Contacts of the strand formed by residues 417 - 422 (chain D) 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 LYS 417 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D THR 3.8 7.2 + - - +
416D SER* 1.3 78.8 - - - +
418D PRO* 1.3 72.0 - - + +
419D LEU 3.4 0.5 + - - -
429D PHE* 4.1 39.1 - - + +
494D LEU* 6.1 0.2 - - - -
633D SER* 4.7 1.3 - - - -
634D LEU* 3.0 30.9 + - - +
636D VAL* 4.0 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D SER 4.4 3.8 - - - +
417D LYS* 1.3 84.2 - - + +
419D LEU* 1.3 60.2 + - - +
420D TYR* 3.7 35.2 + - + +
429D PHE* 3.4 25.9 - - - +
631D TYR* 3.6 28.3 - - + -
632D ILE 3.7 5.4 - - - +
633D SER* 4.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D LYS 3.4 0.4 + - - -
418D PRO* 1.3 71.1 - - - +
420D TYR* 1.3 61.0 + - - +
421D LEU* 3.7 5.2 + - - +
427D LEU* 3.7 33.7 - - + -
428D SER* 3.8 26.2 - - - -
429D PHE* 3.8 31.6 - - + -
487D THR* 4.9 6.1 - - + -
494D LEU* 6.0 0.4 - - + -
519D LEU* 4.7 5.2 - - + -
584D VAL* 3.9 18.8 - - + -
586D VAL* 4.7 3.8 - - + -
631D TYR* 3.3 4.0 - - - -
632D ILE* 2.9 40.2 + - + +
634D LEU* 4.1 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D PRO* 3.7 33.3 - - + +
419D LEU* 1.3 71.8 - - - +
421D LEU* 1.3 66.8 + - - +
422D GLN* 3.6 14.6 - - - +
427D LEU* 3.4 7.1 - - - +
428D SER 2.9 33.7 + - - +
429D PHE 3.7 11.7 - - - -
430D GLN 3.5 16.2 - - - -
431D PRO* 3.6 28.3 - - + +
432D PRO* 3.7 17.7 - - + -
629D PRO* 3.9 25.1 - - + -
630D SER 3.6 2.7 - - - -
631D TYR* 3.7 25.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D LEU 4.0 8.3 - - - +
420D TYR* 1.3 76.4 - - - +
422D GLN* 1.3 64.9 + - - +
426D LYS 4.1 0.4 - - - -
427D LEU* 3.9 18.4 - - + -
432D PRO* 4.5 1.9 - - - +
485D PHE* 3.6 38.6 - - + -
504D LEU* 5.0 3.1 - - + -
586D VAL* 4.4 14.4 - - + -
588D VAL* 4.2 12.8 - - + -
622D VAL* 3.9 17.7 - - + -
624D VAL* 3.4 28.3 - - + +
630D SER* 3.0 28.7 + - - +
631D TYR* 4.1 9.4 - - - -
632D ILE* 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D TYR* 3.6 17.9 - - - +
421D LEU* 1.3 79.4 - - - +
423D ALA* 1.3 67.3 + - - +
425D GLY 3.5 0.5 + - - -
426D LYS* 2.9 37.8 + - + +
427D LEU* 3.9 4.7 - - - +
428D SER* 3.0 16.4 + - - +
430D GLN* 2.7 29.5 + - - +
431D PRO 4.2 1.2 + - - -
432D PRO* 3.4 28.3 - - - +
436D GLN* 4.6 8.1 + - - +
485D PHE* 3.3 22.4 - - - -
624D VAL* 4.1 7.6 - - - +
----------------------------------------------------------
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