Contacts of the helix formed by residues 518 - 534 (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 ASN 518 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517B ILE* 1.3 83.5 + - + +
519B GLU* 1.3 86.3 + - - +
520B SER* 4.2 6.6 + - - -
521B ALA* 3.6 23.5 - - + +
522B ASP* 2.7 25.5 + - - +
559B TYR* 2.9 13.8 + - - -
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Residues in contact with GLU 519 (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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518B ASN* 1.3 87.7 + - - +
520B SER* 1.3 61.9 + - - +
523B MET* 3.7 2.6 + - - +
555B TYR* 2.4 39.9 + - - +
559B TYR* 3.3 32.9 - - + +
561B CYS* 4.5 5.9 - - - -
572B ARG* 3.5 32.4 + - - -
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Residues in contact with SER 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ASN* 4.2 5.3 + - - -
519B GLU* 1.3 78.5 - - - +
521B ALA* 1.3 68.0 + - - +
523B MET* 3.4 5.9 + - - +
524B SER* 3.0 25.6 + - - -
555B TYR* 4.5 1.6 - - - -
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Residues in contact with ALA 521 (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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517B ILE* 5.0 8.1 - - + -
518B ASN* 3.6 25.6 - - + +
519B GLU 3.5 0.4 - - - -
520B SER* 1.3 82.6 + - - +
522B ASP* 1.3 57.1 + - - +
524B SER* 3.8 4.9 - - - -
525B ILE* 2.9 45.6 + - + +
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Residues in contact with ASP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 3.3 16.4 - - + +
515B SER* 3.2 13.7 + - - +
516B GLY* 2.7 26.8 + - - -
517B ILE* 2.9 19.3 + - - +
518B ASN 2.7 14.5 + - - +
520B SER 3.3 0.6 - - - -
521B ALA* 1.3 78.0 - - - +
523B MET* 1.3 58.1 + - - +
525B ILE* 3.3 4.3 + - - +
526B GLY 2.9 25.1 + - - -
551B PHE* 3.2 9.6 - - - -
555B TYR* 4.1 7.4 - - + -
559B TYR* 2.2 33.8 + - - -
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Residues in contact with MET 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLU 3.7 3.5 + - - +
520B SER* 3.4 9.2 + - - +
522B ASP* 1.3 79.4 - - - +
524B SER* 1.3 64.7 + - - +
526B GLY* 3.3 0.9 + - - -
527B VAL* 3.0 42.3 + - + +
548B LEU* 6.3 0.7 - - + -
551B PHE* 3.6 26.0 - - - -
552B ILE* 4.7 20.6 - - + -
555B TYR* 4.1 30.9 - - + +
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Residues in contact with SER 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B SER 3.0 18.1 + - - -
521B ALA* 3.8 6.3 - - - -
523B MET* 1.3 77.0 - - - +
525B ILE* 1.3 56.6 + - - +
527B VAL* 3.2 9.5 - - - +
528B THR* 2.7 42.2 + - - -
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Residues in contact with ILE 525 (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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515B SER* 3.2 26.0 - - - +
517B ILE* 4.0 26.9 - - + -
521B ALA* 2.9 30.7 + - + +
522B ASP 3.8 3.1 - - - +
524B SER* 1.3 76.9 - - - +
526B GLY* 1.3 56.2 + - - +
528B THR* 3.3 5.6 + - - -
529B VAL* 2.9 46.9 + - + +
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Residues in contact with GLY 526 (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 5.9 2.2 - - - -
515B SER* 5.2 1.8 - - - -
522B ASP 2.9 16.0 + - - -
525B ILE* 1.3 79.7 - - - +
527B VAL* 1.3 58.4 + - - +
529B VAL* 3.3 6.3 + - - +
530B ILE* 3.0 36.4 + - - +
551B PHE* 3.8 22.7 - - - -
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Residues in contact with VAL 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B MET* 3.0 34.1 + - + +
