Contacts of the strand formed by residues 565 - 570 (chain A) in PDB entry 1MPX
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 565 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A LEU 3.4 0.7 - - - +
505A GLN* 3.5 5.5 - - - -
506A ALA 3.0 33.4 + - - +
507A SER* 6.1 0.2 - - - -
550A ARG* 3.8 35.7 - - - +
559A LEU* 3.9 29.2 - - + -
560A THR* 3.9 24.7 - - - +
563A GLN* 3.4 28.9 - - + +
564A PRO* 1.3 79.5 - - - +
566A ALA* 1.3 59.6 + - - +
567A PHE* 3.3 12.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A LEU 3.4 4.9 - - - +
505A GLN* 3.4 23.7 + - - +
550A ARG* 3.0 35.5 + - - +
565A LEU* 1.3 74.1 - - - +
567A PHE* 1.3 61.0 + - - +
568A GLN* 4.4 0.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL 3.5 2.1 - - - +
503A HIS* 3.6 2.6 - - - -
504A LEU* 2.8 47.5 + - + +
506A ALA* 3.6 21.8 - - + -
515A TRP* 3.2 42.0 - + - -
545A PHE* 4.0 13.2 - + + -
547A GLY* 4.0 7.2 - - - -
550A ARG* 3.6 37.9 - - + -
559A LEU* 3.7 22.4 - - + -
565A LEU* 3.3 24.7 - - + -
566A ALA* 1.3 75.2 - - - +
568A GLN* 1.3 61.5 + - - +
569A PHE* 4.4 14.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ASP* 5.4 1.8 + - - -
501A ASP* 3.0 25.3 + - - +
502A VAL 3.2 14.1 - - - +
503A HIS* 3.5 30.6 + - + +
545A PHE* 4.3 10.2 - - - -
550A ARG 6.0 0.2 + - - -
553A PHE* 5.6 2.1 - - - -
566A ALA* 4.3 0.6 + - + -
567A PHE* 1.3 76.6 - - - +
569A PHE* 1.3 66.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.7 18.6 - + + -
501A ASP* 3.2 6.1 - - - -
502A VAL* 2.8 54.5 + - + +
504A LEU* 5.0 1.8 - - + -
515A TRP* 4.0 13.2 - - + -
517A VAL* 3.9 23.1 - - + -
543A ALA* 4.2 19.1 - - + -
545A PHE* 3.5 50.5 - + + -
567A PHE* 4.4 13.9 - - + -
568A GLN* 1.3 83.6 - - - +
570A GLY* 1.3 71.5 + - - +
571A LEU* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.1 32.8 + - - -
499A ALA* 6.1 0.9 - - - -
500A PRO 3.6 6.1 - - - -
501A ASP* 3.4 11.4 + - - -
543A ALA* 3.8 9.7 - - - +
569A PHE* 1.3 74.8 - - - +
571A LEU* 1.3 64.5 + - - -
572A PRO* 4.5 0.5 - - - +
----------------------------------------------------------
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