Contacts of the strand formed by residues 511 - 522 (chain C) in PDB entry 6Q0V
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 511 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497C LEU* 3.4 5.6 - - - -
498C ALA 2.8 35.3 + - - +
500C PRO* 4.2 16.3 - - + +
509C ARG* 4.0 14.4 - - + +
510C PRO* 1.4 76.5 - - - +
512C THR* 1.4 61.9 + - - +
513C TYR* 3.2 33.3 + - + +
538C GLU* 3.4 35.7 + - + +
540C LYS* 5.3 3.2 - - - +
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Residues in contact with THR 512 (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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472C SER* 5.5 2.7 - - - +
495C LEU* 3.9 24.9 - - + -
496C LEU 3.2 15.0 - - - +
497C LEU* 4.6 10.0 - - + +
511C LYS* 1.4 72.3 - - - +
513C TYR* 1.3 61.7 + - - +
538C GLU* 4.0 6.9 - - - +
539C VAL* 3.3 34.1 + - + +
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Residues in contact with TYR 513 (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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467C GLN* 5.9 0.4 - - - -
494C LEU 4.4 0.2 - - - -
495C LEU* 3.5 10.6 - - - +
496C LEU* 3.0 36.8 + - + +
498C ALA* 3.4 37.2 - - + -
499C PHE 4.7 1.6 - - - -
500C PRO* 3.2 32.5 - - + +
511C LYS* 3.2 42.7 + - + +
512C THR* 1.3 72.1 - - - +
514C HIS* 1.3 59.8 + - - +
536C LEU* 3.8 40.4 - - + -
537C THR 3.5 7.2 - - - +
538C GLU* 3.5 33.6 + - + -
539C VAL* 3.9 5.6 - - - -
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Residues in contact with HIS 514 (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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493C GLY* 4.2 3.1 - - - -
494C LEU 3.2 25.7 + - - +
495C LEU* 5.1 1.5 - - + +
496C LEU* 5.6 0.2 - - - -
513C TYR* 1.3 74.4 - - - +
515C THR* 1.3 80.9 + - - +
516C SER* 5.5 1.4 - - - -
535C ASP 3.6 0.3 - - - +
536C LEU* 4.0 0.6 - - - -
537C THR* 2.8 49.4 + - - +
539C VAL* 3.8 9.4 - - + -
547C VAL* 3.6 30.9 - - + +
548C TRP* 4.2 15.6 - + - -
550C SER* 6.5 0.2 - - - -
551C TYR* 4.0 27.0 - + + +
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Residues in contact with THR 515 (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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464C TRP* 3.7 23.5 - - + -
492C ILE 3.7 0.8 - - - +
493C GLY* 3.6 0.7 - - - -
494C LEU* 2.9 42.2 + - + -
496C LEU* 3.7 20.2 - - + -
514C HIS* 1.3 89.3 - - - +
516C SER* 1.3 67.5 + - - +
517C LEU* 4.9 4.3 - - + -
534C GLY* 3.2 19.6 + - - -
535C ASP 3.1 19.0 + - - -
536C LEU* 3.9 7.4 - - - -
537C THR* 5.1 0.2 - - - -
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Residues in contact with SER 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C ASN* 2.6 25.9 + - - -
492C ILE 3.4 5.6 - - - -
514C HIS* 5.5 1.3 - - - -
515C THR* 1.3 77.8 + - - +
517C LEU* 1.4 63.6 + - - +
518C LYS* 3.0 25.6 + - - -
532C SER* 4.1 1.9 + - - +
533C VAL* 3.8 0.7 - - - -
534C GLY* 2.8 35.8 + - - -
551C TYR* 4.7 10.8 - - - -
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Residues in contact with LEU 517 (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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454C ILE* 4.5 8.7 - - + -
