Contacts of the helix formed by residues 549 - 556 (chain A) in PDB entry 2MPF
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 549 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ASN 4.0 0.8 + - - -
548A ALA* 1.3 71.1 - - - +
550A PRO* 1.3 70.1 - - - +
551A ASN* 2.9 32.0 + - - +
552A PHE* 3.0 27.7 + - + +
553A VAL* 3.3 11.9 + - - +
645A TYR* 4.8 11.1 - - + -
647A MET* 4.1 24.7 - - + +
648A MET* 4.1 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ALA 3.6 7.4 - - - +
549A ASP* 1.3 88.7 - - - +
551A ASN* 1.3 63.0 + - - +
553A VAL* 3.5 15.2 - - + +
554A THR* 2.7 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ASP* 2.9 16.4 + - - +
550A PRO* 1.3 83.7 + - - +
552A PHE* 1.3 59.0 - - - +
554A THR* 3.3 5.3 + - - -
555A ALA* 2.9 31.9 + - - +
645A TYR* 3.6 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LEU* 5.7 0.9 - - + -
545A PHE* 4.6 12.3 - + - -
548A ALA* 4.4 6.3 - - + -
549A ASP* 3.0 13.1 + - + +
551A ASN* 1.3 77.4 - - - +
553A VAL* 1.3 71.8 + - + +
554A THR 3.2 0.9 + - - -
555A ALA* 3.3 10.6 + - - +
556A MET* 3.4 42.4 + - + +
638A PHE* 3.8 11.7 - + - -
641A VAL* 4.0 6.6 - - + +
642A LEU* 3.6 40.8 - - + -
645A TYR* 3.6 45.4 - + + -
648A MET* 3.8 30.3 - - + -
652A PHE* 4.8 2.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ARG 5.3 5.6 - - - +
539A VAL* 3.6 15.2 - - + +
540A ALA* 5.4 7.2 - - + -
545A PHE* 3.6 29.6 - - + +
548A ALA* 3.2 35.4 - - + +
549A ASP 3.5 5.6 - - - +
550A PRO* 3.5 23.6 - - + +
552A PHE* 1.3 78.2 - - + +
554A THR* 1.3 65.8 + - - +
556A MET* 3.6 11.5 - - - +
557A LEU* 3.5 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ARG* 5.7 6.6 - - + +
550A PRO 2.7 23.8 + - - -
551A ASN* 3.3 5.8 + - - -
552A PHE 3.2 0.2 - - - -
553A VAL* 1.3 79.4 - - - +
555A ALA* 1.3 61.4 + - - +
556A MET 3.1 4.7 - - - -
557A LEU* 3.1 34.6 + - + +
558A THR* 4.4 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ASN 2.9 20.2 + - - +
552A PHE 3.3 0.6 + - - +
554A THR* 1.3 72.7 - - - +
556A MET* 1.3 59.4 + - - +
557A LEU 3.6 0.3 + - - -
558A THR* 3.7 23.0 + - - +
641A VAL* 3.9 21.9 - - + +
644A GLU* 5.8 2.2 - - + +
645A TYR* 3.5 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A VAL* 4.2 11.2 - - + -
545A PHE* 3.8 19.3 - - + -
552A PHE* 3.4 46.0 + - + +
553A VAL 3.6 11.9 - - - +
554A THR 3.1 0.4 - - - -
555A ALA* 1.3 78.3 - - - +
557A LEU* 1.3 62.6 + - + +
558A THR* 3.3 1.7 + - - -
559A LYS* 4.2 8.3 + - - +
560A LEU* 4.3 0.7 - - + +
581A MET* 5.4 1.1 - - - +
633A LEU* 3.4 34.2 - - + +
637A ASN 5.5 0.2 - - - +
638A PHE* 3.4 39.5 - - + -
641A VAL* 4.0 17.7 - - + +
----------------------------------------------------------
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