Contacts of the helix formed by residues 533 - 547 (chain B) in PDB entry 4WQN
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 PRO 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515B LEU* 4.2 8.7 - - + -
516B GLU* 3.4 35.9 - - - +
517B ASN* 3.0 36.8 - - + +
531B GLU 3.8 0.4 - - - +
532B VAL* 1.4 86.7 - - + +
534B LEU* 1.3 61.8 + - - +
535B GLU* 3.3 12.6 - - - +
536B LYS* 3.0 9.7 + - + +
537B ALA 2.8 24.1 + - - -
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Residues in contact with LEU 534 (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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407B LEU* 4.0 47.8 - - + +
408B LYS 4.3 18.4 - - - +
409B HIS* 4.3 10.3 - - - +
410B GLY 4.1 18.4 - - - +
411B ARG* 5.2 0.4 - - - -
412B VAL* 4.2 13.9 - - + +
532B VAL 3.4 3.1 + - - +
533B PRO* 1.3 71.6 - - - +
535B GLU* 1.3 60.4 + - - +
537B ALA* 3.3 4.0 + - + +
538B LYS* 3.0 35.6 + - + +
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Residues in contact with GLU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B GLU* 2.6 33.7 - - - +
533B PRO* 3.5 13.2 - - - +
534B LEU* 1.3 78.5 + - - +
536B LYS* 1.3 78.8 + - + +
538B LYS* 3.7 19.1 + - + +
539B GLN* 3.4 27.7 + - - +
602B EDO 5.5 0.5 - - - -
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Residues in contact with LYS 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B ILE* 4.1 14.6 - - + +
514B ARG* 2.8 27.6 + - - +
515B LEU* 4.1 4.9 - - + -
516B GLU* 2.6 31.1 + - - +
532B VAL* 4.0 12.3 - - + -
533B PRO* 3.0 11.3 + - + +
535B GLU* 1.3 97.5 - - - +
537B ALA* 1.3 65.3 + - - +
538B LYS 3.2 0.2 - - - -
539B GLN* 3.1 36.2 + - - +
540B VAL* 3.1 16.7 + - - +
602B EDO 3.2 35.6 - - - -
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Residues in contact with ALA 537 (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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407B LEU* 5.2 0.7 - - + -
412B VAL* 3.7 40.2 - - + -
458B LEU* 5.5 0.7 - - - -
532B VAL* 3.5 12.2 - - + +
533B PRO 2.8 13.2 + - - +
534B LEU* 3.5 14.6 - - + +
536B LYS* 1.3 78.2 - - - +
538B LYS* 1.3 61.7 + - - +
540B VAL* 3.3 6.6 + - - +
541B LEU* 3.0 32.0 + - + +
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Residues in contact with LYS 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TRP* 3.1 39.4 - - + +
406B ASN* 4.2 18.4 + - - +
407B LEU* 3.7 34.6 + - + +
408B LYS* 5.2 9.6 - - - +
534B LEU* 3.0 29.9 + - + +
535B GLU* 3.9 15.9 - - - +
536B LYS 3.2 0.2 - - - -
537B ALA* 1.3 75.1 - - - +
539B GLN* 1.3 58.8 + - + +
541B LEU* 3.6 2.4 + - - +
542B LYS* 3.1 29.1 + - - +
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Residues in contact with GLN 539 (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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405B TRP* 6.1 0.2 - - - -
513B ILE* 3.8 25.6 - - + +
535B GLU* 3.4 21.2 + - - +
536B LYS* 3.1 30.6 + - - +
538B LYS* 1.3 76.7 - - + +
540B VAL* 1.3 65.5 + - - +
542B LYS* 3.5 6.2 + - - +
543B ILE* 3.2 29.2 + - + +
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Residues in contact with VAL 540 (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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458B LEU* 3.8 27.1 - - + -
467B PHE* 5.5 2.9 - - + -
510B LEU* 3.8 26.6 - - + +
513B ILE* 3.9 20.6 - - + +
523B VAL* 4.3 20.4 - - + -
532B VAL* 5.0 1.8 - - + -
536B LYS 3.1 18.0 + - - +
537B ALA* 3.3 7.8 + - - +
539B GLN* 1.3 74.6 - - - +
541B LEU* 1.3 58.9 + - - +