457C VAL* 3.6 33.9 - - + -
458C ILE* 4.7 4.3 - - + -
462C ALA* 5.8 0.2 - - + -
464C TRP* 4.7 9.6 - - + -
491C ASN* 3.5 2.9 + - - -
492C ILE* 2.7 68.2 + - + +
494C LEU* 4.2 24.9 - - + -
515C THR* 4.9 3.1 - - + -
516C SER* 1.4 78.7 + - - +
518C LYS* 1.3 62.4 + - - +
519C VAL* 5.0 2.0 - - + -
532C SER 3.5 3.1 - - - +
533C VAL* 3.6 36.1 - - + -
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Residues in contact with LYS 518 (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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479C LEU* 3.9 25.8 - - + -
489C LEU* 4.7 3.8 - - + -
490C ILE 3.4 4.7 - - - +
491C ASN* 3.7 18.3 - - - +
516C SER* 3.0 28.0 + - - +
517C LEU* 1.3 71.9 - - - +
519C VAL* 1.3 63.6 + - - +
530C THR* 3.8 1.7 - - - -
531C VAL* 3.0 39.0 + - + -
532C SER* 2.9 40.7 + - - +
558C MET* 4.4 16.5 - - - -
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Residues in contact with VAL 519 (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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448C LEU* 5.4 1.3 - - + -
453C VAL* 4.0 24.0 - - + -
457C VAL* 4.0 19.3 - - + -
488C VAL 3.5 1.9 - - - +
489C LEU* 3.7 4.9 - - - +
490C ILE* 2.9 42.6 + - + +
492C ILE* 4.0 16.4 - - + -
517C LEU* 4.6 4.0 - - + +
518C LYS* 1.3 80.1 - - - +
520C ALA* 1.3 62.6 + - - +
521C TRP* 4.7 2.2 - - + +
528C PHE* 3.6 33.2 - - + -
529C GLU 3.5 4.0 - - - +
530C THR* 4.1 6.7 - - - -
531C VAL* 3.9 0.8 - - - +
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Residues in contact with ALA 520 (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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487C GLN* 4.3 22.7 - - + +
488C VAL 3.5 7.0 - - - +
489C LEU* 4.5 9.4 - - + -
519C VAL* 1.3 72.8 - - - +
521C TRP* 1.3 58.8 + - - +
522C ASP 4.1 0.9 + - - -
527C ILE 4.2 0.3 - - - +
528C PHE* 3.3 2.6 - - - -
529C GLU* 2.8 46.7 + - - +
531C VAL* 4.3 18.0 - - + +
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Residues in contact with TRP 521 (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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244B LEU* 4.3 6.3 - - + -
251B LEU* 3.6 43.5 - - + -
253B ALA* 4.1 2.7 - - + -
387C VAL* 4.5 0.6 - - - +
446C LEU* 3.3 48.0 - - + -
447C THR 3.9 5.2 - - - -
448C LEU* 3.6 43.7 - - + +
486C ASN 3.8 0.2 - - - +
487C GLN* 3.5 4.0 - - - -
488C VAL* 2.8 53.1 + - + +
490C ILE* 5.5 2.0 - - + -
519C VAL* 5.1 2.5 - - + +
520C ALA* 1.3 72.1 - - - +
522C ASP* 1.4 65.3 + - - +
523C LEU* 3.7 25.3 + - + -
526C GLY* 2.8 33.7 + - - -
527C ILE 4.0 5.8 - - - -
528C PHE* 4.2 4.5 - - + +
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Residues in contact with ASP 522 (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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485C THR 4.5 4.3 - - - +
486C ASN 3.6 6.3 - - - -
487C GLN* 3.9 19.3 + - - +
520C ALA 4.1 1.2 + - - -
521C TRP* 1.4 72.7 - - - +
523C LEU* 1.3 58.7 + - - +
524C ASN* 2.8 45.9 + - - +
525C THR* 3.0 32.9 + - - +
526C GLY* 2.8 30.3 + - - -
527C ILE* 3.1 13.8 + - + +
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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