Contacts of the strand formed by residues 468 - 482 (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 PHE 468 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455C ASN* 4.3 14.6 - - - -
458C ILE* 3.7 42.4 - - + -
464C TRP* 3.5 10.0 + + + +
465C GLY 3.4 17.1 - - - +
466C HIS 3.4 6.1 - - - +
467C GLN* 1.3 79.4 - - - +
469C CYS* 1.3 75.1 + - - +
470C SER* 3.5 28.3 - - - -
471C PHE* 3.5 27.8 - + - -
496C LEU* 4.0 17.7 - - + -
497C LEU 3.9 7.4 - - - -
498C ALA* 4.0 4.5 - - - +
499C PHE* 5.7 0.2 - - - -
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Residues in contact with CYS 469 (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 4.0 1.8 - - - -
468C PHE* 1.3 89.9 - - - +
470C SER* 1.3 63.8 + - - +
497C LEU* 2.8 28.2 + - + +
498C ALA* 4.3 6.3 - - - -
499C PHE* 3.6 37.0 - - - -
510C PRO* 4.7 7.6 - - - -
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Residues in contact with SER 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C PHE* 3.5 12.5 - - - -
469C CYS* 1.3 80.6 - - - +
471C PHE* 1.3 60.0 + - - +
496C LEU* 3.4 1.6 - - - +
497C LEU* 2.7 52.5 + - - +
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Residues in contact with PHE 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C GLU* 3.6 39.7 - - + -
454C ILE* 3.4 31.9 - - + -
455C ASN* 3.5 31.0 - - - -
468C PHE* 3.5 17.3 - + + -
470C SER* 1.3 78.5 - - - +
472C SER* 1.3 68.9 + - - +
474C TYR* 4.0 16.4 - + - -
494C LEU* 4.1 12.8 - - + -
495C LEU 3.4 13.7 - - - +
496C LEU* 3.9 9.6 - - + +
497C LEU* 5.0 0.9 - - - -
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Residues in contact with SER 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C PHE* 1.3 85.9 - - - +
473C ASP* 1.4 76.0 + - - +
474C TYR* 3.7 8.3 - - - -
495C LEU* 2.8 25.5 + - - +
496C LEU 4.9 0.2 - - - -
497C LEU* 3.9 18.0 - - - +
512C THR* 5.5 3.3 - - - +
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Residues in contact with ASP 473 (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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226B TYR* 3.0 29.5 - - - +
227B PRO* 4.0 7.8 - - + +
472C SER* 1.4 90.8 - - - +
474C TYR* 1.3 62.6 + - - +
494C LEU* 4.0 2.6 - - - +
495C LEU* 3.2 33.0 + - + +
544C SER* 5.4 3.1 - - - -
548C TRP* 3.7 22.3 - - + +
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Residues in contact with TYR 474 (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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227B PRO* 4.1 12.5 - - - +
248B SER 3.2 25.1 - - - +
249B TYR* 3.8 25.5 + + - +
450C PHE* 3.8 15.7 - - + -
451C GLU* 2.9 43.9 + - + +
454C ILE* 3.7 17.5 - - + -
471C PHE* 4.0 8.7 - + - -
472C SER 3.7 15.5 - - - -
473C ASP* 1.3 74.3 - - - +
475C ASP* 1.3 60.2 + - - +
476C ILE* 4.0 19.8 + - + +
492C ILE* 4.6 0.2 - - + -
493C GLY 3.2 13.2 - - - +
494C LEU* 3.7 12.6 - - + -
548C TRP* 3.9 3.8 - - - -
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Residues in contact with ASP 475 (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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227B PRO* 3.8 12.5 - - + +
229B PRO* 4.6 5.9 - - - +
230B THR 5.0 0.5 + - - -
246B ASN* 5.3 0.2 + - - -
474C TYR* 1.3 73.2 - - - +
476C ILE* 1.3 67.8 + - - +
477C VAL* 3.8 4.8 - - - +
492C ILE 3.7 0.2 - - - -
493C GLY 2.8 33.8 + - - -
548C TRP* 3.7 23.5 - - + -
551C TYR* 3.0 28.5 + - + -
552C ARG* 2.7 48.3 + - - +
