Contacts of the helix formed by residues 531 - 540 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524D GLU 4.7 1.1 - - - -
525D LEU 3.1 18.4 - - - -
526D ILE 3.9 3.1 - - - -
528D MLY 3.0 15.5 + - - +
529D PRO 3.1 0.2 - - - -
530D MET* 1.3 79.5 - - - +
532D ILE* 1.3 55.2 + - - -
533D PHE 3.3 2.2 - - - -
534D SER* 2.8 28.8 + - - -
535D ILE* 3.2 9.0 + - - -
558D HIS* 3.6 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 532 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D LEU* 4.4 18.6 - - + -
525D LEU* 3.1 21.7 + - + +
526D ILE* 4.4 10.1 - - + +
531D GLY* 1.3 68.6 - - - +
533D PHE* 1.3 59.6 + - + +
535D ILE* 3.4 2.3 + - - +
536D LEU* 2.7 31.1 + - + +
550D PHE* 4.4 7.0 - - + -
554D LEU* 4.1 23.6 - - + -
558D HIS* 4.1 6.7 + - + -
565D PHE* 4.1 20.4 - - + -
579D PHE* 3.7 38.6 - - + -
581D LEU* 4.2 14.4 - - + -
595D TRP* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 533 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D PHE* 4.3 11.7 - + - -
478D LEU* 3.5 37.7 - - + -
479D CYS* 4.3 17.5 - - - -
482D PHE* 4.0 18.4 - + - -
526D ILE* 3.4 35.6 + - + +
527D GLU* 5.1 0.7 - - - -
531D GLY 3.0 1.2 + - - -
532D ILE* 1.3 78.4 - - + +
534D SER* 1.3 51.4 + - - +
536D LEU* 2.8 14.8 + - + +
537D GLU* 2.5 43.0 + - - +
650D SER* 4.1 20.0 - - - -
653D PHE* 4.8 4.9 - + - -
654D ARG* 3.5 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 534 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3509 SER 2.6 20.5 + - - -
3519 THR* 1.6 55.5 + - - +
3539 GLN* 3.3 12.2 - - - +
3549 GLN* 1.4 67.4 + - - -
526D ILE 4.8 0.6 + - - -
528D MLY 4.4 1.9 + - - -
531D GLY 2.8 8.7 + - - -
533D PHE* 1.3 71.9 - - - +
535D ILE* 1.3 46.0 - - - -
537D GLU* 2.7 2.3 + - - -
538D GLU 2.7 3.5 + - - -
654D ARG* 4.9 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 535 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3519 THR* 1.5 51.5 + - + +
3549 GLN* 4.7 5.6 - - + +
530D MET* 3.1 33.9 - - + +
531D GLY 3.2 3.3 + - - +
532D ILE 3.9 1.6 - - - +
534D SER* 1.3 68.7 - - - +
536D LEU* 1.3 59.3 + - - +
538D GLU* 4.8 2.2 - - - +
539D GLU* 3.4 14.6 + - - +
550D PHE* 3.9 11.9 - - + -
553D MLY 3.9 37.5 - - + +
554D LEU* 3.4 32.5 - - + +
557D GLU* 4.2 8.3 - - + -
558D HIS* 3.8 14.6 - - + +
46W GLY* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D PHE* 4.2 16.2 - - + -
532D ILE* 2.7 17.1 + - + +
533D PHE* 2.8 23.0 + - + +
535D ILE* 1.3 81.4 - - - +
537D GLU* 1.3 57.0 + - - +
538D GLU 3.3 0.7 + - - -
539D GLU* 4.3 0.9 - - - +
540D CYS* 3.3 19.2 + - - -
550D PHE* 3.2 34.1 - - + -
595D TRP* 3.9 32.1 - - + -
596D LEU* 3.8 16.8 - - + +
599D ASN* 3.6 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3499 LEU* 1.7 31.1 - - - +
3509 SER* 0.4 131.0 + - - +
3519 THR 2.5 1.6 - - - -
533D PHE* 2.5 32.7 + - - +
534D SER 2.7 0.6 + - - -
536D LEU* 1.3 71.5 - - - +
538D GLU* 1.3 47.7 - - - +
540D CYS* 3.8 4.6 - - - +
599D ASN* 4.4 0.4 - - - +
641D LYS* 5.1 2.4 + - - -
648D THR* 3.2 12.5 - - - +
650D SER* 2.6 31.6 + - - +
651D ALA* 3.5 7.3 + - - +
654D ARG* 2.9 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439 TYR* 3.7 1.7 + - - -
3469 LEU* 4.2 7.0 - - + +
3499 LEU* 1.8 49.4 - - + +
3519 THR* 1.3 104.5 + - - +
3529 PHE* 2.8 17.9 - - + +
3559 MET* 1.9 43.1 - - - +
530D MET* 4.7 2.1 - - - +
534D SER 2.7 0.2 + - - -
535D ILE* 4.0 2.1 - - - +
537D GLU* 1.3 62.1 - - - +
539D GLU* 1.3 55.5 + - - +
541D MET* 2.4 20.3 + - + +
542D PHE* 4.4 5.3 - - + -
553D MLY 4.3 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3519 THR* 2.4 6.1 + - - +
535D ILE* 3.5 14.6 - - - +
536D LEU 4.3 2.9 - - - +
538D GLU* 1.3 78.0 - - - +
540D CYS* 1.3 56.6 + - - +
541D MET 2.8 5.1 + - - -
542D PHE* 3.0 27.6 + - - +
545D ALA* 3.5 14.0 - - + +
549D SER* 2.8 13.6 + - - +
550D PHE* 4.1 11.9 - - + -
553D MLY 3.0 21.5 + - - +
596D LEU* 4.6 11.3 - - + +
600D MLY 3.8 1.6 - - - -
45W VAL* 1.3 56.7 - - + +
46W GLY* 3.2 10.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3499 LEU* 3.3 2.4 - - - +
536D LEU* 3.3 19.6 + - - -
537D GLU* 3.8 13.0 - - - +
538D GLU 2.7 3.2 + - - -
539D GLU* 1.3 75.5 - - - +
541D MET* 1.3 57.6 + - - +
542D PHE 3.4 0.4 - - - -
596D LEU* 3.8 32.5 - - - -
599D ASN* 4.0 21.8 - - - -
600D MLY 3.3 36.8 - - + +
640D LYS* 6.1 0.9 - - - -
647D GLN 3.9 15.4 - - - +
648D THR* 4.4 2.5 - - - -
----------------------------------------------------------
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