Contacts of the helix formed by residues 556 - 564 (chain C) in PDB entry 5DO7
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 556 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C ARG* 3.8 10.1 - - - +
554C GLU 3.9 0.6 - - - +
555C MET* 1.4 91.8 - - + +
557C ILE* 1.3 76.4 + - + +
558C PRO* 3.1 11.2 - - + +
559C PHE* 3.4 20.7 + - + +
560C LYS 3.7 2.3 + - - -
433D PHE* 3.2 25.8 - - + +
434D LEU* 3.6 16.6 - - - +
436D PHE* 4.6 11.0 - - + -
440D SER* 5.0 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 557 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A VAL* 4.1 26.3 - - + +
529A ILE* 4.5 23.1 - - + -
555C MET 3.6 2.9 + - - -
556C PRO* 1.3 70.7 - - + +
558C PRO* 1.3 72.9 - - + +
560C LYS* 2.8 36.6 + - - +
561C ILE* 3.6 6.2 + - + +
440D SER* 3.9 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 558 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C PRO* 3.1 14.6 - - + +
557C ILE* 1.3 97.3 - - + +
559C PHE* 1.3 83.0 + - + +
561C ILE* 2.8 29.3 + - + +
562C ILE* 3.1 17.5 + - + +
433D PHE* 5.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 559 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C VAL* 4.1 18.0 - - + +
555C MET* 3.4 20.4 - - - +
556C PRO* 3.4 14.8 + - + +
558C PRO* 1.3 87.1 - - + +
560C LYS* 1.3 65.3 + - - +
562C ILE* 2.8 26.2 + - + +
563C SER* 2.8 13.5 + - - -
430D THR* 3.8 30.1 - - + -
433D PHE* 3.4 23.8 - + + -
434D LEU* 3.1 48.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 560 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 4.2 25.3 + - + +
524A VAL* 6.4 0.2 - - + -
648A LEU* 5.2 4.4 - - + +
552C ILE* 4.3 14.6 - - + +
553C GLN* 3.6 40.6 + - - +
555C MET* 3.5 25.9 + - + +
556C PRO 3.7 1.4 + - - -
557C ILE* 2.8 22.4 + - - +
559C PHE* 1.3 76.7 - - - +
561C ILE* 1.3 58.9 + - - +
563C SER* 2.3 31.6 + - - +
564C TYR* 3.2 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 561 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A LEU* 4.3 29.4 - - + -
523A ILE* 4.4 14.8 - - + -
524A VAL* 3.8 30.7 - - + -
533A VAL* 5.2 12.3 - - + -
557C ILE* 4.4 4.0 - - + +
558C PRO* 2.8 27.9 + - + +
560C LYS* 1.3 70.0 - - - +
562C ILE* 1.3 79.4 + - + +
564C TYR* 3.1 22.4 + - - +
565C PHE* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 562 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C VAL* 4.6 17.0 - - + -
558C PRO* 3.4 18.2 - - + +
559C PHE* 2.8 26.9 + - + +
561C ILE* 1.3 82.1 - - + +
563C SER* 1.3 69.5 + - - +
565C PHE* 2.5 30.8 + - + +
566C THR* 3.7 9.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 563 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C VAL* 3.7 25.5 - - - +
545C GLY* 4.0 8.3 - - - +
552C ILE* 3.3 29.0 - - - +
555C MET* 4.9 0.7 - - - -
559C PHE 2.8 14.1 + - - -
560C LYS* 2.3 27.9 + - - -
562C ILE* 1.3 72.0 - - - +
564C TYR* 1.3 56.6 + - - -
565C PHE 2.8 10.2 + - - -
566C THR* 2.4 34.5 + - - +
569C LYS* 3.8 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 564 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 3.4 41.7 - - + +
637A LEU* 4.6 5.5 - - + +
641A VAL* 3.7 23.0 + - + +
644A ILE* 3.5 38.9 - - + +
645A ARG* 5.7 0.7 - - - +
648A LEU* 4.1 20.1 - - - +
552C ILE* 5.2 2.5 - - + -
553C GLN* 5.7 0.3 + - - -
560C LYS* 3.2 34.5 - - + +
561C ILE 3.1 7.1 + - - +
562C ILE 2.8 3.2 + - - -
563C SER* 1.3 80.5 + - - +
565C PHE* 1.3 65.1 + - + +
566C THR 3.5 0.7 - - - -
569C LYS* 3.6 24.4 + - - -
570C TYR* 2.4 39.6 + - - +
626C ILE* 5.1 1.0 - - - +
630C PHE* 5.6 0.2 - - - -
----------------------------------------------------------
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