Contacts of the helix formed by residues 544 - 560 (chain D) in PDB entry 6AH0
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 MET 544 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D ALA* 3.4 6.1 - - - +
543D PRO* 1.3 77.7 - - - +
545D ARG* 1.3 60.8 + - - +
546D SER 3.6 1.6 - - - -
547D LEU* 3.5 6.1 + - - +
548D VAL* 3.0 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2333A LEU* 5.8 8.5 - - - +
544D MET* 1.3 67.2 - - - +
546D SER* 1.3 66.8 + - - +
547D LEU 3.1 1.3 - - - -
548D VAL* 2.9 12.7 + - - +
549D GLN* 2.9 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D MET 3.6 0.2 - - - -
545D ARG* 1.3 71.2 - - - +
547D LEU* 1.3 57.1 + - - +
549D GLN* 3.3 2.6 + - - +
550D GLU* 2.9 28.2 + - - -
817D TRP 4.0 10.1 - - - -
818D GLY* 4.9 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D MET* 3.5 8.1 + - - +
545D ARG 3.1 1.0 - - - -
546D SER* 1.3 76.9 - - - +
548D VAL* 1.3 56.5 + - - +
550D GLU* 3.9 0.6 - - - +
551D MET* 2.9 27.0 + - - -
817D TRP* 3.7 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D ALA* 6.2 4.0 - - - +
544D MET 3.0 11.1 + - - -
545D ARG* 2.9 7.9 + - - +
547D LEU* 1.3 73.1 - - - +
549D GLN* 1.3 64.7 + - - +
551D MET* 3.2 2.0 + - - +
552D VAL* 2.9 21.0 + - - -
568D GLU* 5.8 5.0 - - - -
587D VAL* 6.0 7.9 - - - +
588D CYS* 6.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D ARG 2.9 12.3 + - - -
546D SER* 3.7 2.9 - - - +
548D VAL* 1.3 75.8 - - - +
550D GLU* 1.3 62.8 + - - +
552D VAL* 3.1 1.6 + - - -
553D GLY* 3.0 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 550 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D SER 2.9 17.5 + - - -
547D LEU 4.1 0.7 - - - -
549D GLN* 1.3 71.4 - - - +
551D MET* 1.3 56.1 - - - +
553D GLY* 3.2 4.3 + - - +
554D SER* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D LEU 2.9 19.2 + - - -
548D VAL* 3.6 1.3 - - - +
549D GLN 3.1 0.2 - - - -
550D GLU* 1.3 73.9 - - - +
552D VAL* 1.3 60.2 + - - +
554D SER* 5.3 0.4 - - - +
555D PHE* 2.8 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 552 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D VAL 2.9 14.6 + - - -
549D GLN 3.7 2.7 - - - -
551D MET* 1.3 74.7 - - - +
553D GLY* 1.3 58.1 + - - +
555D PHE* 5.1 0.2 - - - +
556D GLY* 3.0 27.5 + - - +
566D VAL 4.7 12.8 - - - +
567D ALA* 5.7 2.0 - - - +
568D GLU* 5.6 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 553 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D GLN 3.0 13.0 + - - -
550D GLU* 3.4 6.3 - - - -
551D MET 3.1 0.4 - - - -
552D VAL* 1.3 77.8 - - - +
554D SER* 1.3 57.7 + - - +
556D GLY* 4.2 1.0 - - - -
557D LYS* 3.7 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 554 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D GLU 2.9 15.7 + - - -
551D MET 4.0 0.2 - - - -
553D GLY* 1.3 69.0 - - - -
555D PHE* 1.3 61.2 + - - +
556D GLY 3.2 1.8 - - - -
557D LYS* 3.2 3.8 + - - +
558D ARG* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 555 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D MET 2.8 21.3 + - - -
552D VAL* 4.1 0.9 - - - +
554D SER* 1.3 70.6 - - - +
556D GLY* 1.3 57.4 + - - +
558D ARG* 4.5 0.9 - - - +
559D LEU* 2.9 29.9 + - - +
566D VAL* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 556 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D VAL 3.0 18.5 + - - -
553D GLY 4.2 1.6 - - - -
554D SER 3.2 0.2 - - - -
555D PHE* 1.3 74.4 - - - +
557D LYS* 1.3 61.8 + - - +
559D LEU 3.9 0.2 - - - -
560D ALA* 3.0 24.6 + - - -
564D ILE 5.3 5.6 - - - +
566D VAL* 5.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 557 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D GLY 3.7 8.8 + - - -
554D SER* 3.2 7.1 + - - +
556D GLY* 1.3 75.3 - - - +
558D ARG* 1.3 64.6 + - - +
560D ALA* 3.4 7.4 + - - -
561D THR 4.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 558 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D GLY* 3.8 31.4 - - - -
554D SER 2.9 15.4 + - - -
555D PHE* 3.9 1.6 - - - +
557D LYS* 1.3 78.4 - - - +
559D LEU* 1.3 60.7 + - - +
560D ALA 3.1 1.4 + - - -
561D THR* 3.8 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 559 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D GLY* 5.8 0.4 - - - -
555D PHE 2.9 18.1 + - - -
556D GLY 3.9 0.7 - - - -
558D ARG* 1.3 67.8 - - - +
560D ALA* 1.3 58.0 + - - +
561D THR 3.1 3.6 - - - -
562D TYR* 2.9 21.8 + - - -
563D GLY 3.4 5.2 + - - -
564D ILE* 3.9 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 560 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D GLY 3.0 18.6 + - - -
557D LYS* 3.4 5.4 + - - +
558D ARG 3.1 2.8 - - - -
559D LEU* 1.3 76.9 - - - +
561D THR* 1.3 55.5 + - - +
562D TYR 3.0 0.2 - - - -
563D GLY* 2.7 27.1 + - - +
564D ILE 4.9 3.8 - - - +
----------------------------------------------------------
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