Contacts of the helix formed by residues 529 - 545 (chain C) in PDB entry 7ATU
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 LYS 529 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C GLU* 5.2 0.7 - - - +
527C ASP* 2.7 27.0 + - - +
528C GLU* 1.3 81.7 - - + +
530C VAL* 1.3 54.0 + - - +
531C ASP 3.0 3.4 - - - -
532C VAL* 2.8 43.6 + - + +
591C PRO* 3.8 39.2 + - + +
592C GLU* 4.4 8.4 + - - +
594C ARG* 3.0 40.9 + - + +
595C PRO 4.9 0.7 - - - +
596C SER* 4.3 16.8 - - - +
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Residues in contact with VAL 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ILE* 3.8 21.8 - - + -
459C ARG* 4.6 11.2 - - + -
517C ALA* 3.5 25.9 + - + +
519C GLU* 3.5 13.5 - - + +
520C MET* 4.4 13.0 - - + -
526C TYR* 3.8 33.7 - - + -
527C ASP 3.3 11.6 + - - +
528C GLU 4.6 0.2 - - - +
529C LYS* 1.3 76.1 - - - +
531C ASP* 1.3 66.9 + - - +
533C PHE* 3.4 5.9 + - - +
534C SER* 3.3 23.1 + - - -
594C ARG* 3.9 7.4 - - - +
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Residues in contact with ASP 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C MET* 3.1 20.1 - - + +
452C HIS* 2.9 30.3 + - - +
457C ILE* 3.6 6.2 - - - +
458C HIS* 2.8 27.0 + - - +
459C ARG* 2.9 27.5 + - - -
460C ASP 4.6 0.2 + - - -
461C LEU* 3.7 8.8 - - + +
528C GLU 3.5 0.4 + - - -
529C LYS 2.9 1.2 + - - -
530C VAL* 1.3 78.7 - - - +
532C VAL* 1.3 59.9 + - - +
534C SER* 3.5 5.8 + - - -
535C PHE* 2.9 28.6 + - - +
597C PHE* 3.4 7.4 - - + -
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Residues in contact with VAL 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C HIS* 4.8 1.6 - - + -
528C GLU 4.7 1.1 - - - +
529C LYS* 2.8 35.2 + - + +
531C ASP* 1.3 71.4 - - - +
533C PHE* 1.3 51.7 + - - +
535C PHE* 3.2 3.6 + - - +
536C GLY 2.7 29.1 + - - -
586C CYS* 3.6 26.0 - - - +
594C ARG* 4.1 7.2 - - + -
595C PRO* 3.2 32.1 - - + +
596C SER* 4.9 1.8 - - - -
597C PHE* 3.5 26.0 - - + -
600C LEU* 3.8 18.4 - - + -
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Residues in contact with PHE 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C TRP 3.6 13.5 - - - -
516C MET 3.6 19.7 - - - -
517C ALA* 3.8 6.1 - - + -
518C PRO* 3.6 19.7 - - + -
529C LYS 3.5 2.2 + - - -
530C VAL 3.4 10.3 + - - +
531C ASP 3.2 0.2 - - - -
532C VAL* 1.3 74.9 - - - +
534C SER* 1.3 57.3 + - - +
536C GLY* 2.5 25.5 + - - -
537C ILE* 2.9 25.5 + - + -
555C ARG* 3.8 15.3 - - - -
559C PHE 3.5 21.1 - - - -
560C GLY* 4.1 6.7 - - - -
586C CYS 3.8 7.0 + - - -
587C CYS* 3.2 34.3 - - + -
588C ASP 3.7 13.0 - - - -
589C LEU* 4.6 0.2 - - + -
594C ARG* 3.7 20.8 - - - +
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Residues in contact with SER 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ARG 5.3 3.1 + - - -
460C ASP* 5.0 2.3 + - - -
461C LEU* 3.0 41.2 + - - -
515C TRP* 2.8 31.7 + - - +
516C MET* 4.5 2.9 - - - -
517C ALA 4.8 0.2 + - - -
530C VAL 3.3 10.3 + - - -
531C ASP* 3.8 6.3 + - - -
533C PHE* 1.3 77.0 - - - +
535C PHE* 1.3 57.1 + - - +
537C ILE 3.3 1.7 + - - +
538C VAL* 2.9 34.3 + - - +
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Residues in contact with PHE 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ALA* 3.2 29.4 - - - -
444C ILE* 3.3 41.5 - - + -
445C ALA* 3.8 6.3 - - + -
461C LEU* 3.7 6.5 - - + +
531C ASP 2.9 15.4 + - - +
532C VAL 3.2 10.1 - - - +
533C PHE 2.9 0.2 + - - -
534C SER* 1.3 75.0 - - - +
536C GLY* 1.3 52.3 + - - +
538C VAL* 3.2 7.2 + - + +
539C LEU* 2.7 60.9 + - + +
586C CYS* 3.8 9.2 - - - -
597C PHE* 3.6 13.2 - + + -
600C LEU* 3.7 30.5 - - + -
604C LEU* 3.7 14.8 - - + -
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Residues in contact with GLY 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C VAL 2.7 10.2 + - - -
533C PHE 2.5 16.0 + - - -
535C PHE* 1.3 70.5 - - - +
537C ILE* 1.3 60.6 + - - -
539C LEU* 3.1 4.7 + - - -
540C CYS* 2.9 21.0 + - - -
583C THR* 3.5 9.7 - - - +
586C CYS* 3.8 14.5 - - - +
587C CYS* 3.5 20.9 - - - -
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Residues in contact with ILE 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C TYR 4.5 2.5 - - - +
515C TRP* 3.4 38.1 - - + -
533C PHE* 2.9 38.4 + - + +
534C SER 3.9 1.1 - - - +
536C GLY* 1.3 71.8 - - - -
538C VAL* 1.3 62.7 + - - +
