Contacts of the helix formed by residues 540 - 556 (chain B) in PDB entry 3QFR
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).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475B CYS* 4.6 4.7 - - - -
535B GLY 3.2 11.2 + - - +
537B GLY 3.1 15.7 + - - +
538B THR 2.9 1.2 - - - +
539B GLY* 1.3 77.3 - - - +
541B ALA* 1.3 59.4 + - - +
543B PHE* 2.7 34.8 + - + +
544B ILE* 3.2 23.2 + - + -
565B LEU* 4.4 25.4 - - + -
567B TYR* 3.6 24.9 - - + -
577B LEU* 4.7 3.1 - - + +
578B TYR* 3.9 28.3 - - + -
582B LEU* 4.7 4.9 - - + -
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Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B SER 3.8 10.1 - - - +
461B ILE 4.2 0.2 - - - -
462B ALA* 2.7 33.5 - - + +
475B CYS* 3.7 21.3 - - + -
538B THR 3.0 17.2 + - - +
539B GLY 3.2 0.2 - - - -
540B VAL* 1.3 83.5 - - - +
542B PRO* 1.3 65.7 - - + +
543B PHE 3.4 0.2 + - - -
544B ILE* 3.5 5.7 + - - -
752B FAD 3.6 19.3 - - - +
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Residues in contact with PRO 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B SER* 5.1 1.4 - - - -
320B GLY* 5.1 7.6 + - - -
460B SER* 4.0 12.1 - - - -
461B ILE 3.6 13.9 - - - +
521B PHE* 4.1 20.2 - - + -
539B GLY 3.1 18.2 - - - +
540B VAL 3.5 0.2 - - - -
541B ALA* 1.3 88.7 - - + +
543B PHE* 1.3 67.9 + - + +
545B GLY* 3.2 5.0 + - - -
546B PHE* 3.0 28.1 + - - -
632B CYS* 3.3 31.9 - - + -
677B ASP* 4.1 4.5 - - - +
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Residues in contact with PHE 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B PHE* 3.9 15.0 - + - -
533B MET* 3.3 46.4 - - + -
534B VAL 3.3 34.3 - - - -
535B GLY* 3.6 5.8 - - - -
539B GLY 3.8 16.8 - - - -
540B VAL* 2.7 21.1 + - + +
542B PRO* 1.3 70.3 - - + +
544B ILE* 1.3 58.8 + - - -
545B GLY 2.9 1.3 - - - -
546B PHE* 3.4 11.2 - + - +
547B ILE* 2.8 38.2 + - + +
565B LEU* 3.7 20.6 - - + -
630B TYR* 3.5 26.0 - - + -
632B CYS* 3.8 12.6 - - + -
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Residues in contact with ILE 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B HIS* 5.9 1.3 - - - +
462B ALA* 3.4 19.7 - - + +
540B VAL* 3.2 21.2 + - + +
541B ALA 3.8 6.5 - - - +
542B PRO 3.3 0.2 - - - -
543B PHE* 1.3 77.5 - - - +
545B GLY* 1.3 57.5 + - - +
547B ILE* 4.2 4.7 - - - +
548B GLN* 2.9 39.5 + - + +
578B TYR* 3.4 63.7 - - + -
581B GLU* 6.0 2.0 - - + -
582B LEU* 3.7 23.3 - - + -
585B PHE* 5.1 9.1 - - + -
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Residues in contact with GLY 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B SER* 3.7 11.0 + - - -
461B ILE 5.0 0.2 - - - -
462B ALA* 3.6 3.4 + - - -
463B SER* 3.8 30.1 - - - -
464B SER* 3.5 14.4 - - - -
542B PRO 3.2 10.2 + - - -
543B PHE 2.9 0.4 - - - -
544B ILE* 1.3 81.2 - - - +
546B PHE* 1.3 63.2 + - - +
548B GLN* 4.1 0.7 - - - -
549B GLU* 3.5 13.5 + - - +
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Residues in contact with PHE 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B SER* 3.7 36.3 - - - -
320B GLY* 4.1 4.7 - - - -
521B PHE* 3.5 26.2 - + - -
522B ARG* 3.8 18.4 - - - -
523B LEU* 3.5 32.9 - - + +
533B MET* 3.5 32.3 - - + -
542B PRO 3.0 17.1 + - - +
543B PHE* 3.1 8.7 + + - +
545B GLY* 1.3 75.9 - - - +
547B ILE* 1.3 65.2 + - - +
549B GLU* 3.3 6.6 + - - +
550B ARG* 3.1 26.2 + - + +
630B TYR* 3.6 30.5 - + - -
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Residues in contact with ILE 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B MET* 3.7 17.7 - - + -
543B PHE 2.8 27.9 + - - +
544B ILE* 4.2 3.8 - - - +
546B PHE* 1.3 73.8 - - - +
548B GLN* 1.3 68.8 + - - +
550B ARG* 3.2 8.1 + - - +
551B ALA* 3.1 18.7 + - - +
563B THR* 5.0 2.7 - - + -
565B LEU* 3.7 20.6 - - + -
582B LEU* 3.5 29.8 - - + -
585B PHE* 3.6 36.1 - - + -
590B ALA 4.5 7.9 - - - +
591B LEU* 3.9 19.3 - - + -
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Residues in contact with GLN 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B ALA 4.6 2.4 + - - -
463B SER* 3.1 13.9 - - - +
