Contacts of the helix formed by residues 548 - 562 (chain A) in PDB entry 3HR4
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 GLY 548 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A THR* 2.9 23.8 + - - +
546A GLU 3.4 2.4 + - - -
547A THR* 1.3 76.5 - - - +
549A LYS* 1.3 61.8 + - - +
550A SER 3.3 2.7 - - - -
551A GLU* 3.6 7.7 + - - +
552A ALA* 3.3 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A THR* 3.4 20.9 - - - +
548A GLY* 1.3 72.1 - - - -
550A SER* 1.3 60.1 + - - +
552A ALA* 3.6 6.1 + - - +
553A LEU* 3.2 28.9 + - - +
626A LEU* 3.5 12.6 - - + -
661A GLU* 3.5 27.1 + - - +
665A GLN* 3.3 18.1 + - - +
999A FMN 2.7 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A PHE* 4.5 1.3 - - - -
544A ALA 3.3 20.4 - - - -
545A THR* 3.7 1.3 - - - -
548A GLY 3.3 0.2 - - - -
549A LYS* 1.3 74.4 - - - +
551A GLU* 1.3 57.0 + - - +
553A LEU 3.4 0.5 + - - -
554A ALA* 2.7 35.3 + - - +
589A VAL* 3.6 19.3 - - - +
590A THR 3.5 0.3 - - - -
591A SER 3.2 20.8 + - - -
626A LEU* 3.4 20.6 - - - +
999A FMN 2.7 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A PHE* 3.3 43.5 - - + -
545A THR* 4.1 10.0 - - + +
548A GLY* 3.6 10.7 + - - +
549A LYS 3.4 0.4 - - - -
550A SER* 1.3 80.1 - - - +
552A ALA* 1.3 58.3 + - - +
554A ALA* 3.4 3.9 - - - +
555A TRP* 2.9 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLY 3.3 15.5 + - - +
549A LYS* 3.8 7.4 - - - +
550A SER 3.2 0.4 - - - -
551A GLU* 1.3 77.3 - - - +
553A LEU* 1.3 67.3 + - + +
555A TRP* 3.3 5.5 + - - +
556A ASP* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A LYS* 3.2 14.7 + - + +
550A SER 3.7 3.8 - - - +
552A ALA* 1.3 80.2 - - + +
554A ALA* 1.3 57.7 + - - +
556A ASP* 3.0 7.9 + - - +
557A LEU 2.8 24.6 + - - -
589A VAL* 4.1 3.8 - - + -
624A PHE* 4.1 4.0 - - + -
626A LEU* 3.5 36.8 - - + -
665A GLN* 4.7 8.5 - - + +
666A GLU* 4.0 23.3 - - + +
669A PHE* 3.0 64.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ILE* 3.9 19.0 - - + +
543A PHE* 3.7 25.4 - - + -
550A SER 2.7 22.6 + - - +
551A GLU* 3.4 7.0 - - - +
552A ALA 3.2 0.2 - - - -
553A LEU* 1.3 74.4 - - - +
555A TRP* 1.3 61.4 + - - +
557A LEU* 3.2 8.1 + - - +
558A GLY 3.2 15.1 + - - -
569A VAL* 3.6 16.9 - - + +
589A VAL* 4.4 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A PHE* 4.2 6.7 - + - -
551A GLU* 2.9 53.6 + - + +
552A ALA* 3.3 4.7 + - - +
554A ALA* 1.3 73.7 - - - +
556A ASP* 1.3 65.8 + - - +
558A GLY* 3.4 3.5 + - - -
559A ALA* 3.2 19.2 + - - +
568A LYS* 5.4 7.4 - - - +
569A VAL* 3.5 53.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ALA* 3.0 19.4 + - - +
553A LEU* 3.0 22.0 + - - +
555A TRP* 1.3 75.2 - - - +
557A LEU* 1.3 65.9 + - - +
558A GLY 3.1 0.4 - - - -
559A ALA* 3.2 8.0 + - - +
560A LEU* 3.2 16.5 + - - +
666A GLU* 4.3 10.4 - - - +
669A PHE* 3.8 7.2 - - + -
697A LEU* 4.9 12.2 - - - +
698A TYR* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ILE* 3.8 10.5 - - + -
553A LEU 2.8 13.3 + - - +
554A ALA* 3.2 11.6 + - - +
556A ASP* 1.3 76.2 - - - +
558A GLY* 1.3 57.8 + - - +
560A LEU* 3.5 4.3 + - + +
561A PHE* 2.9 61.6 + - + +
587A LEU* 3.6 30.1 - - + -
589A VAL* 4.1 15.3 - - + -
669A PHE* 4.0 4.0 - - + -
672A TRP* 3.8 23.8 - - + -
673A ALA* 3.9 30.5 - - + -
698A TYR* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ILE* 3.6 15.7 - - - +
554A ALA 3.2 11.3 + - - -
555A TRP* 3.4 7.1 + - - -
556A ASP 3.1 0.4 - - - -
557A LEU* 1.3 76.0 - - - +
559A ALA* 1.3 59.2 + - - +
562A SER* 2.9 34.9 + - - -
567A PRO* 3.6 11.6 - - - +
569A VAL* 4.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A TRP 3.2 12.6 + - - +
556A ASP* 3.2 14.2 + - - +
558A GLY* 1.3 76.1 - - - +
560A LEU* 1.3 63.8 + - - +
562A SER* 3.2 19.4 + - - -
563A CYS* 3.8 9.7 - - - -
695A PRO* 4.7 12.3 - - + +
698A TYR* 5.3 1.8 - - + +
42B ASN* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ASP 3.2 10.0 + - - +
557A LEU* 3.7 7.4 - - + +
559A ALA* 1.3 79.5 - - - +
561A PHE* 1.3 66.6 + - + +
562A SER 3.3 0.7 + - - -
563A CYS* 3.3 14.0 + - - -
673A ALA* 3.5 45.1 - - + +
674A VAL* 3.9 4.7 - - - +
677A PHE* 3.5 36.6 - - + -
694A ILE* 3.9 27.8 - - + -
695A PRO* 4.3 9.3 - - - +
698A TYR* 4.0 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A VAL* 4.3 11.7 - - + -
541A ILE* 5.0 0.9 - - + -
557A LEU* 2.9 52.9 + - + +
558A GLY 3.3 0.2 + - - -
560A LEU* 1.3 73.7 - - + +
562A SER* 1.3 57.9 + - - +
563A CYS 3.0 6.4 + - - -
564A ALA 3.4 1.3 + - - -
565A PHE* 2.8 57.8 + + + +
567A PRO* 4.0 21.5 - - + -
585A LEU* 4.1 7.0 - - + -
587A LEU* 3.7 21.5 - - + -
673A ALA 4.4 0.4 - - - -
676A THR* 4.0 10.5 - - + -
677A PHE* 3.5 40.2 - + + -
680A ALA* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A MET* 5.4 5.3 - - - +
536A ARG* 2.6 25.6 + - - -
558A GLY 2.9 20.2 + - - -
559A ALA* 3.4 11.7 - - - -
560A LEU 3.2 1.0 - - - -
561A PHE* 1.3 76.8 - - - +
563A CYS* 1.3 53.0 + - - +
564A ALA 3.2 1.8 - - - -
565A PHE 3.8 8.7 - - - -
567A PRO* 3.6 11.9 - - - +
42B ASN* 3.5 22.2 + - - +
----------------------------------------------------------
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