Contacts of the helix formed by residues 650 - 666 (chain M) in PDB entry 1MVW
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 SER 650 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475M PHE* 4.3 7.0 - - - -
479M CYS* 5.9 0.2 - - - -
533M PHE* 4.1 27.5 - - - -
537M GLU* 2.6 25.5 + - - +
599M ASN* 2.7 29.3 + - - -
648M THR* 3.3 1.2 - - - -
649M VAL* 1.0 81.8 - - - +
651M ALA* 1.3 64.4 + - - +
652M LEU 3.2 2.9 + - - -
653M PHE* 3.6 9.9 - - - +
654M ARG* 3.2 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 651 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537M GLU* 3.9 11.7 - - - +
641M LYS* 5.0 10.8 - - - +
646M PHE* 5.4 2.5 - - + -
647M GLN 4.9 4.0 - - - +
648M THR* 2.9 39.6 + - + +
650M SER* 1.3 79.0 - - - +
652M LEU* 1.3 61.1 + - + +
654M ARG* 4.1 9.8 + - - +
655M GLU* 3.7 19.1 + - - +
4Z GLU* 4.9 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 652 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646M PHE* 2.6 54.5 - - + -
648M THR 4.5 4.5 + - - +
649M VAL* 5.6 9.0 - - + +
650M SER 3.2 0.6 - - - +
651M ALA* 1.3 76.0 - - + +
653M PHE* 1.3 57.1 - - - +
654M ARG 2.8 2.5 - - - -
655M GLU* 2.3 44.8 + - - +
656M ASN* 2.6 36.9 + - - +
4Z GLU* 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 653 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268M TYR* 5.5 9.9 - + + -
269M LEU* 3.6 31.4 - - + -
479M CYS* 3.2 57.4 - - + -
482M PHE* 4.2 7.2 - + - -
483M THR* 3.3 13.0 - - + -
533M PHE* 4.8 5.8 - + - -
649M VAL 4.3 6.0 + - - +
650M SER* 3.6 19.5 - - - +
652M LEU* 1.3 76.7 - - - +
654M ARG* 1.3 58.9 + - + +
656M ASN* 3.4 7.4 + - + +
657M LEU* 2.7 57.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 654 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482M PHE* 4.7 10.3 - - + -
527M GLU* 3.9 25.0 + - + +
528M MLY 5.2 1.8 + - - -
533M PHE* 3.5 44.3 - - + +
534M SER* 4.9 7.3 + - - +
537M GLU* 2.9 33.6 + - - -
650M SER 3.2 17.2 + - - +
651M ALA* 4.1 11.4 + - - +
652M LEU 2.8 0.8 + - - -
653M PHE* 1.3 84.0 - - + +
655M GLU* 1.3 49.5 + - - +
657M LEU* 3.0 7.6 + - - +
658M ASN* 2.6 46.9 + - - +
350Z SER 4.9 3.0 + - - -
353Z GLN* 4.9 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 655 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651M ALA 3.7 8.4 + - - +
652M LEU* 2.3 39.0 + - + +
654M ARG* 1.3 71.8 - - - +
656M ASN* 1.3 64.4 + - - +
658M ASN* 3.4 7.0 + - - +
659M MLY 3.2 23.9 + - - +
1Z ASP* 1.5 62.5 + - + +
2Z GLU* 4.4 9.2 - - - +
4Z GLU* 3.2 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 656 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M GLU* 4.6 4.3 - - - +
267M THR 5.4 2.4 - - - +
268M TYR* 4.2 24.6 + - + -
652M LEU* 2.6 37.8 + - - +
653M PHE* 3.8 8.2 + - + +
655M GLU* 1.3 76.2 - - - +
657M LEU* 1.3 58.8 + - - +
658M ASN 3.0 8.8 + - - -
659M MLY 3.1 31.6 + - - +
660M LEU* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 657 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268M TYR* 5.0 2.6 - - - -
482M PHE* 3.5 40.6 - - + -
483M THR* 3.9 30.5 - - + +
486M MLY 4.3 10.7 - - + -
487M LEU* 6.0 0.2 - - + -
653M PHE* 2.7 41.8 + - + +
654M ARG* 3.3 6.3 - - - +
656M ASN* 1.3 72.9 - - - +
658M ASN* 1.3 61.8 + - - +
660M LEU* 3.9 15.7 - - + -
661M MET* 3.4 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 658 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486M MLY 3.1 35.0 - - - -
