Contacts of the helix formed by residues 433 - 452 (chain C) in PDB entry 1RR8
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 SER 433 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C TRP* 3.9 4.3 + - - -
348C GLU* 3.4 29.2 - - - -
429C LEU* 3.5 24.7 - - - +
430C ASN* 2.7 24.7 + - - +
432C SER* 1.3 83.8 + - - +
434C ARG* 1.3 60.3 + - - +
435C ILE* 3.8 1.6 - - - +
436C LYS* 3.7 14.4 + - - +
437C GLY* 3.2 24.8 + - - -
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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
----------------------------------------------------------
203C TRP* 3.8 27.9 - - + -
205C TRP* 3.9 38.0 - - + +
211C TYR* 3.6 51.1 - - - +
216C LYS* 3.5 24.2 + - - +
343C MET* 4.2 19.4 + - - +
344C ASP* 4.7 7.1 + - - +
348C GLU* 3.1 11.8 + - - +
433C SER* 1.3 72.9 - - - +
435C ILE* 1.3 86.1 + - - +
438C GLU* 3.0 49.3 + - - +
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Residues in contact with ILE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LYS* 3.7 21.1 - - + +
343C MET* 3.9 21.3 - - + -
348C GLU* 4.9 0.6 + - - -
411C THR* 3.8 38.4 - - + +
429C LEU* 4.0 26.0 - - + +
433C SER* 3.8 11.4 - - - +
434C ARG* 1.3 109.2 - - - +
436C LYS* 1.3 69.1 + - + +
438C GLU* 4.9 1.6 - - - +
439C LYS* 3.8 22.7 + - - +
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Residues in contact with LYS 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A C 4.6 14.1 - - - +
9A T 4.2 15.8 - - - +
411C THR* 5.4 3.4 - - - -
428C MET* 3.5 36.6 - - - -
429C LEU 3.7 26.5 - - - +
430C ASN 3.8 7.0 - - - +
431C PRO* 4.1 11.9 - - + +
433C SER* 3.7 13.9 + - - +
434C ARG 3.3 0.4 - - - -
435C ILE* 1.3 87.0 - - + +
437C GLY* 1.3 61.5 + - - +
438C GLU 3.4 0.7 - - - -
439C LYS* 3.4 6.5 + - + +
440C ASP* 3.0 26.2 + - - +
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Residues in contact with GLY 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TRP* 3.4 18.2 - - - -
431C PRO 4.0 8.2 + - - -
433C SER 3.2 16.3 + - - -
436C LYS* 1.3 79.5 - - - +
438C GLU* 1.3 58.5 - - - +
440C ASP* 3.3 7.7 + - - +
441C TRP* 2.9 28.4 + - - +
751C LYS 5.4 0.7 - - - -
754C TRP* 4.1 9.6 + - - -
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Residues in contact with GLU 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TRP* 3.5 26.1 - - + +
210C ARG* 3.8 27.2 - - - +
211C TYR* 3.4 38.0 + - - +
434C ARG* 3.0 36.7 + - - +
435C ILE* 4.9 2.0 - - - +
437C GLY* 1.3 74.6 - - - +
439C LYS* 1.3 59.0 + - + +
441C TRP* 3.4 12.0 + - + +
442C GLN* 3.0 46.3 + - + +
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Residues in contact with LYS 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A C 5.2 7.5 + - - -
9A T 3.7 33.4 + - - +
216C LYS* 4.4 19.0 - - - +
435C ILE 3.8 15.4 + - - +
436C LYS* 3.4 11.5 + - + +
437C GLY 3.2 0.6 - - - -
438C GLU* 1.3 80.1 - - + +
440C ASP* 1.3 55.7 + - - +
442C GLN* 3.4 25.8 + - + +
443C LYS* 3.0 27.4 + - - +
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Residues in contact with ASP 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A T 4.7 0.2 + - - -
436C LYS 3.0 18.0 + - - +
437C GLY* 3.5 9.9 - - - +
438C GLU 3.2 0.2 - - - -
439C LYS* 1.3 75.4 - - - +
441C TRP* 1.3 61.7 + - - +
443C LYS* 2.9 36.0 + - - +
444C TYR* 3.0 45.1 + - - -
721C LEU 4.8 1.3 - - - +
751C LYS* 3.7 26.4 + - - +
752C PHE* 4.1 8.8 - - - -
754C TRP* 4.5 8.8 + - + +
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Residues in contact with TRP 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C TRP* 4.0 20.0 - + - -
206C TRP* 4.0 32.8 - - + -
210C ARG* 5.4 14.8 - - + -
437C GLY 2.9 14.7 + - - +
438C GLU* 3.6 15.0 - - + +
440C ASP* 1.3 76.6 - - - +
442C GLN* 1.3 58.2 + - + +
444C TYR* 3.2 4.7 + - - +
445C GLU* 3.0 40.8 + - + +
727C ARG* 3.3 28.9 - - - +
754C TRP* 3.8 27.7 - + + -
758C MET* 3.8 27.1 - - + -
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Residues in contact with GLN 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ARG* 3.5 39.5 + - - +
438C GLU* 3.0 31.4 + - - +
439C LYS* 3.5 35.5 - - + +
440C ASP 3.4 0.2 - - - -
441C TRP* 1.3 75.9 - - + +
443C LYS* 1.3 59.1 + - - +
445C GLU* 3.7 9.1 - - + +
446C THR* 3.0 33.5 + - - +
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Residues in contact with LYS 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A T 4.4 3.6 - - - +
