Contacts of the helix formed by residues 481 - 493 (chain B) in PDB entry 3MY0
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 THR 481 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B HIS* 5.9 0.7 - - - -
394B LYS* 6.3 1.3 - - - +
395B TRP* 5.6 7.4 - - - +
398B ILE* 3.9 4.7 - - - -
479B ARG 4.8 4.5 - - - +
480B LEU* 1.3 78.6 - - - +
482B ALA* 1.3 65.2 + - - +
483B LEU* 3.6 9.3 + - - +
484B ARG* 3.2 24.3 + - + +
485B ILE* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA* 4.1 3.8 - - - +
310B LEU* 3.7 24.5 - - + +
311B ALA* 3.5 32.2 - - - +
314B HIS* 4.0 15.1 + - + +
398B ILE* 3.6 10.5 - - + +
481B THR* 1.3 69.9 - - - +
483B LEU* 1.3 61.1 + - - +
485B ILE* 3.3 8.1 + - - +
486B LYS* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA* 3.9 17.7 - - + +
315B VAL* 5.3 18.2 - - + -
481B THR* 3.2 8.9 + - - +
482B ALA* 1.3 77.4 - - - +
484B ARG* 1.3 57.4 + - - +
486B LYS* 3.3 12.7 + - + +
487B LYS* 2.9 64.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 3.7 23.3 - - + -
481B THR* 3.2 26.5 + - + +
483B LEU* 1.3 79.0 - - - +
485B ILE* 1.3 57.7 + - - +
487B LYS* 3.8 37.6 - - - +
488B THR* 3.0 44.6 + - - +
491B LYS* 4.3 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA* 3.9 5.6 - - + -
310B LEU* 5.9 0.7 - - + -
398B ILE* 4.3 15.3 - - + -
401B PHE* 3.7 24.5 - - + -
467B MET* 3.3 33.7 - - + -
471B CYS* 3.8 27.4 - - - -
480B LEU* 3.8 25.6 - - + -
481B THR 3.1 15.3 + - - +
482B ALA* 3.6 8.5 - - - +
483B LEU 3.3 0.2 - - - -
484B ARG* 1.3 74.3 - - - +
486B LYS* 1.3 67.1 + - - +
488B THR* 3.3 3.7 + - - -
489B LEU* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B HIS* 5.4 5.9 + - - -
304B VAL* 4.3 2.0 - - - +
307B ALA* 3.8 22.6 - - + +
308B CYS* 4.1 33.9 + - - +
311B ALA* 4.3 10.5 - - + +
482B ALA 2.9 13.8 + - - +
483B LEU* 3.3 19.7 - - + +
485B ILE* 1.3 76.6 - - - +
487B LYS* 1.3 67.3 + - + +
489B LEU* 3.3 3.3 + - - +
490B GLN* 3.0 56.2 + - - +
254C ASP* 5.7 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 2.9 52.0 + - + +
484B ARG* 3.8 27.3 - - - +
486B LYS* 1.3 78.6 - - + +
488B THR* 1.3 63.5 + - - +
490B GLN* 3.2 20.7 + - - +
491B LYS* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B GLY* 5.9 3.6 - - - +
467B MET* 4.4 21.1 - - + -
480B LEU* 5.3 3.7 - - + +
484B ARG* 3.0 31.3 + - - +
485B ILE* 3.7 4.2 - - - -
487B LYS* 1.3 75.4 - - - +
489B LEU* 1.3 54.5 + - - +
491B LYS* 2.8 52.7 + - + +
492B ILE* 3.6 15.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 3.3 38.3 - - + +
303B ALA* 3.5 33.7 - - + +
304B VAL* 4.0 12.8 - - + +
307B ALA* 4.3 1.6 - - + -
401B PHE* 5.0 0.2 - - + -
405B LEU* 4.9 0.7 - - + -
460B VAL 5.5 0.7 - - - +
464B LEU* 3.3 28.5 - - + +
467B MET* 3.2 35.9 - - + -
485B ILE* 3.0 19.5 + - + +
486B LYS 3.8 2.9 - - - +
488B THR* 1.3 73.1 - - - +
490B GLN* 1.3 64.4 + - - +
492B ILE* 3.8 14.7 + - + +
493B SER* 3.4 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B VAL* 3.9 15.9 - - + +
308B CYS* 4.5 2.9 - - - -
486B LYS* 3.0 58.1 + - - +
487B LYS* 3.2 19.1 + - - +
489B LEU* 1.3 78.3 - - - +
491B LYS* 1.3 59.8 + - - +
493B SER* 2.8 21.0 + - - +
494B ASN* 3.2 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ARG* 4.3 19.1 - - - +
487B LYS* 3.2 9.3 + - - +
488B THR* 2.8 44.7 + - + +
490B GLN* 1.3 72.9 - - - +
492B ILE* 1.3 61.7 + - + +
493B SER 3.6 0.2 + - - -
494B ASN* 3.8 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 4.0 5.7 - - + +
459B PRO* 4.3 13.0 - - + +
460B VAL* 3.0 45.4 - - + +
463B GLY* 4.2 24.9 - - - -
464B LEU 5.2 0.2 - - - +
488B THR* 3.6 22.9 + - + +
489B LEU* 3.8 19.0 + - + +
490B GLN 3.5 0.4 - - - -
491B LYS* 1.3 78.0 - - + +
493B SER* 1.3 55.3 + - - +
494B ASN 3.1 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 3.2 27.1 - - - -
304B VAL* 5.4 6.2 - - - +
489B LEU 3.4 7.7 + - - -
490B GLN* 2.8 31.2 + - - +
491B LYS 3.4 1.2 - - - -
492B ILE* 1.3 75.3 - - - +
494B ASN* 1.3 65.2 + - - +
----------------------------------------------------------
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