Contacts of the helix formed by residues 540 - 559 (chain B) in PDB entry 6QNW
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 540 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A GLN* 6.0 1.6 - - - +
593A GLU* 3.2 25.8 + - - +
597A GLU* 4.2 10.5 + - - -
539B LEU* 1.3 83.6 - - - +
541B PRO* 1.3 76.3 - - - +
542B ALA 3.4 0.2 - - - -
543B THR* 3.4 3.3 + - - -
544B ALA 3.1 17.2 + - - -
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Residues in contact with PRO 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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435A ILE* 4.0 28.0 - - + +
438A ILE* 5.8 2.2 - - + -
439A ALA* 3.6 20.4 - - + +
442A ARG* 4.5 5.8 - - - +
593A GLU* 3.2 8.3 - - - +
597A GLU* 3.6 15.0 - - - +
534B MET* 4.9 11.4 - - + -
539B LEU 4.5 1.1 - - - +
540B GLY* 1.3 85.1 - - - +
542B ALA* 1.3 57.3 + - - +
544B ALA* 3.2 8.3 + - + +
545B GLN* 2.9 31.0 + - - +
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Residues in contact with ALA 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ALA* 3.5 30.0 - - - +
442A ARG* 3.6 21.3 - - + -
443A ARG* 4.1 6.5 - - + +
589A LEU* 3.4 17.7 - - + +
593A GLU* 2.7 23.4 + - - +
541B PRO* 1.3 71.6 - - - +
543B THR* 1.3 64.0 + - - +
545B GLN* 3.2 4.4 + - - +
546B MET* 2.9 19.6 + - - +
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Residues in contact with THR 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU* 3.5 24.1 - - + +
589A LEU* 3.7 10.6 - - - +
590A GLN* 3.5 35.3 + - + +
593A GLU* 2.4 26.6 + - - -
509B LEU* 4.8 11.7 - - + -
539B LEU* 4.7 13.9 - - + -
540B GLY 3.6 10.5 + - - -
541B PRO 3.3 0.2 - - - -
542B ALA* 1.3 77.2 - - - +
544B ALA* 1.3 56.4 + - - +
546B MET 3.4 0.7 + - - -
547B ALA* 2.9 29.2 + - + +
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Residues in contact with ALA 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ILE* 4.0 11.3 - - + +
534B MET* 3.5 32.5 - - + -
539B LEU* 3.7 19.2 - - + +
540B GLY 3.1 8.2 + - - +
541B PRO 3.5 8.5 - - - +
542B ALA 3.2 0.2 - - - -
543B THR* 1.3 73.9 - - - +
545B GLN* 1.3 59.7 + - + +
547B ALA* 3.3 7.0 + - - +
548B LEU* 2.9 31.0 + - - +
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Residues in contact with GLN 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 3.4 27.1 - - + +
431A ASP* 4.5 7.9 + - - -
436A GLU* 3.5 24.7 + - - +
439A ALA* 3.4 23.9 - - + +
440A SER* 3.3 15.4 + - - +
443A ARG* 2.6 41.9 + - - +
541B PRO 2.9 16.2 + - - +
542B ALA 3.2 8.9 + - - +
544B ALA* 1.3 77.5 - - - +
546B MET* 1.3 57.6 + - - +
548B LEU* 3.3 3.7 + - - +
549B GLN* 2.9 23.4 + - - +
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Residues in contact with MET 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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425A LEU* 4.6 12.3 - - + -
443A ARG* 4.4 10.2 - - + +
446A PHE* 3.6 28.0 - - + -
447A THR* 3.8 18.8 - - - +
585A LEU* 4.1 28.7 - - + -
586A LEU* 3.6 23.1 - - + -
589A LEU* 3.7 19.1 - - + -
542B ALA 2.9 15.6 + - - +
545B GLN* 1.3 76.1 - - - +
547B ALA* 1.3 57.8 + - - +
549B GLN* 3.2 13.7 + - - +
550B LEU* 2.9 36.2 + - + +
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Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU* 3.5 23.5 - - + +