540C CYS* 3.1 7.2 + - - +
541C GLU* 3.0 25.8 + - - +
548C ALA* 3.5 23.6 - - + -
553C LEU* 3.9 16.8 - - + -
555C ARG* 3.8 29.4 - - - +
561C LEU* 5.5 2.7 - - + -
587C CYS* 4.0 13.0 - - - -
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Residues in contact with VAL 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU* 3.8 28.3 - - + -
444C ILE* 4.1 15.7 - - + -
461C LEU* 4.6 5.4 - - + -
462C ASN* 3.7 26.0 - - - +
463C SER* 5.0 1.1 - - - -
466C CYS* 5.1 0.7 - - - -
515C TRP* 3.6 16.6 - - + +
534C SER 2.9 23.0 + - - +
535C PHE* 3.2 13.4 + - + +
537C ILE* 1.3 77.4 - - - +
539C LEU* 1.3 60.7 + - + +
541C GLU* 3.2 12.4 + - + +
542C ILE* 3.1 25.5 + - + +
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Residues in contact with LEU 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ALA* 3.6 14.6 - - + -
535C PHE* 2.7 53.5 + - + +
536C GLY* 3.1 5.6 + - - +
538C VAL* 1.3 70.6 - - + +
540C CYS* 1.3 65.7 + - - +
542C ILE* 4.6 8.1 - - + -
543C ILE* 3.0 29.6 + - - +
579C PHE* 3.4 39.0 - - + +
582C ILE* 4.4 17.7 - - + -
583C THR* 3.4 27.8 - - + +
586C CYS* 4.9 1.1 - - - -
604C LEU* 4.7 1.8 - - + -
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Residues in contact with CYS 540 (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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536C GLY 2.9 11.3 + - - -
537C ILE* 3.4 10.1 - - - +
539C LEU* 1.3 77.0 - - - +
541C GLU* 1.3 62.3 + - - +
543C ILE* 4.6 1.1 - - - -
544C GLY* 3.0 23.0 + - - -
546C VAL* 4.7 1.4 - - - +
553C LEU* 3.6 19.7 - - + -
561C LEU* 3.6 35.7 - - - -
566C PHE* 3.8 26.2 - - + -
580C PHE* 4.5 1.1 - - - -
583C THR* 3.5 22.0 - - - -
587C CYS* 4.5 3.6 - - - -
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Residues in contact with GLU 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ARG* 4.5 7.3 + - - -
425C ILE* 3.2 19.7 - - + +
463C SER* 3.2 30.2 + - - -
515C TRP* 2.3 41.2 + - - +
537C ILE 3.0 13.8 + - - +
538C VAL* 3.2 11.3 + - + +
540C CYS* 1.3 75.1 - - - +
542C ILE* 1.3 57.3 + - - +
545C ARG* 3.0 23.1 + - - -
546C VAL* 3.6 30.1 + - - +
547C ASN* 4.7 0.5 - - - -
548C ALA* 3.9 14.5 + - + +
553C LEU* 4.5 4.0 - - + +
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Residues in contact with ILE 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU* 3.9 21.1 - - + -
425C ILE* 3.7 21.5 - - + -
428C MET* 4.4 2.2 - - + +
437C ARG* 3.2 57.7 + - + +
440C PHE* 3.9 28.7 - - + -
441C ALA* 4.5 6.7 - - - +
444C ILE* 5.4 0.4 - - + -
538C VAL* 3.1 18.7 + - + +
539C LEU* 3.9 11.9 - - + +
540C CYS 3.2 0.2 - - - -
541C GLU* 1.3 76.7 - - - +
543C ILE* 1.3 66.7 + - - +
544C GLY 3.1 2.7 + - - -
545C ARG* 3.6 7.3 + - - +
579C PHE* 4.3 11.2 - - + -
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Residues in contact with ILE 543 (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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434C TRP* 3.2 24.8 - - + -
437C ARG* 3.6 3.3 + - - -
539C LEU 3.0 15.8 + - - +
540C CYS 3.9 1.6 - - - +
542C ILE* 1.3 77.3 - - - +
544C GLY* 1.3 57.9 + - - +
545C ARG* 5.0 1.2 + - - -
566C PHE* 3.7 28.0 - - + -
571C CYS* 4.4 6.3 - - - -
572C PRO* 3.3 25.3 - - + +
575C CYS* 4.8 3.4 - - + -
579C PHE* 3.3 45.3 - - + +
580C PHE* 3.8 15.3 - - + +
583C THR* 3.2 28.7 - - + +
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Residues in contact with GLY 544 (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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540C CYS 3.0 13.2 + - - -
543C ILE* 1.3 81.0 - - - +
545C ARG* 1.3 80.2 + - - +
546C VAL* 3.1 17.3 - - - +
566C PHE* 4.5 4.3 - - - -
570C TYR* 4.1 22.6 - - - +
572C PRO* 5.4 0.2 - - - -
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Residues in contact with ARG 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ARG* 5.1 0.7 + - - -
425C ILE* 3.5 21.0 - - + +
428C MET* 3.5 41.6 + - + +
429C ASP 3.1 19.1 + - - -
430C SER* 3.3 43.4 + - - +
437C ARG* 3.8 13.7 - - - +
541C GLU 3.0 14.4 + - - -
542C ILE 4.1 4.7 - - - +
543C ILE 5.0 0.6 + - - -
544C GLY* 1.3 85.2 + - - +
546C VAL* 1.3 58.5 + - - +
570C TYR* 5.4 1.2 - - - -
572C PRO* 4.7 19.0 - - - +
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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