Contacts of the strand formed by residues 541 - 551 (chain C) in PDB entry 1S9K
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 ARG 541 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C ALA* 3.9 19.8 + - + +
464C ASP* 3.8 26.4 + - - +
471C HIS* 3.1 17.3 + - - -
538C LYS* 2.8 30.5 + - - +
539C ASN* 3.8 7.1 + - - +
540C THR* 1.3 81.7 + - - +
542C VAL* 1.3 70.6 + - - +
566C PRO* 4.9 6.7 - - + -
567C ILE 3.3 18.6 - - - +
568C GLU* 3.6 24.2 + - + +
577C LEU* 3.9 23.3 - - - +
667C ARG 5.1 4.6 + - - -
669C GLN* 3.7 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 542 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C ILE* 3.2 40.8 - - + -
461C GLY 3.6 3.4 - - - +
463C ALA* 3.7 3.8 - - - -
471C HIS* 3.3 20.9 - - + -
474C TYR* 3.9 18.2 - - + -
518C ILE* 4.8 7.2 - - + -
541C ARG* 1.3 87.4 - - - +
543C ARG* 1.3 83.3 + - - +
566C PRO* 3.1 6.1 - - - +
567C ILE* 2.5 52.8 + - + +
569C CYS* 4.4 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 543 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460C ILE 3.6 0.3 - - - -
461C GLY* 2.7 34.4 + - - +
462C THR 2.8 22.4 + - - +
463C ALA* 3.5 21.2 + - + +
464C ASP 4.7 2.7 + - - -
466C ARG 4.2 7.5 + - - -
467C ILE 4.8 0.2 - - - -
468C LEU* 3.0 42.5 - - + +
542C VAL* 1.3 89.5 - - - +
544C LEU* 1.3 58.2 + - - +
545C VAL* 4.9 0.7 - - + -
563C ALA* 4.2 15.0 - - + +
564C SER* 3.0 31.8 + - - +
565C ASN 3.7 5.8 - - - +
566C PRO* 3.7 13.2 - - + -
567C ILE* 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C PRO* 3.6 29.2 - - + -
433C VAL* 4.1 23.8 - - + -
441C PRO* 4.8 9.0 - - + -
458C ILE* 5.4 4.9 - - + -
459C PHE 4.0 2.5 - - - +
460C ILE* 3.4 24.9 - - + -
476C VAL* 4.8 6.1 - - + -
513C ILE* 5.6 1.1 - - + -
516C ALA* 4.5 21.1 - - + -
518C ILE* 5.4 1.1 - - + -
543C ARG* 1.3 70.1 - - - +
545C VAL* 1.3 60.6 + - - +
546C PHE* 3.0 34.1 - - + -
563C ALA* 3.3 0.3 - - - -
564C SER* 2.7 32.4 + - - +
567C ILE* 4.3 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C GLN 3.7 0.3 - - - +
458C ILE* 3.0 5.4 - - - +
459C PHE* 2.8 70.7 + - + +
461C GLY* 3.5 32.5 - - - +
468C LEU* 3.8 17.0 - - + -
543C ARG 3.8 1.6 - - - +
544C LEU* 1.3 75.5 - - - +
546C PHE* 1.3 63.3 + - - +
561C GLN* 3.7 24.7 - - + +
562C THR 3.4 10.5 - - - +
563C ALA* 4.3 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 3.6 8.8 - - + +
412C ILE* 3.5 28.5 - - + -
416C PRO* 5.8 0.7 - - + -
441C PRO* 5.8 3.4 - - + -
443C VAL* 3.9 27.1 - - + -
456C LEU* 3.5 22.9 - - + -
457C GLN 3.1 4.5 - - - +
458C ILE* 3.1 29.2 - - + -
459C PHE* 5.6 0.2 - - - -
513C ILE* 4.3 16.8 - - + -
544C LEU* 3.0 48.7 - - + -
545C VAL* 1.3 73.6 - - - +
547C ARG* 1.3 62.5 + - - +
561C GLN* 3.0 4.1 - - - +
562C THR* 2.7 53.6 + - - -
564C SER* 4.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 547 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C TRP* 2.9 74.4 + - - +
401C LEU 3.3 19.2 + - - -
403C SER* 4.7 10.5 + - - -
410C LEU* 4.3 0.2 - - - -
455C GLY 3.8 0.2 - - - +
456C LEU* 2.9 19.4 - - - +
457C GLN* 2.8 49.8 + - + +
459C PHE* 4.7 13.5 - - + -
546C PHE* 1.3 72.9 - - - +
548C VAL* 1.3 64.2 + - - +
549C HIS* 4.2 12.4 + - - +
559C SER* 6.0 0.7 - - - -
560C LEU 3.1 16.8 - - - +
561C GLN* 2.7 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 548 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 3.4 29.8 - - + -
445C LEU* 4.4 17.9 - - + -
454C LEU* 5.0 8.5 - - + -
455C GLY 3.9 8.3 - - - +
456C LEU* 3.7 13.9 - - + +
503C LEU* 3.7 29.2 - - + -
547C ARG* 1.3 81.9 - - - +
549C HIS* 1.3 67.0 + - - +
550C ILE* 3.9 3.0 - - + +
558C VAL 3.7 1.6 - - - +
559C SER* 3.4 2.3 - - - -
560C LEU* 2.7 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 549 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C TRP* 4.5 17.8 - + - -
454C LEU* 3.9 11.4 - - - +
455C GLY 4.8 5.7 + - - +
457C GLN* 3.0 32.1 + - - -
547C ARG* 4.2 18.9 + - + +
548C VAL* 1.3 77.2 + - - +
550C ILE* 1.3 61.4 + - - +
551C PRO* 3.0 16.1 - - + +
557C ILE* 3.8 18.5 - - + +
558C VAL 3.9 3.4 - - - -
559C SER* 2.8 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 550 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C TYR* 3.6 52.7 - - + +
445C LEU* 3.9 17.9 - - + -
448C TYR* 4.0 25.6 - - + -
454C LEU* 4.1 12.8 - - + -
548C VAL* 4.6 5.8 - - + +
549C HIS* 1.3 73.4 - - - +
551C PRO* 1.3 74.5 - - + +
552C GLU* 3.6 4.0 + - + +
556C ARG 3.3 2.9 - - - +
557C ILE* 4.2 1.6 - - - -
558C VAL* 3.0 42.1 + - + +
560C LEU* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 551 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C TYR* 5.9 1.4 - - - +
454C LEU* 4.6 12.6 - - + -
549C HIS* 3.0 11.7 - - + +
550C ILE* 1.3 92.2 - - + +
552C GLU* 1.3 62.5 + - - +
555C GLY 6.0 0.9 - - - -
556C ARG 3.2 7.2 - - - +
557C ILE* 3.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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