Contacts of the helix formed by residues 540 - 551 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 4.0 29.6 - - + +
303A TRP* 5.1 10.5 - - + +
306A PHE* 3.7 32.4 - - + -
291B GLU* 5.0 0.6 - - + +
539B THR* 1.3 84.3 + - - +
541B SER* 1.3 60.7 + - - +
542B THR 3.1 6.5 + - - -
543B ALA* 3.2 20.7 + - - +
544B VAL* 3.9 5.6 + - - +
563B VAL* 4.0 8.3 - - + -
564B ILE* 3.9 23.1 - - + -
567B ASN* 3.4 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 5.3 0.7 - - - -
284B GLY* 4.5 0.8 - - - -
287B LEU* 3.6 32.3 - - - -
288B PHE* 3.6 22.4 - - - +
291B GLU* 2.9 25.5 + - - -
539B THR* 2.8 5.1 + - - +
540B VAL* 1.3 79.5 - - - +
542B THR* 1.3 62.2 + - - +
543B ALA 3.3 0.2 - - - -
544B VAL* 3.2 21.9 + - - +
545B ILE* 3.3 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B PHE* 5.1 6.2 - - - -
484B PHE* 3.6 20.7 - - + -
488B PHE* 5.7 0.7 - - + -
530B ALA* 3.9 6.1 - - - +
533B THR* 3.6 32.1 - - + +
534B GLY* 3.8 17.5 - - - +
537B SER* 3.4 8.1 + - - -
539B THR* 3.3 20.6 - - - +
540B VAL 3.1 1.3 - - - -
541B SER* 1.3 76.4 + - - +
543B ALA* 1.3 59.7 + - - +
545B ILE* 3.3 10.6 - - - +
546B CYS* 2.9 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 6.4 0.7 - - + -
530B ALA* 4.2 7.2 - - + -
540B VAL 3.2 13.6 + - - +
542B THR* 1.3 78.9 - - - +
544B VAL* 1.3 58.9 + - + +
546B CYS* 3.4 8.2 - - - +
547B PHE* 3.0 35.8 + - + -
559B MET* 3.8 15.4 - - + +
560B MET* 5.1 9.2 - - + -
563B VAL* 3.7 29.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.9 17.3 - - + -
306A PHE* 5.7 6.5 - - + -
283B LEU* 3.9 19.5 - - + -
284B GLY* 3.6 28.9 - - - +
287B LEU* 3.9 21.1 - - + -
540B VAL 4.3 3.8 - - - +
541B SER* 3.2 17.4 + - - +
543B ALA* 1.3 78.9 - - + +
545B ILE* 1.3 58.9 + - - +
547B PHE* 3.4 22.5 + - + -
548B GLU* 3.0 27.3 + - - +
560B MET* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 5.0 13.0 - - + -
279B PHE* 4.2 15.3 - - + -
281B THR* 3.4 28.0 - - + +
284B GLY* 3.6 26.7 - - - +
288B PHE* 5.8 6.7 - - + -
484B PHE* 3.6 37.7 - - + -
541B SER 3.3 4.2 + - - +
542B THR* 3.3 21.3 - - - +
544B VAL* 1.3 75.9 - - - +
546B CYS* 1.3 56.8 + - - +
548B GLU* 3.8 6.7 - - - -
549B LEU* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B PHE* 4.2 23.3 - - + -
526B VAL* 3.3 39.2 - - - +
530B ALA* 3.6 26.2 - - + -
542B THR* 2.9 18.8 + - + +
543B ALA 3.4 5.8 - - - +
544B VAL 3.1 0.2 - - - -
545B ILE* 1.3 78.8 - - - +
547B PHE* 1.3 64.3 + - - +
549B LEU* 3.3 6.0 + - - +
550B THR* 3.0 20.1 + - - -
559B MET* 4.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.2 19.3 - - + -
547A PHE* 4.5 19.3 - + - -
553A ILE* 4.3 6.9 - - + +
283B LEU* 5.3 3.4 - - + -
543B ALA* 3.0 26.9 + - + -
544B VAL* 3.4 40.4 - - + -
546B CYS* 1.3 77.4 - - - +
548B GLU* 1.3 71.3 + - + +
550B THR* 3.3 25.1 + - + +
551B GLY* 3.3 6.4 + - - -
552B GLN 4.2 2.8 - - - +
553B ILE* 3.5 31.0 - - + -
556B ILE* 3.5 27.1 - - + -
559B MET* 4.0 22.6 - - + -
560B MET* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ILE* 5.1 7.0 - - + +
556A ILE* 4.2 25.2 - - + +
560A MET* 4.4 0.3 - - - +
280B GLY 3.9 4.5 - - - +
281B THR* 3.3 39.4 - - + +
282B PRO* 3.2 19.8 - - - +
283B LEU* 3.3 28.4 - - - +
284B GLY 4.1 2.4 + - - -
331B ALA* 3.3 22.2 - - + +
544B VAL* 3.0 18.0 + - - +
545B ILE 4.0 0.2 - - - +
547B PHE* 1.3 87.3 - - + +
549B LEU* 1.3 60.9 + - - +
551B GLY* 4.0 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 3.3 58.1 - - + +
281B THR* 4.2 6.3 - - + -
331B ALA* 4.5 3.1 - - + +
332B LEU* 3.7 27.1 + - + +
333B PHE* 3.3 45.5 + - + +
484B PHE* 5.6 3.4 - - + -
488B PHE* 4.9 19.3 - - + -
545B ILE* 2.9 22.7 + - + +
546B CYS* 4.0 2.9 - - - +
548B GLU* 1.3 78.8 - - - +
550B THR* 1.3 62.5 + - - +
551B GLY 3.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PHE* 2.8 18.1 - - - +
335B THR* 3.0 35.1 + - - +
337B PHE* 4.8 2.1 - - - -
428B PHE* 4.7 5.1 - - - -
526B VAL* 3.6 32.1 - - + +
546B CYS 3.0 11.2 + - - -
547B PHE* 3.3 21.1 - - + +
549B LEU* 1.3 78.2 - - - +
551B GLY* 1.3 55.8 + - - +
552B GLN* 3.2 28.4 + - + +
559B MET* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A MET* 5.6 0.9 - - - +
553A ILE* 3.3 30.6 + - - +
554A ALA* 5.2 0.9 + - - -
331B ALA* 5.0 9.2 - - - -
333B PHE 4.3 4.3 - - - -
334B ARG* 5.2 6.9 - - - +
335B THR 5.7 0.7 - - - -
547B PHE 3.3 4.8 + - - -
548B GLU 4.0 3.9 + - - -
549B LEU 3.3 4.2 - - - -
550B THR* 1.3 77.2 - - - +
552B GLN* 1.3 65.3 + - - +
----------------------------------------------------------
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