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Residues in contact with ILE 476 (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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230B THR* 4.5 3.5 + - - -
232B GLN* 4.4 3.8 - - - +
246B ASN* 3.0 28.3 + - - +
248B SER 5.0 1.3 - - - +
251B LEU* 5.9 2.0 - - + -
450C PHE* 3.4 47.8 - - + -
474C TYR* 4.0 15.0 - - + -
475C ASP* 1.3 79.9 + - - +
477C VAL* 1.3 67.9 + - - +
478C ILE* 4.4 1.2 + - + -
490C ILE* 3.8 35.4 - - + -
491C ASN 3.4 8.7 - - - +
492C ILE* 3.5 35.9 - - + -
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Residues in contact with VAL 477 (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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230B THR* 3.9 14.8 - - + +
232B GLN* 3.6 19.5 - - - +
475C ASP* 3.8 20.6 - - - +
476C ILE* 1.3 78.4 - - - +
478C ILE* 1.4 66.3 + - - +
479C LEU* 3.6 2.3 + - + +
490C ILE* 3.7 1.5 - - - -
491C ASN* 2.8 35.4 + - - +
551C TYR* 3.9 10.4 + - + +
552C ARG* 4.2 10.5 - - + -
555C CYS* 3.7 34.8 - - + -
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Residues in contact with ILE 478 (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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232B GLN* 2.9 37.2 + - - +
235B PHE* 3.4 21.8 - - + -
236B GLN* 4.2 24.5 - - + -
244B LEU* 4.3 22.4 - - + -
246B ASN* 6.4 0.9 - - + -
251B LEU* 4.5 12.8 - - + -
476C ILE* 4.3 1.3 - - + +
477C VAL* 1.4 73.1 - - - +
479C LEU* 1.3 62.1 + - - +
480C GLU 3.5 23.1 - - - +
481C VAL* 3.7 15.5 - - + -
488C VAL* 4.0 6.7 - - + -
489C LEU 3.7 7.2 - - - +
490C ILE* 4.1 15.9 - - + -
559C VAL* 5.4 1.6 - - - +
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Residues in contact with LEU 479 (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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235B PHE* 3.1 20.9 - - - -
477C VAL* 3.6 1.3 + - + +
478C ILE* 1.3 77.5 - - - +
480C GLU* 1.3 61.6 + - - +
489C LEU* 2.8 32.2 + - + +
491C ASN* 3.6 35.2 - - + +
518C LYS* 3.9 21.3 - - + -
555C CYS* 4.0 34.5 - - + +
558C MET* 4.1 31.9 - - + -
559C VAL* 4.3 13.9 - - + +
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Residues in contact with GLU 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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235B PHE* 3.9 12.4 - - - -
238B LYS* 3.3 20.8 + - - +
478C ILE* 3.5 4.5 - - - +
479C LEU* 1.3 81.8 - - - +
481C VAL* 1.3 91.8 + - - +
482C CYS* 4.3 5.6 - - + +
487C GLN 4.6 0.7 - - - -
489C LEU* 2.8 46.8 + - + -
562C TRP* 5.6 4.3 - - - +
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Residues in contact with VAL 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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235B PHE* 3.3 24.6 - - + +
238B LYS* 3.2 42.8 - - + +
239B LYS* 4.2 20.2 - - + +
244B LEU* 3.8 18.2 - - + -
478C ILE* 3.7 17.0 - - + -
480C GLU* 1.3 90.6 + - - +
482C CYS* 1.3 64.8 + - - +
483C PRO* 3.3 6.2 - - - +
487C GLN 3.5 7.4 - - - +
488C VAL* 4.3 8.3 - - + -
523C LEU* 5.7 2.5 - - + -
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Residues in contact with CYS 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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480C GLU* 4.3 6.5 - - + -
481C VAL* 1.3 73.7 - - - +
483C PRO* 1.4 62.5 - - - +
484C GLU* 3.3 9.4 + - - -
485C THR* 3.1 41.1 - - - +
486C ASN* 2.8 25.5 + - - -
487C GLN* 2.8 23.4 + - + +
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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