510B PRO* 5.4 11.0 - - + -
512B PHE* 4.6 7.3 - - + +
530B ILE* 3.9 16.3 - - + +
539B LEU* 6.3 2.5 - - + -
543B THR* 2.9 19.4 + - + +
544B ALA* 3.6 8.7 - - - +
546B MET* 1.3 73.8 - - - +
548B LEU* 1.3 59.8 + - - +
550B LEU* 3.3 3.5 + - - +
551B PHE* 2.9 29.6 + - - +
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Residues in contact with LEU 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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427A GLU 4.7 0.2 - - - +
428A ILE* 3.6 39.9 - - + -
523B MET* 6.3 0.4 - - + -
527B VAL* 4.6 21.5 - - + -
530B ILE* 3.5 20.5 - - + +
544B ALA 2.9 16.5 + - - +
545B GLN* 3.7 3.1 - - - +
547B ALA* 1.3 76.1 - - - +
549B GLN* 1.3 57.0 + - - +
551B PHE* 3.7 2.3 - - + +
552B ILE* 2.9 55.2 + - + +
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Residues in contact with GLN 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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425A LEU* 3.3 41.1 + - + +
426A ASP* 2.4 45.1 + - - +
427A GLU* 4.7 1.1 - - - +
428A ILE* 4.1 16.2 - - + +
443A ARG* 3.7 32.3 - - - +
545B GLN 2.9 9.9 + - - +
546B MET* 3.4 14.4 - - - +
547B ALA 3.2 0.2 - - - -
548B LEU* 1.3 80.7 - - - +
550B LEU* 1.3 63.1 + - - +
552B ILE* 3.3 5.6 + - - +
553B LYS* 3.0 23.8 + - - +
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Residues in contact with LEU 550 (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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425A LEU* 4.1 22.2 - - + -
582A ARG* 4.0 44.0 + - + +
585A LEU* 4.8 8.5 - - + -
586A LEU* 3.7 36.1 - - + -
512B PHE* 3.7 24.9 - - + -
546B MET* 2.9 21.6 + - + +
547B ALA 3.8 3.8 - - - +
549B GLN* 1.3 76.3 - - - +
551B PHE* 1.3 58.7 + - - +
553B LYS* 3.3 10.5 + - + +
554B ASP* 2.9 28.9 + - - +
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Residues in contact with PHE 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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511B SER 5.1 1.8 - - - -
512B PHE* 3.1 28.2 + - - +
513B GLY 3.9 9.0 - - - -
514B VAL* 4.1 19.5 - - + -
515B SER* 4.9 1.8 - - - -
522B ASP 3.2 28.7 - - - -
523B MET* 3.6 35.9 - - - -
526B GLY* 3.8 19.5 - - - -
527B VAL* 4.3 8.5 - - + -
530B ILE* 4.5 8.1 - - + -
547B ALA 2.9 17.8 + - - +
548B LEU* 3.7 5.8 - - + +
549B GLN 3.2 0.2 - - - -
550B LEU* 1.3 77.5 - - - +
552B ILE* 1.3 67.2 + - + +
554B ASP* 3.3 1.8 + - - +
555B TYR* 2.8 39.5 + + + +
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Residues in contact with ILE 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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426A ASP* 3.8 18.6 - - + +
427A GLU* 4.5 11.2 - - - +
523B MET* 4.7 22.7 - - + -
548B LEU* 2.9 47.5 + - + +
549B GLN* 3.8 3.8 - - - +
551B PHE* 1.3 83.5 - - + +
553B LYS* 1.3 60.3 + - - +
555B TYR* 3.7 8.0 - - + +
556B ARG* 2.9 48.7 + - + +
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Residues in contact with LYS 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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423A ILE* 5.7 0.6 - - - +
424A GLU* 3.4 58.5 + - + +
425A LEU* 5.5 2.5 - - + -
426A ASP* 3.1 22.7 + - + +
