Contacts of the strand formed by residues 514 - 522 (chain C) 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 ASP 514 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C SER* 1.3 74.5 - - - +
515C TRP* 1.3 63.3 + - - +
544C ILE* 3.8 26.3 - - + +
545C PHE 3.4 4.0 - - - +
546C ARG* 2.9 48.4 + - - -
590C SER* 3.1 46.6 + - - +
591C SER* 5.6 1.0 - - - -
597C ASP 3.9 4.5 - - - +
598C ARG* 5.2 0.2 - - - -
599C ASN* 3.0 31.1 + - - +
601C GLN* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 515 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C TYR* 3.3 28.5 - + - -
504C LEU* 3.8 25.4 - - + -
506C ALA* 3.7 22.0 - - + -
507C SER 3.7 28.5 - - - -
508C THR* 4.4 2.9 - - + -
513C SER* 4.1 27.5 + - - -
514C ASP* 1.3 75.8 - - - +
516C VAL* 1.3 62.4 + - - +
517C VAL* 5.4 0.7 - - + -
544C ILE* 3.5 1.7 - - - -
545C PHE* 2.9 39.0 + + - +
547C GLY* 4.5 0.9 - - - -
559C LEU* 4.6 0.6 - - - +
567C PHE* 3.3 47.2 - + + -
569C PHE* 3.9 16.0 - - + -
588C VAL* 4.6 5.2 - - + -
589C GLN 3.7 1.8 - - - -
590C SER* 3.6 7.6 - - - -
620C GLN* 3.7 18.4 - - + -
621C ARG 4.8 0.2 - - - -
622C VAL* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 516 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C TRP* 1.3 73.2 - - - +
517C VAL* 1.3 64.3 + - - +
518C LYS* 4.4 14.6 - - + -
542C LEU* 5.1 2.5 - - + -
543C ALA 3.4 10.3 - - - +
544C ILE* 3.6 33.2 - - + -
587C GLN 3.6 0.9 - - - +
588C VAL* 3.2 8.3 - - - +
589C GLN* 2.8 55.0 + - + +
590C SER 4.7 0.4 - - - -
591C SER 4.0 20.6 - - - +
592C LEU* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C VAL* 4.0 32.5 - - + -
504C LEU* 4.9 10.1 - - + -
515C TRP 4.1 0.6 + - - -
516C VAL* 1.3 79.1 - - - +
518C LYS* 1.3 67.6 + - - +
542C LEU* 3.2 4.2 - - - +
543C ALA 3.0 31.2 + - - -
569C PHE* 4.0 20.0 - - + -
571C LEU* 3.9 8.3 - - + +
586C VAL* 3.9 22.4 - - + -
587C GLN 3.4 2.5 - - - -
588C VAL* 4.5 15.5 - - + -
632C ILE* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 518 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C TRP* 6.6 0.2 - - - -
473C GLN* 2.7 36.0 + - + +
476C VAL* 3.5 11.3 - - - +
516C VAL* 4.4 10.5 - - + -
517C VAL* 1.3 79.7 - - - +
519C LEU* 1.3 59.7 + - - +
520C ILE* 3.7 14.5 + - + +
539C PRO* 5.0 1.8 - - + -
541C SER 3.7 4.0 - - - -
542C LEU* 3.8 23.6 - - + -
585C MSE 3.5 0.5 - - - +
586C VAL* 3.1 10.4 - - - +
587C GLN* 2.8 57.0 + - + +
589C GLN* 3.0 37.0 + - - +
592C LEU* 4.9 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C LEU* 4.8 2.5 - - + -
496C ILE* 3.9 20.0 - - + -
500C PRO* 4.1 17.0 - - + -
517C VAL 4.2 0.4 - - - -
518C LYS* 1.3 70.8 - - - +
520C ILE* 1.3 60.5 + - - +
539C PRO* 3.6 2.1 - - - +
540C VAL* 2.9 27.2 + - + -
541C SER* 2.7 26.7 + - - +
571C LEU* 4.1 12.4 - - + +
578C PHE* 4.4 9.6 - - + -
584C VAL* 3.8 28.7 - - + -
585C MSE 3.6 4.3 - - - +
586C VAL* 4.4 11.4 - - + +
632C ILE* 4.8 4.3 - - + -
634C LEU* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 520 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C GLN* 4.2 11.0 - - + -
518C LYS* 4.0 16.8 - - + +
519C LEU* 1.3 79.4 - - - +
521C ASP* 1.3 74.7 + - - +
522C VAL* 3.9 9.9 - - + -
537C GLU* 3.7 21.3 - - + -
538C LEU 3.3 8.5 - - - +
539C PRO* 3.9 15.5 - - + -
540C VAL* 4.6 0.2 - - - -
578C PHE* 3.6 7.2 - - - -
584C VAL* 3.6 6.4 - - - +
585C MSE 2.8 46.2 + - + +
587C GLN* 3.6 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 521 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C ILE* 1.3 73.4 - - - +
522C VAL* 1.3 63.2 + - - +
523C TYR* 3.6 8.7 + - - -
536C TYR 3.3 3.5 - - - +
538C LEU* 2.8 37.0 + - + +
540C VAL* 3.8 7.1 - - + +
576C HIS* 2.7 38.1 + - + +
577C THR 4.3 0.9 - - - +
578C PHE* 3.7 25.1 - - + -
582C HIS* 2.7 37.7 + - - +
583C ARG 3.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 522 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C VAL* 4.4 0.4 - - + -
520C ILE* 3.9 6.7 - - + -
521C ASP* 1.3 73.7 - - - +
523C TYR* 1.3 73.8 + - - +
535C GLY* 3.9 19.7 - - - +
536C TYR 3.4 3.4 - - - +
537C GLU* 4.3 6.7 - - + +
582C HIS* 3.2 6.1 - - - +
583C ARG* 2.9 57.3 + - + +
585C MSE 3.5 48.5 - - + -
----------------------------------------------------------
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