 65.4 + - - +
545B ARG* 3.9 4.3 + - - +
579B PHE* 4.5 10.1 - - + -
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Residues in contact with ILE 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B TRP* 3.6 10.7 - - + -
437B ARG* 3.6 4.2 + - - -
539B LEU 2.9 18.2 + - - +
540B CYS* 4.1 2.2 - - - +
542B ILE* 1.3 78.7 - - - +
544B GLY* 1.3 60.3 + - - +
566B PHE* 3.9 19.3 - - + -
571B CYS* 4.4 2.2 - - - -
572B PRO* 3.2 37.8 - - + +
575B CYS* 3.9 15.0 - - - -
579B PHE* 3.6 47.8 - - + +
580B PHE* 4.2 8.3 - - + -
583B THR* 3.2 31.2 - - + +
640B CL 4.1 0.9 - - - +
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Residues in contact with GLY 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B CYS 2.9 15.5 + - - -
543B ILE* 1.3 76.4 - - - +
545B ARG* 1.3 77.9 + - - +
546B VAL* 3.1 11.7 + - - +
566B PHE* 3.8 9.2 - - - -
570B TYR* 3.6 29.4 - - - +
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Residues in contact with ARG 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ARG* 5.2 2.0 + - - -
425B ILE* 3.8 19.3 - - + +
428B MET* 2.8 49.3 + - + -
429B ASP* 3.4 25.7 - - - +
430B SER* 3.7 21.4 - - - +
437B ARG* 3.6 17.9 - - - +
541B GLU 2.8 12.3 + - - -
542B ILE 3.9 0.9 + - - +
543B ILE 3.4 0.2 - - - -
544B GLY* 1.3 79.7 + - - +
546B VAL* 1.3 57.3 + - - +
570B TYR* 5.7 0.5 - - - -
640B CL 3.2 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