460A MET* 4.2 11.1 - - - +
582A ARG* 3.1 35.8 - - - +
549B GLN 3.0 14.0 + - - +
550B LEU* 3.6 16.6 - - + +
552B ILE* 1.3 78.1 - - - +
554B ASP* 1.3 57.1 + - - +
556B ARG* 3.3 2.3 + - - +
557B TYR* 2.9 32.2 + - + +
562B HIS* 5.5 0.5 - - - -
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Residues in contact with ASP 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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582A ARG* 6.0 4.2 - - - +
512B PHE* 4.1 15.0 - - + -
513B GLY* 3.2 32.0 - - - -
514B VAL* 3.8 8.2 + - - +
550B LEU 2.9 16.5 + - - +
551B PHE 3.3 3.6 + - - +
553B LYS* 1.3 76.3 - - - +
555B TYR* 1.3 53.1 + - - +
557B TYR* 3.8 16.8 - - - -
558B THR* 2.2 48.1 + - - -
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Residues in contact with TYR 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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514B VAL* 4.3 19.9 - - + +
519B GLU* 2.4 44.9 + - - +
520B SER* 4.5 0.9 - - - -
522B ASP* 4.1 4.3 - - + -
523B MET* 4.1 35.0 - - + +
551B PHE* 2.8 30.5 + + + +
552B ILE* 3.7 10.3 - - + +
554B ASP* 1.3 75.7 - - - +
556B ARG* 1.3 69.9 + - + +
558B THR* 4.0 3.9 - - - -
559B TYR* 3.4 44.1 + + - +
561B CYS* 4.1 11.2 - - - -
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Residues in contact with ARG 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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426A ASP* 3.3 26.7 + - - +
427A GLU* 2.3 47.6 + - - -
552B ILE* 2.9 28.9 + - + +
553B LYS 3.9 2.9 - - - +
555B TYR* 1.3 81.4 - - + +
557B TYR* 1.3 61.2 + - - +
560B ARG* 3.4 2.9 + - - -
561B CYS* 3.1 45.8 + - - +
562B HIS* 3.0 46.9 + - - +
563B ARG* 4.1 20.1 - - - +
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Residues in contact with TYR 557 (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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298A GLU* 6.2 0.4 - - - -
299A GLY* 5.8 9.0 - - - -
467A THR* 4.7 15.1 - - - +
553B LYS* 2.9 20.8 + - + +
554B ASP* 3.8 18.8 - - - +
556B ARG* 1.3 77.1 - - - +
558B THR* 1.3 66.9 + - + +
559B TYR 3.5 0.2 + - - -
560B ARG* 2.9 50.4 + - - -
562B HIS* 4.0 16.4 + + + -
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Residues in contact with THR 558 (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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514B VAL* 3.4 25.5 - - + +
516B GLY* 6.0 0.9 - - - -
554B ASP* 2.2 38.6 + - - -
555B TYR* 3.5 5.1 + - - -
556B ARG 3.4 0.2 - - - -
557B TYR* 1.3 85.0 - - - +
559B TYR* 1.3 84.2 + - + +
560B ARG* 3.7 14.4 + - - +
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Residues in contact with TYR 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 4.5 2.9 - - + -
516B GLY* 3.9 5.3 - - - -
517B ILE 3.8 3.3 + - - -
518B ASN* 2.9 29.8 + - - -
519B GLU* 3.3 39.5 - - + +
522B ASP* 2.2 28.2 + - - -
555B TYR* 3.4 28.2 + + - +
558B THR* 1.3 101.7 - - + +
560B ARG* 1.3 72.5 + - - +
561B CYS* 3.1 18.5 + - - -
572B ARG* 3.2 19.3 + - - +
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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
------------------------------------------------------------
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