Contacts of the helix formed by residues 650 - 666 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475P PHE* 4.3 7.0 - - - -
479P CYS* 5.7 0.4 - - - -
533P PHE* 4.1 26.6 - - - -
537P GLU* 2.6 25.2 + - - +
599P ASN* 2.7 29.7 + - - -
648P THR* 3.3 1.0 - - - -
649P VAL* 1.0 82.7 - - - +
651P ALA* 1.3 63.8 + - - +
652P LEU 3.2 3.3 + - - -
653P PHE* 3.6 8.8 - - - +
654P ARG* 3.2 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 651 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 ASP 5.5 0.3 + - - -
41 GLU* 4.9 11.5 - - + +
537P GLU* 3.9 11.0 - - - +
641P LYS* 5.0 10.5 - - - +
646P PHE* 5.4 2.9 - - + -
647P GLN 4.9 4.5 - - - +
648P THR* 2.9 39.6 + - + +
650P SER* 1.3 78.6 - - - +
652P LEU* 1.3 61.8 + - + +
654P ARG* 4.1 10.1 + - - +
655P GLU* 3.7 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 652 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41 GLU* 5.3 1.1 - - - +
646P PHE* 2.6 53.6 - - + -
648P THR 4.5 4.5 + - - +
649P VAL* 5.6 8.5 - - + +
650P SER 3.2 0.8 - - - +
651P ALA* 1.3 75.6 - - + +
653P PHE* 1.3 57.9 - - - +
654P ARG 2.8 2.2 - - - -
655P GLU* 2.3 45.5 + - - +
656P ASN* 2.6 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 653 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268P TYR* 5.5 9.9 - + + -
269P LEU* 3.6 30.1 - - + -
479P CYS* 3.2 56.3 - - + -
482P PHE* 4.2 7.4 - + - -
483P THR* 3.3 14.1 - - + -
533P PHE* 4.8 6.3 - + - -
649P VAL* 4.3 6.0 + - + +
650P SER* 3.6 19.0 - - - +
652P LEU* 1.3 77.8 - - - +
654P ARG* 1.3 58.6 + - + +
656P ASN* 3.4 8.0 + - + +
657P LEU* 2.7 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 654 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3501 SER 4.9 3.0 + - - -
3531 GLN* 4.9 14.3 - - - +
482P PHE* 4.7 10.3 - - + -
527P GLU* 3.9 25.9 + - + +
528P MLY 5.3 1.4 + - - -
529P PRO* 6.1 0.2 - - - +
533P PHE* 3.5 43.7 - - + +
534P SER* 4.9 6.7 + - - +
537P GLU* 2.9 34.7 + - - -
650P SER 3.2 18.1 + - - +
651P ALA* 4.1 11.5 + - - +
652P LEU 2.8 0.6 + - - -
653P PHE* 1.3 81.6 - - + +
655P GLU* 1.3 49.1 + - - +
657P LEU* 3.0 8.3 + - - +
658P ASN* 2.6 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 655 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 ASP* 1.5 62.9 + - + +
21 GLU* 4.4 8.7 - - - +
41 GLU* 3.2 19.0 - - - +
651P ALA 3.7 9.0 + - - +
652P LEU* 2.3 39.2 + - + +
654P ARG* 1.3 71.0 - - - +
656P ASN* 1.3 63.3 + - - +
658P ASN* 3.4 7.4 + - - +
659P MLY 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 656 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P GLU* 4.6 4.5 - - - +
267P THR 5.4 2.8 - - - +
268P TYR* 4.2 24.2 + - + -
652P LEU* 2.6 35.7 + - - +
653P PHE* 3.8 8.2 + - + +
655P GLU* 1.3 76.0 - - - +
657P LEU* 1.3 58.8 + - - +
658P ASN 3.0 9.4 + - - -
659P MLY 3.1 31.0 + - - +
660P LEU* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 657 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268P TYR* 5.0 2.4 - - - -
482P PHE* 3.5 40.2 - - + -
483P THR* 3.9 31.2 - - + +
486P MLY 4.3 11.7 - - + -
487P LEU* 6.0 0.2 - - + -
653P PHE* 2.7 41.3 + - + +
654P ARG* 3.3 7.0 - - - +
656P ASN* 1.3 73.1 - - - +
658P ASN* 1.3 61.6 + - - +
660P LEU* 3.9 16.4 - - + -
661P MET* 3.4 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 658 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21 GLU* 5.9 2.4 + - - +