524B SER* 3.2 17.3 - - - +
526B GLY* 1.3 76.3 - - - +
528B THR* 1.3 64.6 + - - +
530B ILE* 3.4 9.2 + - + +
531B LYS* 2.9 27.6 + - - +
548B LEU* 4.6 20.6 - - + -
551B PHE* 4.3 13.0 - - + -
552B ILE* 6.0 0.4 - - + -
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Residues in contact with THR 528 (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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524B SER* 2.7 30.4 + - - -
525B ILE* 3.8 4.7 - - - -
526B GLY 3.3 0.2 - - - -
527B VAL* 1.3 78.2 - - - +
529B VAL* 1.3 60.3 + - + +
531B LYS* 3.3 23.9 + - - +
532B ASN* 2.9 49.7 + - - +
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Residues in contact with VAL 529 (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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510B PRO* 3.6 29.4 - - + -
511B SER 5.2 3.8 - - - +
525B ILE* 2.9 34.0 + - + +
526B GLY* 3.6 7.0 - - - +
528B THR* 1.3 76.1 - - + +
530B ILE* 1.3 60.4 + - + +
532B ASN* 3.3 9.2 + - - +
533B ASN* 2.9 34.8 + - - +
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Residues in contact with ILE 530 (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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510B PRO* 5.1 10.5 - - + -
512B PHE* 6.5 0.4 - - - -
526B GLY 3.0 21.5 + - - +
527B VAL* 3.7 8.7 - - - +
529B VAL* 1.3 78.6 - - + +
531B LYS* 1.3 62.3 + - - +
533B ASN* 3.4 5.7 + - - +
534B MET* 3.2 25.7 + - + +
539B LEU* 5.0 3.5 - - + +
544B ALA* 4.0 32.1 - - + +
547B ALA* 3.9 13.5 - - + +
548B LEU* 3.5 41.5 - - + +
551B PHE* 4.5 10.5 - - + -
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Residues in contact with LYS 531 (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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527B VAL 2.9 17.6 + - - +
528B THR* 3.7 22.5 + - - +
529B VAL 3.3 0.2 - - - -
530B ILE* 1.3 78.3 - - - +
532B ASN* 1.3 75.4 + - - +
534B MET* 3.3 24.8 + - + +
535B ILE* 3.6 17.2 - - + +
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Residues in contact with ASN 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B THR* 2.9 38.6 + - - +
529B VAL* 3.3 10.5 + - - +
531B LYS* 1.3 89.1 - - - +
533B ASN* 1.3 59.0 + - - +
534B MET 3.1 0.7 + - - -
535B ILE* 3.1 14.1 + - - +
536B ASN* 2.9 46.1 + - - +
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Residues in contact with ASN 533 (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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506B SER 5.3 0.9 - - - +
508B GLU 5.6 1.7 + - - +
510B PRO* 3.3 40.1 - - + +
529B VAL* 2.9 23.2 + - - +
530B ILE* 3.4 4.7 + - - +
531B LYS 3.4 0.2 - - - -
532B ASN* 1.3 76.0 - - - +
534B MET* 1.3 56.3 + - - +
535B ILE 3.3 0.7 - - - -
536B ASN* 5.1 0.6 - - - +
537B ASN* 2.6 60.6 + - - +
539B LEU* 3.2 24.6 + - + +
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Residues in contact with MET 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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530B ILE* 3.2 20.3 + - + +
531B LYS* 3.6 16.6 - - + +
532B ASN 3.1 1.4 - - - -
533B ASN* 1.3 78.0 - - - +
535B ILE* 1.3 64.5 + - + +
538B ASP* 4.4 9.2 - - - +
539B LEU* 3.9 28.9 - - + +
540B GLY 4.9 1.6 - - - +
541B PRO* 4.9 11.4 - - + -
544B ALA* 3.5 26.2 - - + -
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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