543B ILE* 3.2 5.2 + - - +
544B ILE* 2.9 40.6 + - + +
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Residues in contact with LEU 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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403B PHE* 4.2 19.9 - - + -
405B TRP* 3.9 16.4 - - + -
407B LEU* 3.8 30.3 - - + -
412B VAL* 4.9 4.3 - - + -
456B TYR* 4.4 12.8 - - + -
458B LEU* 4.0 26.2 - - + -
470B VAL* 4.0 26.9 - - + -
501B PHE* 5.6 2.1 - - + -
537B ALA* 3.0 25.1 + - + +
538B LYS* 4.1 1.3 - - - +
540B VAL* 1.3 74.3 - - + +
542B LYS* 1.3 61.5 + - - +
544B ILE* 3.9 5.0 - - + +
545B ALA* 2.9 34.0 + - - +
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Residues in contact with LYS 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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405B TRP* 3.4 59.7 - - + +
538B LYS 3.1 19.3 + - - +
539B GLN* 3.8 7.0 - - - +
541B LEU* 1.3 75.0 - - - +
543B ILE* 1.3 59.7 + - + +
545B ALA* 3.9 1.4 - - - +
546B SER* 2.8 42.1 + - - +
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Residues in contact with ILE 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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505B VAL* 4.7 4.3 - - + -
509B GLN* 3.3 49.6 - - + +
510B LEU* 3.8 18.6 - - + -
513B ILE* 3.9 14.4 - - + -
539B GLN* 3.2 16.4 + - + +
540B VAL 3.2 7.6 + - - +
542B LYS* 1.3 79.5 - - + +
544B ILE* 1.3 57.8 + - - +
546B SER* 3.9 4.2 + - - -
547B TYR* 2.9 34.6 + - + +
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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
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458B LEU* 4.9 6.3 - - + -
467B PHE* 4.8 19.7 - - + -
469B GLY* 5.1 5.8 - - - +
470B VAL* 3.9 33.2 - - + -
501B PHE* 4.5 14.4 - - + -
503B LYS* 3.0 31.4 + - + +
505B VAL* 4.1 31.4 - - + +
510B LEU* 4.6 4.5 - - + -
540B VAL* 2.9 39.3 + - + +
541B LEU* 3.9 6.3 - - + +
543B ILE* 1.3 76.3 - - - +
545B ALA* 1.3 62.4 + - - +
546B SER 3.4 0.2 + - - -
547B TYR* 3.5 2.6 + - - +
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Residues in contact with ALA 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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400B PRO 5.2 2.4 - - - +
403B PHE* 4.5 12.1 - - + +
405B TRP* 5.1 6.1 - - + -
501B PHE* 3.5 37.9 - - + -
503B LYS* 3.4 12.6 + - - -
541B LEU 2.9 20.3 + - - +
542B LYS* 3.9 4.5 - - - +
544B ILE* 1.3 77.5 - - - +
546B SER* 1.3 59.1 + - - +
548B LYS* 5.6 1.7 + - - -
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Residues in contact with SER 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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542B LYS* 2.8 30.2 + - - +
543B ILE* 3.9 4.0 + - - -
545B ALA* 1.3 75.5 - - - +
547B TYR* 1.3 69.5 + - - +
548B LYS* 3.4 10.4 + - - +
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Residues in contact with TYR 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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503B LYS* 3.0 25.2 + - - -
504B ASP 3.5 26.5 - - - -
505B VAL* 4.0 13.7 - - + -
506B PRO* 3.4 24.8 - - + +
509B GLN* 3.6 42.8 - - + -
543B ILE 2.9 20.2 + - - +
544B ILE 3.9 7.6 - - - +
545B ALA 3.5 1.8 - - - -
546B SER* 1.3 78.7 + - - +
548B LYS* 1.3 86.5 + - - +
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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
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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