Contacts of the strand formed by residues 479 - 484 (chain C) 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 LYS 479 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437C PHE* 3.5 8.5 - - + -
466C PHE* 2.9 42.6 - - + +
467C ARG* 5.0 2.2 - - - +
468C GLY* 5.0 3.1 - - - +
474C LEU* 3.0 39.3 + - + -
475C LEU* 4.7 3.2 - - - +
477C LYS 2.8 27.1 + - - +
478C PRO* 1.3 74.5 - - - +
480C LEU* 1.3 64.9 + - - +
481C PHE* 3.7 19.5 - - + -
517D ALA 3.9 5.9 + - - -
518D ASP* 2.8 20.0 + - - +
519D PHE* 3.2 30.2 - - + -
520D LEU 3.1 20.8 + - - -
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Residues in contact with LEU 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C PHE* 4.7 2.9 - - + -
436C CYS* 5.1 3.1 - - + -
437C PHE* 2.8 16.7 + - - +
438C ALA* 3.3 9.8 - - + -
439C CYS 2.9 25.4 + - - -
478C PRO* 3.9 14.8 - - + +
479C LYS* 1.3 74.7 - - - +
481C PHE* 1.3 70.4 + - - +
482C PHE* 3.8 28.7 - - + -
520D LEU* 3.5 26.2 - - + +
558D ILE* 5.0 2.9 - - + -
595D LEU* 4.7 3.4 - - + -
599D LEU* 3.7 24.2 - - + -
601D PHE* 3.8 31.9 - - + -
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Residues in contact with PHE 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C LEU* 5.1 4.7 - - + -
437C PHE* 4.0 9.6 - + - -
439C CYS* 3.2 34.5 - - + +
441C LEU* 5.2 7.4 - - + -
462C LEU* 5.0 1.1 - - + -
463C THR* 3.4 34.3 - - + -
466C PHE* 3.9 28.5 - + - -
479C LYS* 3.7 18.2 - - + -
480C LEU* 1.3 79.1 - - - +
482C PHE* 1.3 63.2 + - - +
483C ILE* 3.8 10.9 + - + +
519D PHE* 3.7 23.3 - + - -
520D LEU* 2.9 10.1 + - - +
521D PHE* 3.5 22.4 - + + -
522D ALA 2.9 25.9 + - - +
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Residues in contact with PHE 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C PHE* 3.7 25.6 - + - -
438C ALA* 4.6 2.9 - - + -
439C CYS 2.8 10.6 + - - +
440C ILE* 3.1 32.5 - - + +
441C LEU 2.8 25.8 + - - -
480C LEU* 3.8 35.4 - - + -
481C PHE* 1.3 74.4 - - - +
483C ILE* 1.3 61.6 + - - +
484C GLN 4.2 0.2 - - - -
520D LEU* 5.3 1.8 - - + -
522D ALA* 3.5 26.2 - - + +
541D PHE* 4.6 4.9 - + + -
545D LEU* 3.5 35.2 - - + -
549D LEU* 5.7 1.6 - - + -
558D ILE* 4.6 12.1 - - + -
562D LEU* 4.1 16.8 - - + -
601D PHE* 5.3 2.5 - + - -
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Residues in contact with ILE 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C LEU* 3.6 29.2 - - + +
450C ILE* 5.2 2.2 - - + -
459C ILE* 3.9 29.8 - - + -
481C PHE* 4.1 12.1 - - + +
482C PHE* 1.3 80.3 - - - +
484C GLN* 1.3 60.0 + - - +
485C ALA* 4.1 20.4 - - + +
487C ARG* 6.4 0.4 - - + -
521D PHE* 4.3 13.0 - - + -
522D ALA 2.9 11.3 + - - +
523D TYR* 3.8 39.3 - - + -
524D SER* 2.9 30.6 + - - -
541D PHE* 4.4 3.5 - - - -
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Residues in contact with GLN 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C ARG* 3.9 8.3 - - - +
393C ASP* 4.8 0.4 - - - +
440C ILE* 5.6 0.2 - - - +
441C LEU 2.8 8.8 + - - +
442C LEU* 3.6 21.3 - - + +
443C SER 3.0 25.8 + - - +
482C PHE 4.1 1.0 + - - -
483C ILE* 1.3 70.0 - - - +
485C ALA* 1.3 69.8 + - - +
524D SER* 3.0 20.5 - - - -
531D SER* 2.8 26.5 + - - -
532D TRP 4.2 2.3 + - - +
539D SER* 3.3 37.9 + - - +
541D PHE* 3.5 11.8 + - + +
542D VAL* 4.0 9.0 - - + -
587D GLN* 4.9 0.2 + - - -
805F ASJ 3.2 25.4 + - - +
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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