10A T 2.7 41.2 + - - +
439C LYS 3.0 16.9 + - - +
440C ASP* 2.9 28.4 + - - +
441C TRP 3.2 0.2 - - - -
442C GLN* 1.3 76.5 - - - +
444C TYR* 1.3 81.9 + - - +
446C THR* 3.5 7.6 + - - +
447C ALA* 3.3 19.6 + - - +
587C LYS* 3.8 17.3 - - - +
588C VAL* 5.2 3.5 - - + +
591C THR* 4.5 12.7 - - + +
722C ASN* 2.8 22.8 + - - +
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Residues in contact with TYR 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C ASP* 3.0 42.3 + - - -
441C TRP 3.2 6.9 + - - +
443C LYS* 1.3 86.7 + - - +
445C GLU* 1.3 58.1 + - - +
447C ALA* 3.2 5.6 + - - +
448C ARG* 3.0 33.0 + - - +
591C THR* 3.7 23.3 - - + -
595C SER* 4.0 2.7 - - - -
721C LEU 4.5 3.6 + - - -
722C ASN* 3.4 13.2 + - - -
723C PTR 3.1 31.2 - - - -
724C LEU 3.4 9.8 + - - -
725C ASP* 3.3 44.9 - - + +
726C PRO* 3.9 17.7 - - + +
727C ARG* 3.9 3.8 - - - +
752C PHE* 5.2 1.6 - + - -
754C TRP* 4.3 7.2 - + - -
765C PHE* 4.1 3.3 - + + -
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Residues in contact with GLU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C TRP* 3.0 35.7 + - + +
442C GLN* 3.7 10.1 - - + +
444C TYR* 1.3 75.6 - - - +
446C THR* 1.3 57.3 + - - +
448C ARG* 2.9 38.1 + - - +
449C ARG* 3.0 35.5 + - + +
727C ARG* 3.0 22.2 + - - -
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Residues in contact with THR 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C GLN* 3.0 17.8 + - - +
443C LYS* 3.7 8.2 - - - -
444C TYR 3.3 0.2 - - - -
445C GLU* 1.3 76.4 - - - +
447C ALA* 1.3 56.8 + - - +
449C ARG* 3.2 19.1 + - - +
450C LEU* 3.1 22.5 + - - +
581C MET* 3.5 19.7 - - + +
583C GLY* 3.5 24.8 + - - +
588C VAL* 3.9 21.1 - - + -
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Residues in contact with ALA 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C LYS 3.3 10.6 + - - +
444C TYR 3.2 10.0 + - - +
446C THR* 1.3 79.7 - - - +
448C ARG* 1.3 60.1 + - - +
450C LEU* 3.6 5.7 + - - +
451C LYS 3.5 13.5 + - - -
588C VAL* 3.8 14.8 - - + +
591C THR* 3.9 21.8 - - + -
592C TYR* 3.8 16.5 - - - +
765C PHE* 3.8 24.7 - - + -
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Residues in contact with ARG 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C TYR 3.0 16.7 + - - +
445C GLU* 2.9 43.8 + - - +
446C THR 3.2 0.2 - - - -
447C ALA* 1.3 77.3 - - - +
449C ARG* 1.3 62.8 + - + +
450C LEU 3.2 0.7 - - - -
451C LYS* 3.4 22.4 + - - +
452C LYS* 3.7 14.3 - - - +
727C ARG* 3.7 5.6 - - - +
763C TYR* 3.1 39.1 + - - -
764C GLU 3.0 21.2 + - - -
765C PHE* 3.2 37.9 + - + +
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Residues in contact with ARG 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C GLU* 3.0 20.6 + - + +
446C THR* 3.2 22.7 + - - +
448C ARG* 1.3 77.8 - - + +
450C LEU* 1.3 61.1 + - - +
451C LYS 3.6 0.2 + - - -
452C LYS* 3.7 24.4 + - - +
453C CYS* 3.7 15.6 - - - +
581C MET* 3.5 30.7 - - + +
582C GLU* 2.7 42.0 + - - +
583C GLY* 4.6 2.2 - - - -
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Residues in contact with LEU 450 (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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446C THR 3.1 12.9 + - - +
447C ALA* 3.7 8.7 - - - +
448C ARG 3.2 0.4 - - - -
449C ARG* 1.3 76.3 - - - +
451C LYS* 1.3 57.6 + - - +
452C LYS 3.3 0.2 - - - -
453C CYS* 3.8 1.1 - - - -
454C VAL* 2.8 34.0 + - + +
457C ILE* 3.8 26.7 - - + -
581C MET* 3.7 9.6 - - - -
584C LEU* 3.7 22.2 - - + -
588C VAL* 3.8 37.2 - - + +
589C PHE* 3.9 25.8 - - + -
592C TYR* 3.9 17.5 - - + -
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Residues in contact with LYS 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ALA 3.5 6.1 + - - +
448C ARG* 3.4 17.7 + - - +
449C ARG 3.3 0.4 - - - -
450C LEU* 1.3 78.9 - - - +
452C LYS* 1.3 68.7 + - - +
453C CYS 3.2 4.2 + - - -
454C VAL* 3.5 16.3 + - - +
455C ASP* 5.0 0.5 + - - -
592C TYR* 3.7 30.3 - - + +
596C ILE* 4.3 11.4 - - + -
765C PHE* 3.0 49.4 + - + +
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Residues in contact with LYS 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C ARG* 3.7 18.6 - - - +
449C ARG* 3.8 23.7 - - - +
450C LEU 3.3 0.2 - - - -
451C LYS* 1.3 84.6 - - - +
453C CYS* 1.3 65.2 + - - +
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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