486P MLY 3.1 35.1 - - - -
527P GLU* 4.7 2.0 + - - +
654P ARG* 2.6 31.2 + - - +
655P GLU* 3.7 8.3 - - - +
656P ASN 3.0 0.4 - - - -
657P LEU* 1.3 77.6 - - - +
659P MLY 1.3 63.9 + - - +
660P LEU 2.9 4.5 - - - -
661P MET* 3.5 2.4 + - - +
662P ALA* 3.1 25.5 + - - +
665P ARG* 5.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 659 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266P GLU* 2.5 43.6 + - - +
655P GLU 3.2 14.7 + - - +
656P ASN* 3.5 27.4 - - - +
658P ASN* 1.3 78.8 + - - +
660P LEU* 1.3 57.8 + - - +
662P ALA* 3.8 5.6 - - - +
663P ASN* 3.3 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 660 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249P PHE* 3.9 29.2 - - + -
266P GLU* 6.0 0.4 - - - -
268P TYR* 3.5 33.9 - - + +
462P LEU* 4.3 17.5 - - + -
464P ILE* 4.5 8.7 - - + -
483P THR* 5.2 2.7 - - + -
487P LEU* 5.5 2.9 - - + -
656P ASN 3.0 16.1 + - - +
657P LEU* 3.8 21.1 - - + +
659P MLY 1.3 74.6 + - - -
661P MET* 1.3 54.0 + - + +
662P ALA 2.9 3.4 - - - -
663P ASN* 2.8 27.1 + - - +
664P LEU* 2.8 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 661 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486P MLY 4.2 27.8 - - + +
487P LEU* 3.6 35.9 - - + -
490P PHE* 4.1 30.3 - - + -
657P LEU* 3.4 32.0 + - + +
658P ASN* 3.5 3.3 + - - +
660P LEU* 1.3 79.2 - - + +
662P ALA* 1.3 57.7 + - - +
664P LEU* 3.5 14.6 - - + +
665P ARG* 3.1 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 662 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658P ASN 3.1 16.5 + - - +
659P MLY 3.8 8.5 - - - +
660P LEU 2.9 0.2 - - - -
661P MET* 1.3 75.4 - - - +
663P ASN* 1.3 65.9 + - - +
664P LEU 3.1 1.6 - - - -
665P ARG* 3.3 21.5 + - - +
666P SER* 3.1 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 663 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249P PHE* 4.2 22.4 - - + -
251P ARG* 3.6 36.6 + - - +
458P PHE* 4.3 12.1 - - + -
659P MLY 3.3 26.0 + - - +
660P LEU* 2.8 9.5 + - - +
662P ALA* 1.3 80.4 - - - +
664P LEU* 1.3 61.7 + - - +
665P ARG 3.4 0.3 + - - -
666P SER* 3.7 12.2 + - - -
667P THR* 2.7 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 664 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P SER* 4.7 14.4 - - - +
176P LEU* 4.4 13.7 - - + -
249P PHE* 4.0 28.9 - - + -
462P LEU* 4.7 5.6 - - + -
487P LEU* 3.9 15.0 - - + -
490P PHE* 3.3 33.8 - - + -
660P LEU* 2.8 28.1 + - + +
661P MET* 3.5 35.4 - - + +
663P ASN* 1.3 79.9 - - - +
665P ARG* 1.3 53.7 + - - +
667P THR* 2.8 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 665 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486P MLY 4.8 17.8 + - - -
489P GLN* 5.8 2.4 + - - -
490P PHE* 4.3 18.5 - - + -
658P ASN 5.6 0.6 + - - -
661P MET* 3.1 49.6 + - - +
662P ALA* 3.3 14.4 + - - +
663P ASN 3.2 0.6 - - - -
664P LEU* 1.3 73.6 - - - +
666P SER* 1.3 52.2 + - - +
667P THR 2.6 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 666 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172P ASN* 3.2 30.7 + - - +
458P PHE* 5.0 3.9 - - - -
662P ALA 3.1 15.3 + - - -
663P ASN* 3.7 10.1 + - - -
664P LEU 3.6 0.2 - - - -
665P ARG* 1.3 73.2 - - - +
667P THR* 1.3 60.4 + - - +
----------------------------------------------------------
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