Contacts of the helix formed by residues 549 - 559 (chain A) in PDB entry 1HHS
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 LEU 549 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A PHE* 3.2 37.5 + - + +
548A GLY* 1.3 71.9 - - - +
550A ALA* 1.3 65.6 + - - +
551A TRP 3.0 3.1 - - - -
552A ALA* 2.9 20.8 + - - +
553A SER 3.7 2.8 + - - -
591A LEU* 4.0 8.7 - - + -
594A ASP* 4.0 3.1 - - + -
595A THR* 3.7 39.7 - - - +
598A LEU* 4.2 11.7 - - + -
611A LEU* 4.2 10.8 - - + -
619A LEU* 3.9 27.1 - - + +
622A LEU* 3.7 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLN* 5.5 9.5 - - + +
547A PRO 3.4 9.0 + - - +
548A GLY 3.3 1.4 - - - -
549A LEU* 1.3 76.6 - - - +
551A TRP* 1.3 62.7 + - - +
553A SER* 3.3 12.3 + - - +
554A MET* 3.1 23.9 + - - +
587A ARG* 4.9 4.7 - - - +
619A LEU 4.8 2.0 - - - -
620A GLU* 4.3 11.2 - - - +
623A ALA* 3.9 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLN* 3.8 12.6 - - - -
548A GLY 3.2 14.4 + - - +
549A LEU 3.0 1.0 - - - -
550A ALA* 1.3 80.1 - - - +
552A ALA* 1.3 61.7 + - - +
553A SER 3.4 0.3 + - - -
554A MET* 3.4 57.9 + - + +
555A LYS 4.9 0.5 + - - -
568A LEU* 4.0 13.0 - - + -
583A TYR* 3.5 36.1 - + - -
584A ARG* 4.0 28.7 - - + +
587A ARG* 3.3 43.0 - - + +
588A GLU* 4.0 19.3 + - + +
591A LEU* 4.2 17.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
549A LEU 2.9 12.0 + - - +
551A TRP* 1.3 80.7 - - - +
553A SER* 1.3 57.2 + - - +
555A LYS* 5.1 2.8 + - - +
556A ASP* 5.5 1.2 + - - +
591A LEU* 3.8 27.6 - - + +
611A LEU* 4.0 9.4 - - + -
619A LEU* 3.6 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A LEU 3.7 0.8 + - - -
550A ALA* 3.3 14.1 + - - -
552A ALA* 1.3 77.1 - - - +
554A MET* 1.3 60.1 + - - +
555A LYS 3.4 2.7 - - - -
556A ASP* 3.3 9.6 + - - +
557A THR* 2.9 28.6 + - - -
616A PRO* 3.7 31.2 - - - -
619A LEU* 3.8 13.2 - - - +
620A GLU* 2.6 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A MET* 3.7 25.6 - - - +
525A GLN* 3.5 23.1 - - - +
550A ALA 3.1 12.0 + - - +
551A TRP* 3.4 59.5 + - + +
553A SER* 1.3 77.5 - - - +
555A LYS* 1.3 58.1 + - - +
558A TYR* 2.7 40.1 + - + +
564A TYR* 3.4 19.7 - - + +
568A LEU* 3.9 16.8 - - + -
620A GLU* 4.6 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A TRP 4.9 1.0 + - - -
552A ALA 5.1 2.6 + - - +
553A SER 3.4 0.8 - - - -
554A MET* 1.3 78.6 - - + +
556A ASP* 1.3 61.3 + - - +
559A GLY* 2.6 40.8 + - - -
564A TYR* 3.4 42.7 + - + +
565A SER* 5.5 2.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
307A ARG* 4.4 15.6 + - - -
552A ALA 5.5 1.3 + - - +
553A SER* 3.5 11.6 - - - +
555A LYS* 1.3 82.5 - - - +
557A THR* 1.3 63.0 + - - +
559A GLY 4.5 0.7 + - - -
560A ALA 5.6 0.7 + - - -
616A PRO* 3.2 41.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ARG* 4.4 8.9 - - - +
499A ASP* 5.0 2.4 - - - +
516A GLY* 3.6 19.7 + - - -
553A SER* 2.9 13.7 + - - -
556A ASP* 1.3 81.7 + - - +
558A TYR* 1.3 95.4 + - + +
560A ALA 5.3 0.2 + - - -
616A PRO* 5.1 2.6 - - - +
620A GLU* 3.1 31.0 + - + +
631A LYS* 6.2 3.8 - - - -
632A TRP* 5.8 2.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A GLY* 4.5 4.5 - - - -
517A ASN 3.2 41.1 - - - -
518A ILE* 4.2 5.4 - - + -
520A SER* 3.8 10.5 - - - -
521A MET* 3.5 50.0 + - + -
524A ASN* 3.9 14.3 + - + +
554A MET* 2.7 26.4 + - + +
557A THR* 1.3 99.4 - - + +
559A GLY* 1.3 64.5 + - - +
560A ALA 3.1 3.6 - - - -
561A CYS* 2.9 19.9 + - + +
564A TYR* 3.4 23.2 - - + -
620A GLU* 4.6 11.1 + - - -
627A LYS* 5.3 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A MET 3.7 1.0 + - - -
555A LYS* 2.6 43.9 + - - -
556A ASP 4.5 0.2 + - - -
557A THR 3.8 0.6 - - - -
558A TYR* 1.3 70.2 - - - +
560A ALA* 1.3 60.1 + - - +
561A CYS 3.5 6.1 + - - +
564A TYR* 3.9 23.6 - - - +
----------------------------------------------------------
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