Contacts of the helix formed by residues 547 - 557 (chain A) in PDB entry 3I5Y
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 547 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASP 5.6 1.2 + - - -
486A PRO* 5.3 3.0 - - - +
545A ARG 4.1 0.8 + - - -
546A PHE* 1.3 71.0 - - - +
548A GLU* 1.3 56.8 + - - +
549A ARG* 3.3 25.6 + - - +
550A ARG* 3.1 40.4 + - - -
551A ILE* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ARG* 4.2 17.7 + - - +
541A ILE* 3.7 20.2 - - + +
546A PHE 3.6 5.5 + - - -
547A SER* 1.3 71.8 + - - +
549A ARG* 1.3 61.9 + - - +
551A ILE* 3.8 8.5 - - - -
552A LEU* 3.3 49.2 + - + +
553A PRO* 3.6 1.2 - - - +
582A LEU* 5.0 5.6 - - - +
587A ILE* 3.8 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A SER* 3.3 16.0 + - - +
548A GLU* 1.3 79.1 - - - +
550A ARG* 1.3 89.3 + - + +
553A PRO* 3.2 19.8 - - - +
587A ILE* 3.6 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASP* 3.4 25.8 + - + +
547A SER* 3.1 30.7 + - - +
549A ARG* 1.3 118.6 - - + +
551A ILE* 1.3 65.0 + - - +
552A LEU 3.4 0.6 + - - -
553A PRO* 3.5 4.0 - - - +
554A GLU* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A CYS* 4.9 2.0 - - - -
483A ASP* 3.5 37.9 - - + +
484A GLU* 3.9 17.0 - - + -
537A TYR* 4.1 19.7 - - + -
541A ILE* 4.0 4.3 - - + -
546A PHE* 3.9 30.5 - - + -
547A SER 2.8 32.8 + - - +
548A GLU* 3.8 5.8 - - - -
550A ARG* 1.3 73.6 - - - +
552A LEU* 1.3 75.9 + - + +
554A GLU* 3.3 4.3 + - + +
555A ILE* 3.1 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ILE* 4.4 15.2 - - + +
537A TYR* 4.3 9.2 - - + -
538A ARG* 4.2 35.4 - - + +
541A ILE* 3.9 12.3 - - + -
548A GLU* 3.3 38.6 + - + +
551A ILE* 1.3 91.9 - - + +
553A PRO* 1.4 68.9 - - + +
555A ILE* 3.4 5.1 + - + +
556A ALA* 3.1 28.4 + - - +
582A LEU* 5.5 5.2 - - + -
587A ILE* 4.3 4.3 - - + -
591A MET* 3.9 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLU 3.6 4.0 - - - +
549A ARG 3.2 27.8 - - - +
550A ARG 3.5 5.6 - - - +
552A LEU* 1.4 92.9 - - + +
554A GLU* 1.3 58.0 + - - +
556A ALA* 3.8 1.4 - - + +
557A SER* 2.9 30.5 + - - -
587A ILE* 4.0 16.6 - - + -
590A ALA* 4.4 22.1 - - + +
591A MET* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A GLU 4.5 3.0 - - - +
351A LYS* 2.7 41.9 + - - +
352A PHE* 2.7 34.2 + - + +
353A ALA 4.5 0.9 + - - -
481A CYS* 4.2 14.1 - - + -
483A ASP* 3.7 20.1 - - + +
550A ARG 3.4 12.2 + - - +
551A ILE* 3.3 10.7 + - + +
552A LEU 3.3 0.6 - - - -
553A PRO* 1.3 76.9 - - - +
555A ILE* 1.3 65.8 + - + +
557A SER* 2.8 18.4 + - - -
558A THR* 3.6 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 3.9 25.1 - - + -
481A CYS* 5.5 0.4 - - - -
484A GLU* 5.5 0.7 - - - -
530A VAL* 3.5 4.5 - - - +
533A LEU* 3.5 44.9 - - + -
534A ILE* 3.9 9.0 - - + +
537A TYR* 3.7 46.7 - - + -
551A ILE* 3.1 23.8 + - + +
552A LEU* 3.8 6.7 - - + +
553A PRO 3.4 0.2 - - - -
554A GLU* 1.3 76.2 - - + +
556A ALA* 1.3 58.8 + - - +
558A THR* 2.6 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A VAL* 3.8 10.3 - - - +
534A ILE* 4.0 7.8 - - + +
552A LEU 3.1 17.2 + - - +
553A PRO 3.8 2.7 - - - +
554A GLU 3.3 0.2 - - - -
555A ILE* 1.3 76.7 - - - +
557A SER* 1.3 56.9 + - - +
558A THR 3.1 0.4 - - - -
559A TYR* 3.2 27.7 + - - +
569A LYS* 6.2 0.2 - - - -
570A ILE* 3.8 11.8 - - + +
591A MET* 3.7 41.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LYS* 2.8 30.9 + - - -
553A PRO 2.9 15.7 + - - -
554A GLU* 2.8 16.4 + - - -
555A ILE 3.2 0.2 - - - -
556A ALA* 1.3 71.9 - - - +
558A THR* 1.3 63.2 + - - +
559A TYR 3.1 2.2 - - - -
560A GLY* 3.2 6.7 + - - +
561A VAL* 3.2 24.2 + - - +
566A PRO 5.2 10.1 - - - +
568A LEU 5.8 2.5 - - - -
----------------------------------------------------------
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