Contacts of the strand formed by residues 519 - 523 (chain D) in PDB entry 2QLF
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 PHE 519 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463C THR* 3.7 22.9 - - - -
466C PHE* 3.2 29.6 - - + -
467C ARG* 3.8 15.3 - - + -
479C LYS* 3.2 27.6 - - + -
481C PHE* 3.7 24.9 - + - -
515D VAL 4.1 3.8 - - - -
516D GLU* 3.3 26.0 - - - +
517D ALA 3.4 6.7 - - - -
518D ASP* 1.3 78.8 - - - +
520D LEU* 1.3 56.5 + - - +
521D PHE* 3.7 31.2 - + + -
594D MET* 2.8 41.6 + - + +
595D LEU* 3.3 4.8 - - - +
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Residues in contact with LEU 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479C LYS 3.1 6.9 + - - +
480C LEU* 3.7 19.5 - - + -
481C PHE* 2.9 28.2 + - - +
482C PHE* 5.3 2.9 - - + -
519D PHE* 1.3 77.3 - - - +
521D PHE* 1.3 66.4 + - - +
522D ALA* 4.0 12.6 - - + +
558D ILE* 4.0 22.7 - - + -
559D MET* 4.1 17.7 - - - -
562D LEU* 3.8 22.2 - - + -
591D VAL* 4.6 3.1 - - + -
592D VAL 3.2 10.8 - - - +
593D SER* 4.4 2.7 - - - +
595D LEU* 3.4 35.9 - - + -
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Residues in contact with PHE 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ILE* 4.6 6.5 - - + -
463C THR* 3.3 37.0 - - + -
481C PHE* 3.5 19.3 - + + +
483C ILE* 4.3 8.1 - - + -
519D PHE* 3.7 38.6 - + + -
520D LEU* 1.3 77.7 - - - +
522D ALA* 1.3 60.0 + - - +
523D TYR* 3.4 35.2 + + + -
590D CYS 3.5 0.9 - - - +
591D VAL* 3.5 2.4 - - - +
592D VAL* 2.7 45.2 + - + +
594D MET* 3.7 20.2 - - + -
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Residues in contact with ALA 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C PHE 2.9 9.0 + - - +
482C PHE* 3.5 30.6 - - + -
483C ILE* 2.9 24.9 + - - -
520D LEU* 4.0 4.8 - - + +
521D PHE* 1.3 70.3 - - - +
523D TYR* 1.3 62.4 + - - +
541D PHE* 3.6 10.2 - - + -
562D LEU* 4.0 28.5 - - + -
590D CYS 4.0 2.7 - - - -
591D VAL* 4.6 6.3 - - + +
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Residues in contact with TYR 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C ASN* 5.9 2.3 + - - -
459C ILE* 3.8 38.8 - - + +
483C ILE* 3.8 27.6 - - + -
485C ALA 6.0 0.2 - - - -
487C ARG* 3.2 58.2 + - + +
521D PHE* 3.4 34.8 - + + -
522D ALA* 1.3 75.1 - - - +
524D SER* 1.3 60.1 + - - +
525D THR 3.1 6.3 - - - +
541D PHE* 4.0 3.4 - - - -
589D PRO* 3.3 6.6 - - - +
590D CYS 2.8 43.1 + - - +
592D VAL* 4.0 13.9 - - + -
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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