464B SER* 2.9 34.1 + - - -
467B VAL* 4.5 12.7 - - + +
468B HIS* 3.1 34.3 + - - -
473B HIS* 5.2 3.0 + - - -
544B ILE* 2.9 26.6 + - + +
545B GLY 3.8 4.7 - - - +
546B PHE 3.2 0.4 - - - -
547B ILE* 1.3 81.8 - - - +
549B GLU* 1.3 58.6 + - - +
550B ARG 2.9 4.5 + - - -
551B ALA* 2.9 13.5 + - - +
552B TRP* 3.0 10.7 + - - +
585B PHE* 4.2 23.1 - - + -
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Residues in contact with GLU 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B GLU* 4.4 6.2 - - - +
319B SER* 3.4 16.6 + - - -
464B SER* 2.4 33.7 + - - +
465B SER 4.4 0.3 + - - -
466B LYS* 3.7 30.0 + - + +
467B VAL* 4.9 0.4 - - - -
523B LEU* 3.7 26.0 - - + +
545B GLY 3.5 4.0 + - - +
546B PHE 3.3 8.2 + - - +
548B GLN* 1.3 78.7 - - - +
550B ARG* 1.3 56.6 + - - +
552B TRP* 3.8 10.8 - - + +
553B LEU* 3.0 39.5 + - + +
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Residues in contact with ARG 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LEU* 4.2 17.4 - - + +
524B PRO* 4.4 9.3 + - - +
527B ALA* 3.3 22.2 + - - +
529B THR 3.1 24.5 + - - -
531B VAL* 3.9 18.9 - - + +
546B PHE 3.1 19.8 + - - +
547B ILE* 3.6 9.0 - - - +
548B GLN 2.9 0.8 + - - -
549B GLU* 1.3 73.0 - - - +
551B ALA* 1.3 67.4 + - - +
552B TRP 3.1 1.6 - - - -
553B LEU* 3.0 24.9 + - - +
554B ARG* 3.2 20.0 + - - +
560B VAL* 3.2 18.5 - - + +
561B GLY 3.4 9.7 + - - -
562B GLU 3.2 12.5 + - - -
563B THR* 2.7 32.5 + - + +
590B ALA 4.3 13.5 - - - +
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Residues in contact with ALA 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547B ILE 3.1 8.4 + - - +
548B GLN 2.9 9.7 + - - +
550B ARG* 1.3 75.2 - - - +
552B TRP* 1.3 57.8 + - - +
554B ARG* 3.3 9.6 + - - +
555B GLN* 3.1 36.9 + - - +
585B PHE* 4.3 12.8 - - + -
588B ASP* 6.0 1.8 - - + +
590B ALA* 3.3 31.5 - - + +
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Residues in contact with TRP 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B LYS* 3.2 60.0 + - + -
467B VAL* 3.7 21.3 - - + -
548B GLN 3.0 13.4 + - - +
549B GLU* 3.8 7.6 - - - +
551B ALA* 1.3 75.9 - - - +
553B LEU* 1.3 88.0 + - + +
554B ARG 3.3 0.2 - - - -
555B GLN* 3.3 25.7 - - - +
556B GLN* 3.2 54.9 + - + +
558B LYS* 5.8 3.4 - - - -
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Residues in contact with LEU 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B LEU* 5.9 3.4 - - + -
524B PRO 6.1 0.4 - - - +
527B ALA* 3.4 30.1 - - + -
549B GLU* 3.0 29.4 + - + +
550B ARG* 3.0 27.7 + - - +
552B TRP* 1.3 98.2 - - + +
554B ARG* 1.3 61.7 + - - +
556B GLN* 3.5 8.2 + - - +
558B LYS* 3.2 45.5 + - + +
560B VAL* 3.6 12.8 - - + -
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Residues in contact with ARG 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B ARG* 3.2 17.0 + - - +
551B ALA* 3.6 13.5 + - - +
553B LEU* 1.3 75.2 - - - +
555B GLN* 1.3 57.8 + - + +
557B GLY* 2.5 30.5 + - - -
558B LYS 3.6 10.7 - - - +
560B VAL* 3.5 28.5 + - + +
588B ASP 2.9 24.4 + - - -
589B GLY* 3.7 19.1 + - - -
590B ALA* 3.8 17.3 - - - +
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Residues in contact with GLN 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B VAL* 5.8 0.2 - - - +
551B ALA* 3.1 19.3 + - - +
552B TRP* 3.3 35.5 - - - +
554B ARG* 1.3 78.3 - - + +
556B GLN* 1.3 60.4 + - - +
557B GLY* 2.8 11.4 + - - -
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Residues in contact with GLN 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B TRP* 3.2 55.8 + - + +
553B LEU* 3.5 13.5 - - - +
554B ARG 3.1 0.6 - - - -
555B GLN* 1.3 81.5 + - - +
557B GLY* 1.3 58.3 + - - +
558B LYS* 3.4 16.6 + - + +
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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
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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) + - + + + + + -
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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