Contacts of the helix formed by residues 544 - 560 (chain A) in PDB entry 4HBN
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 544 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LYS 3.7 3.6 - - - +
543A LEU* 1.3 97.0 - - + +
545A PRO* 1.3 70.4 - - + +
546A ASP* 4.3 6.5 - - + +
547A THR* 3.3 21.0 + - - +
548A ARG* 3.0 23.6 + - - +
550A ARG* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU 4.3 1.3 - - - +
544A PRO* 1.3 87.4 - - + +
546A ASP* 1.3 65.9 + - - +
548A ARG* 3.7 10.1 - - + +
549A GLN* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A PRO* 3.4 3.1 - - + -
545A PRO* 1.3 83.9 - - - +
547A THR* 1.3 59.2 + - - +
549A GLN* 3.7 4.9 - - - +
550A ARG* 2.9 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 4.0 16.6 - - + -
544A PRO* 3.3 31.5 + - + +
546A ASP* 1.3 78.4 - - - +
548A ARG* 1.3 60.2 + - - +
550A ARG* 3.1 24.3 + - + +
551A ILE* 2.8 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLU 4.7 1.6 + - - -
538A MET* 3.7 35.6 - - + +
539A SER* 3.4 36.3 + - - +
542A LYS* 3.4 31.7 - - - +
543A LEU* 2.7 25.7 + - + +
544A PRO 3.0 15.7 + - - +
545A PRO* 3.2 9.3 + - + +
547A THR* 1.3 72.9 - - - +
549A GLN* 1.3 59.1 + - - +
551A ILE* 3.1 3.1 + - - +
552A HIS* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PRO 2.9 17.0 + - - +
546A ASP* 3.7 6.5 - - - +
548A ARG* 1.3 77.0 - - - +
550A ARG* 1.3 54.7 + - + +
552A HIS* 3.0 20.2 + - - +
553A ASP* 2.8 66.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
544A PRO* 5.6 0.4 - - - +
546A ASP* 2.9 42.8 + - - +
547A THR* 3.1 37.0 + - + +
549A GLN* 1.3 76.7 - - + +
551A ILE* 1.3 63.6 + - + +
553A ASP* 4.1 4.5 + - - +
554A TYR* 3.1 21.0 + - - +
617A GLN* 3.2 30.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
531A TYR* 4.9 0.9 - - + -
534A VAL* 4.1 7.6 - - + -
537A TYR* 6.0 3.6 - - + -
538A MET* 3.4 30.3 - - + -
543A LEU* 3.9 20.0 - - + -
547A THR* 2.8 37.3 + - + +
548A ARG 3.6 4.5 - - - +
550A ARG* 1.3 71.3 - - + +
552A HIS* 1.3 68.4 + - - +
554A TYR* 3.3 7.1 + - + +
555A TYR* 3.2 43.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 4.9 0.5 + - - -
531A TYR* 3.2 38.0 + + - +
548A ARG 2.8 11.6 + - - +
549A GLN* 3.1 24.4 + - - +
551A ILE* 1.3 78.0 - - - +
553A ASP* 1.3 82.1 + - - +
555A TYR* 3.2 4.2 + - - +
556A GLU* 3.1 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLN* 2.8 44.8 + - - +
550A ARG* 4.1 6.5 + - - +
552A HIS* 1.3 89.9 - - - +
554A TYR* 1.3 61.7 + - - +
556A GLU* 3.4 5.8 - - - +
557A HIS* 3.0 33.2 + - + +
617A GLN* 4.6 0.4 + - - +
678A TYR* 3.2 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ARG 3.1 19.4 + - - +
551A ILE* 3.6 7.0 - - + +
552A HIS 3.2 0.2 - - - -
553A ASP* 1.3 75.6 - - - +
555A TYR* 1.3 98.5 + + - +
557A HIS* 2.7 18.3 + - - +
558A ARG* 2.8 49.5 + - + +
559A TYR* 4.8 7.1 + + - -
615A VAL* 3.6 40.6 + - + -
617A GLN* 3.6 24.8 - - + +
678A TYR* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 3.3 25.7 + + - +
530A LYS* 4.8 14.5 - - + +
531A TYR* 3.8 18.2 - + + -
534A VAL* 3.2 35.5 - - + +
551A ILE* 3.2 36.9 + - + -
552A HIS 3.2 7.9 + - - +
554A TYR* 1.3 93.9 - + - +
556A GLU* 1.3 64.8 + - - +
558A ARG 2.9 11.8 + - - -
559A TYR* 2.9 51.0 + + - +
560A GLN 3.9 0.2 + - - -
563A MET* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 3.7 8.3 + - - +
552A HIS* 3.1 19.5 + - + +
553A ASP* 3.4 15.3 - - - +
554A TYR 3.2 0.2 - - - -
555A TYR* 1.3 76.7 - - - +
557A HIS* 1.3 63.0 + - + +
560A GLN* 2.9 36.5 + - - +
561A GLY 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ASP* 3.0 27.0 + - + +
554A TYR* 2.7 13.8 + - - +
556A GLU* 1.3 79.7 - - + +
558A ARG* 1.3 58.5 + - - +
559A TYR 3.5 0.2 - - - -
560A GLN* 4.5 11.7 + - - -
613A PHE* 5.6 0.9 - - - -
615A VAL* 4.1 20.6 - - + +
678A TYR* 3.2 58.9 + + + +
680A ARG* 4.9 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A TYR* 2.8 51.2 + - + +
555A TYR 4.0 2.0 - - - +
557A HIS* 1.3 75.6 - - - +
559A TYR* 1.3 106.2 + - + +
560A GLN* 3.8 4.5 - - - +
613A PHE* 3.7 53.7 + - - +
614A GLU* 5.1 2.4 - - - +
615A VAL* 4.2 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 3.9 14.4 - + + -
554A TYR* 4.8 6.7 + + - -
555A TYR* 2.9 49.0 + + - +
558A ARG* 1.3 125.8 + - + +
560A GLN* 1.3 63.2 + - - +
561A GLY 2.5 16.4 + - - -
562A LYS* 3.0 34.7 + - - +
563A MET* 4.1 26.4 - - + -
564A PHE* 6.0 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ARG* 3.8 9.7 + - - -
555A TYR 3.9 0.2 + - - -
556A GLU* 2.9 25.2 + - - +
557A HIS* 4.6 12.2 + - - +
558A ARG 4.8 2.1 - - - +
559A TYR* 1.3 78.7 + - - +
561A GLY* 1.3 54.2 + - - +
562A LYS* 3.7 12.0 + - + +
680A ARG* 5.8 6.8 - - - +
----------------------------------------------------------
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