Contacts of the helix formed by residues 540 - 551 (chain A) in PDB entry 6QVC
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 VAL 540 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 5.7 0.2 - - + -
539A THR* 1.3 83.6 + - - +
541A SER* 1.3 59.9 + - - +
542A THR* 3.1 7.0 + - - -
543A ALA* 3.2 20.6 + - - +
544A VAL* 3.9 5.4 + - - +
563A VAL* 4.0 7.9 - - + -
564A ILE* 3.9 22.2 - - + -
567A ASN* 3.4 21.3 - - + +
302B TYR* 4.0 29.2 - - + +
303B TRP* 5.1 10.3 - - + +
306B PHE* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLY* 4.5 1.2 - - - -
287A LEU* 3.6 32.8 - - - -
288A PHE* 3.6 22.5 - - - -
291A GLU* 2.9 25.4 + - - -
539A THR* 2.8 4.7 + - - +
540A VAL* 1.3 80.1 - - - +
542A THR* 1.3 63.2 + - - +
543A ALA 3.3 0.2 - - - -
544A VAL* 3.2 22.2 + - - +
545A ILE* 3.3 17.6 + - - +
302B TYR* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PHE* 5.1 6.3 - - - -
484A PHE* 3.6 21.4 - - + -
488A PHE* 5.7 0.4 - - + -
529A ALA 5.1 0.2 - - - +
530A ALA* 3.9 5.8 - - - +
533A THR* 3.6 31.2 - - + +
534A GLY* 3.8 18.2 - - - +
537A SER* 3.4 8.5 + - - -
539A THR* 3.3 19.6 - - - +
540A VAL 3.1 1.0 - - - -
541A SER* 1.3 75.8 + - - +
543A ALA* 1.3 61.1 + - - +
545A ILE* 3.3 10.8 - - - +
546A CYS* 2.9 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ALA* 4.2 7.9 - - + -
540A VAL 3.2 12.9 + - - +
542A THR* 1.3 78.9 - - - +
544A VAL* 1.3 58.3 + - + +
546A CYS* 3.4 7.6 - - - +
547A PHE* 3.0 36.0 + - + -
559A MET* 3.8 15.6 - - + +
560A MET* 5.1 9.6 - - + -
563A VAL* 3.7 29.5 - - + +
306B PHE* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.9 19.3 - - + -
284A GLY* 3.6 28.0 - - - +
287A LEU* 3.9 16.4 - - + -
540A VAL 4.3 4.3 - - - +
541A SER* 3.2 17.9 + - - +
542A THR 3.2 0.6 - - - -
543A ALA* 1.3 78.3 - - + +
545A ILE* 1.3 56.9 + - - +
546A CYS 3.3 0.2 + - - -
547A PHE* 3.4 21.6 + - + -
548A GLU* 3.0 27.4 + - - +
560A MET* 5.8 1.3 - - + -
283B LEU* 3.9 22.2 - - + -
306B PHE* 5.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 5.0 12.6 - - + -
279A PHE* 4.2 15.7 - - + -
281A THR* 3.4 27.1 - - + +
284A GLY* 3.6 27.8 - - - +
288A PHE* 5.8 7.4 - - + -
484A PHE* 3.6 37.0 - - + -
541A SER 3.3 4.2 + - - +
542A THR* 3.3 22.4 - - - +
544A VAL* 1.3 76.0 - - - +
546A CYS* 1.3 56.7 + - - +
548A GLU* 4.2 6.7 - - - -
549A LEU* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A PHE* 4.2 24.1 - - + -
526A VAL* 3.3 39.4 - - - +
530A ALA* 3.6 25.8 - - + -
542A THR* 2.9 18.8 + - + +
543A ALA 3.4 5.6 - - - +
544A VAL 3.1 0.2 - - - -
545A ILE* 1.3 78.0 - - - +
547A PHE* 1.3 63.3 + - - +
549A LEU* 3.3 4.9 + - - +
550A THR* 3.0 20.6 + - - -
559A MET* 4.6 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 5.3 4.0 - - + -
543A ALA* 3.0 28.2 + - + -
544A VAL* 3.4 40.4 - - + -
546A CYS* 1.3 77.0 - - - +
548A GLU* 1.3 70.4 + - + +
550A THR* 3.3 25.2 + - + +
551A GLY* 3.3 6.8 + - - -
552A GLN 4.2 3.4 - - - +
553A ILE* 3.5 32.1 - - + -
556A ILE* 3.5 28.3 - - + -
559A MET* 4.0 21.4 - - + -
560A MET* 4.6 4.0 - - + -
283B LEU* 4.2 17.9 - - + -
547B PHE* 4.5 19.5 - + - -
553B ILE* 4.4 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY 3.9 4.0 - - - +
281A THR* 3.3 37.7 - - + +
282A PRO* 3.2 20.6 - - - +
283A LEU* 3.3 27.6 - - - +
284A GLY 4.1 2.4 + - - -
331A ALA* 3.3 22.6 - - + +
544A VAL* 3.0 18.7 + - - +
545A ILE 4.0 0.2 - - - +
546A CYS 3.2 0.4 - - - -
547A PHE* 1.3 87.6 - - + +
549A LEU* 1.3 59.8 + - - +
551A GLY* 4.0 2.9 + - - -
553B ILE* 5.1 8.9 - - + +
556B ILE* 4.2 24.2 - - + +
560B MET* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 3.3 57.0 - - + +
281A THR* 4.2 6.1 - - + -
331A ALA* 4.5 3.5 - - + +
332A LEU* 3.7 27.3 + - + +
333A PHE* 3.3 46.0 + - + +
484A PHE* 5.6 3.8 - - + -
488A PHE* 4.9 19.1 - - + -
545A ILE* 2.9 23.5 + - + +
546A CYS* 4.0 3.4 - - - +
548A GLU* 1.3 79.1 - - - +
550A THR* 1.3 62.7 + - - +
551A GLY 3.3 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A PHE* 2.8 16.7 - - - +
335A THR* 3.0 35.5 + - - +
337A PHE* 4.8 1.9 - - + -
428A PHE* 4.7 5.4 - - - -
526A VAL* 3.6 30.8 - - + +
546A CYS 3.0 11.6 + - - -
547A PHE* 3.3 21.1 + - + +
549A LEU* 1.3 78.0 - - - +
551A GLY* 1.3 56.3 + - - +
552A GLN* 3.2 27.8 + - + +
559A MET* 5.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA* 5.0 9.2 - - - -
333A PHE 4.3 4.0 - - - -
334A ARG* 5.2 6.5 - - - +
335A THR 5.7 0.4 - - - -
547A PHE 3.3 5.1 + - - -
548A GLU 4.0 4.1 + - - -
549A LEU 3.3 4.0 - - - -
550A THR* 1.3 78.0 - - - +
552A GLN* 1.3 64.9 + - - +
339B MET* 5.6 1.2 - - - +
553B ILE* 3.3 30.6 + - - +
554B ALA 5.3 0.3 + - - -
----------------------------------------------------------
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