Contacts of the helix formed by residues 531 - 540 (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 GLY 531 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524M GLU 4.7 1.3 - - - -
525M LEU* 3.1 18.2 - - - -
526M ILE 3.9 2.9 - - - -
528M MLY 3.0 16.0 + - - +
530M MET* 1.3 80.3 - - - +
532M ILE* 1.3 55.0 - - - -
533M PHE 3.3 2.0 - - - -
534M SER* 2.8 29.6 + - - -
535M ILE* 3.2 9.3 + - - -
558M HIS* 3.6 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 532 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478M LEU* 4.4 17.9 - - + -
525M LEU* 3.1 22.6 + - + +
526M ILE* 3.8 10.5 + - + +
531M GLY* 1.3 68.0 - - - +
533M PHE* 1.3 59.3 + - + +
535M ILE* 3.4 1.7 + - - +
536M LEU* 2.7 31.2 + - + +
550M PHE* 4.4 7.3 - - + -
554M LEU* 4.1 24.7 - - + -
558M HIS* 4.1 6.2 + - + -
565M PHE* 4.1 20.4 - - + -
579M PHE* 3.7 40.4 - - + -
581M LEU* 4.2 14.1 - - + -
595M TRP* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 533 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475M PHE* 4.3 12.1 - + - -
478M LEU* 3.5 38.6 - - + -
479M CYS* 4.3 17.0 - - - -
482M PHE* 4.0 18.8 - + - -
526M ILE* 3.4 35.4 + - + +
527M GLU* 5.1 0.2 - - - -
531M GLY 3.0 1.2 + - - -
532M ILE* 1.3 78.4 - - + +
534M SER* 1.3 51.4 + - - +
536M LEU* 2.8 13.2 + - + +
537M GLU* 2.5 42.5 + - - +
650M SER* 4.1 20.6 - - - -
653M PHE* 4.8 5.4 - + - -
654M ARG* 3.5 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 534 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526M ILE 4.8 0.6 + - - -
528M MLY 4.4 2.3 + - - -
529M PRO* 4.5 0.2 - - - -
531M GLY 2.8 8.2 + - - -
533M PHE* 1.3 71.3 - - - +
535M ILE* 1.3 45.1 - - - -
537M GLU* 2.7 2.3 + - - +
538M GLU 2.6 3.3 + - - -
654M ARG* 4.9 5.3 + - - +
350Z SER 2.6 20.8 + - - -
351Z THR* 1.6 55.9 + - - +
353Z GLN* 3.3 11.8 - - - +
354Z GLN* 1.4 68.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 535 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530M MET* 3.1 34.1 - - + +
531M GLY 3.2 2.9 + - - +
532M ILE 3.9 2.0 - - - +
534M SER* 1.3 68.7 - - - +
536M LEU* 1.3 58.3 + - - +
538M GLU* 4.8 2.0 - - - +
539M GLU* 3.4 15.2 + - - +
550M PHE* 3.9 12.2 - - + -
553M MLY 3.9 37.7 - - + +
554M LEU* 3.4 31.6 - - + -
557M GLU* 4.2 8.5 - - + -
558M HIS* 3.8 14.8 - - + +
351Z THR* 1.5 53.0 + - + +
354Z GLN* 4.7 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475M PHE* 4.2 16.2 - - + -
532M ILE* 2.7 16.3 + - + +
533M PHE* 2.8 23.7 + - + +
535M ILE* 1.3 80.4 - - - +
537M GLU* 1.3 58.0 + - - +
538M GLU 3.3 1.0 + - - -
539M GLU* 4.3 1.2 - - - +
540M CYS* 3.3 19.0 + - - -
550M PHE* 3.2 35.2 - - + -
595M TRP* 3.9 33.0 - - + -
596M LEU* 3.8 17.7 - - + +
599M ASN* 3.6 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 537 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533M PHE* 2.5 32.6 + - - +
534M SER 2.7 0.6 + - - -
536M LEU* 1.3 70.9 - - - +
538M GLU* 1.3 47.5 - - - +
540M CYS* 3.8 4.9 - - - +
599M ASN* 4.4 0.7 - - - +
641M LYS* 5.1 3.1 + - - -
648M THR* 3.2 12.6 - - - +
650M SER* 2.6 32.2 + - - +
651M ALA* 3.5 6.9 + - - +
654M ARG* 2.9 34.9 + - - -
349Z LEU* 1.7 32.3 - - - +
350Z SER* 0.4 130.2 + - - +
351Z THR 2.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 538 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530M MET* 4.7 2.1 - - - +
534M SER 2.6 0.4 + - - -
535M ILE* 4.8 2.3 - - - +
537M GLU* 1.3 61.9 - - - +
539M GLU* 1.3 56.0 + - - +
541M MET* 2.4 20.1 + - + +
542M PHE* 3.9 5.9 - - + -
553M MLY 4.3 22.5 - - - +
143Z TYR* 3.7 1.6 + - - -
346Z LEU* 4.2 6.9 - - + +
349Z LEU* 1.8 47.0 - - + +
351Z THR* 1.3 105.2 + - - +
352Z PHE* 2.8 17.7 - - + +
355Z MET* 1.9 42.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 539 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432 VAL* 4.2 1.7 - - - +
535M ILE* 3.5 15.2 - - - +
536M LEU 4.3 2.7 - - - +
538M GLU* 1.3 78.3 - - - +
540M CYS* 1.3 57.3 + - - +
541M MET 2.8 5.2 + - - -
542M PHE* 3.0 28.8 + - - +
545M ALA* 3.5 19.6 - - + +
549M SER* 2.8 30.7 + - - +
550M PHE* 4.1 12.8 - - + -
553M MLY 3.0 58.4 + - - +
596M LEU* 4.6 11.6 - - + +
600M MLY 3.8 1.6 - - - -
351Z THR* 2.4 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 540 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536M LEU* 3.3 19.7 + - - -
537M GLU 3.8 12.8 - - - +
538M GLU 2.7 0.8 + - - -
539M GLU* 1.3 77.4 - - - +
541M MET* 1.3 57.1 + - - +
542M PHE 3.4 0.2 - - - -
596M LEU* 3.8 32.3 - - - -
599M ASN* 4.0 22.0 - - - -
600M MLY 3.3 36.2 - - + +
640M LYS* 6.1 0.7 - - - -
647M GLN 3.9 15.7 - - - +
648M THR* 4.4 2.5 - - - -
349Z LEU* 3.3 2.4 - - - +
----------------------------------------------------------
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