Contacts of the helix formed by residues 605 - 611 (chain A) in PDB entry 5TFM
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 ASP 605 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLU* 3.7 1.1 - - - -
550A ASN* 4.7 2.7 - - - +
583A PHE* 5.2 4.5 - - + -
604A LEU* 1.3 74.7 - - - +
606A TYR* 1.3 65.3 + - - +
607A GLU* 3.0 17.7 - - - +
608A GLN* 2.7 50.5 + - + +
609A ILE* 3.5 16.7 - - - +
903A CA 2.0 35.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLU* 2.8 37.3 + - + +
605A ASP* 1.3 71.2 - - - +
607A GLU* 1.3 58.6 + - - +
609A ILE* 3.2 33.4 + - + +
611A ASN* 4.5 3.3 - - - -
612A GLY* 3.5 28.6 + - - -
638A VAL* 3.2 32.5 - - + -
639A PHE 3.8 2.0 - - - -
640A ASP* 3.3 39.0 - - + +
677A ARG* 3.6 19.7 + - + -
678A SER* 3.4 31.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLU* 3.0 3.3 - - - +
605A ASP* 3.1 10.4 - - - +
606A TYR* 1.3 79.0 - - - +
608A GLN* 1.3 58.4 + - - +
609A ILE 3.5 0.4 - - - -
640A ASP* 2.7 11.4 - - - +
643A ASP* 3.1 1.0 - - - +
644A ASN* 3.7 8.1 + - - +
675A LEU* 3.3 26.2 - - + +
676A ASP* 3.0 9.4 - - - +
677A ARG* 3.1 41.8 + - + +
902A CA 2.2 26.9 - - - -
903A CA 2.3 31.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA* 5.5 1.4 - - - +
583A PHE* 3.7 34.1 - - + -
605A ASP* 2.7 42.6 + - + +
607A GLU* 1.3 79.2 - - - +
609A ILE* 1.3 62.4 + - - +
610A SER 4.4 0.2 + - - -
677A ARG* 3.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA* 5.5 4.9 - - + -
583A PHE* 4.1 14.4 - - + -
604A LEU* 4.5 11.2 - - + -
605A ASP 3.5 19.3 - - - +
606A TYR* 3.2 10.8 + - - +
607A GLU 3.5 1.2 - - - -
608A GLN* 1.3 83.9 - - - +
610A SER* 1.3 68.4 + - - +
611A ASN 3.4 1.0 + - - -
612A GLY* 4.0 7.4 + - - +
613A LEU 3.5 35.4 - - - +
614A ILE* 3.9 17.9 - - + -
638A VAL* 3.8 30.1 - - + -
677A ARG* 2.8 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A GLN 4.4 0.2 + - - -
609A ILE* 1.3 75.6 - - - +
611A ASN* 1.3 72.1 + - - +
612A GLY 3.3 1.6 + - - -
613A LEU* 3.7 12.8 + - - +
677A ARG* 4.2 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A TYR* 4.5 5.7 + - - -
609A ILE 3.4 2.8 + - - -
610A SER* 1.3 74.0 - - - +
612A GLY* 1.3 62.1 + - - +
613A LEU* 3.2 30.3 + - + +
615A TYR* 4.9 2.8 + - - +
677A ARG* 4.7 6.4 - - - +
----------------------------------------------------------
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