Contacts of the helix formed by residues 538 - 545 (chain W) 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 LEU 538 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536W ASP 4.4 0.2 + - - -
537W ILE* 1.3 67.8 - - - +
539W PRO* 1.3 60.8 - - - +
540W GLN 3.3 2.7 - - - -
541W MET* 2.8 24.1 + - - +
542W ILE* 3.2 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 539 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474W PRO* 4.5 9.1 - - - +
484W LEU* 4.8 10.5 - - - -
526W TRP* 6.3 0.7 - - - -
537W ILE 3.1 9.3 - - - +
538W LEU* 1.3 70.7 - - - +
540W GLN* 1.3 57.1 + - - +
541W MET 3.0 5.9 + - - -
542W ILE* 3.1 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 540 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474W PRO* 4.0 24.3 - - - +
476W THR* 5.9 1.3 - - - +
484W LEU* 4.5 11.6 - - - +
538W LEU 3.3 1.0 + - - -
539W PRO* 1.3 73.7 - - - +
541W MET* 1.3 54.0 + - - +
542W ILE 3.6 0.2 - - - -
543W THR 4.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 541 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538W LEU 2.8 15.5 + - - -
540W GLN* 1.3 70.8 - - - +
542W ILE* 1.3 67.1 + - - +
543W THR 3.2 2.9 - - - -
544W LEU* 3.0 17.3 + - - +
545W SER 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 542 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538W LEU 3.2 6.4 + - - -
539W PRO* 3.1 15.0 + - - -
541W MET* 1.3 74.0 - - - +
543W THR* 1.3 57.6 + - - +
544W LEU 2.9 6.6 + - - -
545W SER* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 543 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470W ILE* 5.6 1.4 - - - -
471W VAL 4.8 20.1 + - - +
472W ASN* 5.5 3.9 + - - +
473W PHE 5.5 1.1 - - - +
474W PRO* 4.8 18.5 - - - +
539W PRO 4.7 1.4 + - - -
540W GLN 4.9 1.4 + - - -
541W MET* 3.1 2.8 + - - +
542W ILE* 1.3 73.3 - - - +
544W LEU* 1.3 54.2 + - - +
545W SER 3.0 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541W MET* 3.0 12.8 + - - +
542W ILE 2.9 1.2 + - - -
543W THR* 1.3 75.0 - - - +
545W SER* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 545 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471W VAL 5.7 1.6 + - - -
504W VAL* 6.3 0.7 - - - +
505W HIS 5.8 0.2 - - - -
541W MET 4.4 0.6 + - - -
542W ILE 3.1 13.6 + - - +
543W THR* 3.0 17.8 - - - +
544W LEU* 1.3 77.6 - - - +
546W GLU* 1.3 61.2 + - - +
547W ALA* 3.0 9.1 + - - -
----------------------------------------------------------
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