Contacts of the strand formed by residues 541 - 548 (chain B) in PDB entry 3QNF
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 541 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B THR 3.7 1.7 - - - +
537B VAL* 3.6 2.8 - - - +
538B ARG* 3.0 51.9 + - + +
539B GLY* 4.9 0.6 - - - -
540B ARG* 1.3 82.0 - - - +
542B VAL* 1.3 60.5 + - - +
543B HIS* 3.8 1.1 + - - +
588B VAL* 4.6 13.6 - - + +
589B LEU 3.8 4.3 - - - -
590B ILE* 3.6 22.3 - - - +
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Residues in contact with VAL 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ILE* 4.1 15.9 - - + -
536B THR 3.9 1.8 - - - -
537B VAL* 4.0 13.2 - - + -
540B ARG 3.9 1.3 - - - +
541B ASN* 1.3 73.0 - - - +
543B HIS* 1.3 63.3 + - - +
544B MET* 3.7 3.8 - - + +
588B VAL* 3.4 4.0 - - - +
589B LEU* 2.8 48.0 + - + +
591B LEU* 3.5 39.5 - - + -
598B ILE* 3.7 9.4 - - + -
600B PHE* 3.8 34.1 - - + -
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Residues in contact with HIS 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B THR 3.5 1.1 - - - +
535B ILE* 3.4 8.7 - - - +
536B THR* 2.7 56.7 + - + +
538B ARG* 6.0 2.9 - - - -
541B ASN 3.8 1.5 + - - +
542B VAL* 1.3 73.1 - - - +
544B MET* 1.3 68.0 + - - +
545B LYS* 4.6 5.6 - - + +
586B THR* 4.0 26.8 - - - +
587B ASP* 3.8 11.4 + - - -
588B VAL* 3.8 18.7 - - + +
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Residues in contact with MET 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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533B ILE* 5.0 1.8 - - + -
534B THR 3.6 3.6 - - - -
535B ILE* 3.7 20.0 - - + -
542B VAL* 3.7 4.7 - - + +
543B HIS* 1.3 78.9 - - - +
545B LYS* 1.3 59.3 + - - +
567B LEU* 3.7 17.9 - - + -
580B PHE* 3.5 34.1 - - + -
582B LEU* 4.3 18.4 - - + +
586B THR* 3.1 7.3 - - - -
587B ASP 2.9 33.8 + - - +
588B VAL* 3.5 10.5 - - - -
589B LEU* 3.4 54.3 - - + +
600B PHE* 4.3 6.1 - - + -
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Residues in contact with LYS 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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533B ILE* 3.4 7.4 - - - +
534B THR* 2.9 47.2 + - + +
543B HIS* 5.0 6.7 - - + -
544B MET* 1.3 75.8 - - - +
546B GLN* 1.3 69.8 + - - +
547B GLU* 4.2 20.6 - - - +
582B LEU* 4.5 2.0 - - - -
585B LYS* 3.4 12.1 - - + +
586B THR* 3.8 19.7 - - + -
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Residues in contact with GLN 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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531B PRO* 4.5 3.1 - - + -
532B LEU 3.4 4.3 - - - +
533B ILE* 3.8 11.9 - - + -
545B LYS* 1.3 79.1 - - - +
547B GLU* 1.3 54.6 + - - +
561B TYR 4.4 2.1 - - - +
562B LEU* 3.6 13.2 - - + +
563B TRP* 2.7 60.7 + - - +
565B VAL* 3.9 8.5 - - - +
582B LEU* 3.5 21.3 + - + +
584B THR 3.2 28.2 + - - +
585B LYS* 2.7 46.1 + - - +
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Residues in contact with GLU 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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531B PRO* 3.3 4.7 - - - +
532B LEU* 2.6 56.9 + - + +
534B THR* 3.4 21.8 + - - -
545B LYS* 4.2 14.2 - - + +
546B GLN* 1.3 80.0 + - - +
548B HIS* 1.3 65.2 + - - +
549B TYR* 5.7 0.2 - - - -
561B TYR 5.2 2.9 - - - -
563B TRP* 4.5 1.3 - - - -
585B LYS* 3.5 15.0 - - - +
651B LYS* 5.0 7.4 - - - +
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Residues in contact with HIS 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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411B ASP 5.1 2.9 - - - -
412B ALA 5.6 1.1 - - - -
528B LYS* 4.0 18.1 - - + +
529B GLY* 3.9 25.1 - - - -
530B PHE 3.6 2.5 + - - -
547B GLU* 1.3 79.7 - - - +
549B TYR* 1.3 80.8 + - - +
550B MET* 3.8 29.5 + - + +
559B THR* 3.6 28.3 - - - -
561B TYR* 3.9 30.6 + + + +
563B TRP* 3.6 24.0 - + + -
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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