527M GLU* 4.7 2.0 + - - +
654M ARG* 2.6 31.1 + - - +
655M GLU* 3.7 8.1 - - - +
656M ASN 3.0 0.2 - - - -
657M LEU* 1.3 77.8 - - - +
659M MLY 1.3 64.1 + - - +
660M LEU 2.9 4.3 - - - -
661M MET* 3.5 2.4 + - - +
662M ALA* 3.1 25.8 + - - +
665M ARG* 5.6 0.9 + - - -
2Z GLU* 5.9 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 659 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M GLU* 2.5 44.3 + - - +
655M GLU 3.2 14.5 + - - +
656M ASN* 3.5 27.1 - - - +
658M ASN* 1.3 79.0 + - - +
660M LEU* 1.3 58.0 + - - +
662M ALA* 3.8 5.8 - - - +
663M ASN* 3.3 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 660 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249M PHE* 3.9 28.3 - - + -
266M GLU* 6.0 0.2 - - - -
268M TYR* 3.5 34.3 - - + +
462M LEU* 4.3 17.9 - - + -
464M ILE* 4.5 8.1 - - + -
483M THR* 5.2 2.7 - - + -
487M LEU* 5.5 2.9 - - + -
656M ASN 3.0 15.7 + - - +
657M LEU* 3.8 21.5 - - + +
659M MLY 1.3 75.0 + - - -
661M MET* 1.3 55.1 + - + +
662M ALA 2.9 4.0 - - - -
663M ASN* 2.8 27.3 + - - +
664M LEU* 2.8 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 661 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486M MLY 4.2 27.1 - - + +
487M LEU* 3.6 35.7 - - - -
490M PHE* 4.1 30.3 - - + -
657M LEU* 3.4 31.2 + - + +
658M ASN* 3.5 3.3 + - - +
660M LEU* 1.3 80.6 - - + +
662M ALA* 1.3 57.9 + - - +
664M LEU* 3.5 14.7 - - + +
665M ARG* 3.1 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 662 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658M ASN 3.1 18.7 + - - +
659M MLY 3.8 8.3 - - - +
660M LEU 2.9 0.4 - - - -
661M MET* 1.3 75.0 - - - +
663M ASN* 1.3 65.3 + - - +
664M LEU 3.1 1.3 - - - -
665M ARG* 3.3 21.4 + - - +
666M SER* 3.1 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 663 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249M PHE* 4.2 22.2 - - + -
251M ARG* 3.6 37.0 + - - +
458M PHE* 4.3 11.3 - - + -
659M MLY 3.3 25.1 + - - +
660M LEU* 2.8 9.7 + - - +
662M ALA* 1.3 80.2 - - - +
664M LEU* 1.3 63.2 + - - +
665M ARG 3.4 0.3 + - - -
666M SER* 3.7 11.2 + - - -
667M THR* 2.7 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 664 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174M SER* 4.7 14.1 - - - +
176M LEU* 4.4 12.6 - - + -
249M PHE* 4.0 28.9 - - + -
462M LEU* 4.7 5.8 - - + -
487M LEU* 3.9 15.7 - - + -
490M PHE* 3.3 33.8 - - + -
660M LEU* 2.8 28.7 + - + +
661M MET* 3.5 35.9 - - + +
663M ASN* 1.3 79.8 - - - +
665M ARG* 1.3 55.1 + - - +
667M THR* 2.8 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 665 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486M MLY 4.8 17.6 + - - -
489M GLN* 5.8 2.4 + - - -
490M PHE* 4.3 19.0 - - + -
658M ASN 5.6 0.4 + - - -
661M MET* 3.1 48.8 + - - +
662M ALA* 3.3 14.2 + - - +
663M ASN 3.2 0.6 - - - -
664M LEU* 1.3 73.3 - - - +
666M SER* 1.3 52.0 + - - +
667M THR 2.6 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 666 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172M ASN* 3.2 30.9 + - - +
458M PHE* 5.0 4.1 - - - -
662M ALA 3.1 15.3 + - - -
663M ASN* 3.9 9.9 + - - -
664M LEU 3.6 0.2 - - - -
665M ARG* 1.3 72.1 - - - +
667M THR* 1.3 59.9 + - - +
----------------------------------------------------------
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