Contacts of the helix formed by residues 476 - 485 (chain C) in PDB entry 6T8B
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 VAL 476 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464C VAL* 4.6 10.1 - - + -
472C LYS 2.8 19.6 + - - +
473C SER* 4.3 11.4 - - - +
474C VAL 3.9 0.2 - - - +
475C GLY* 1.3 80.0 - - - +
477C ASN* 1.3 60.6 + - - +
478C ALA 3.2 1.1 - - - -
479C MET* 3.2 7.7 + - + +
480C LEU* 2.9 35.9 + - + +
504C LEU* 4.6 7.9 - - + -
593C VAL* 3.9 28.3 - - + -
595C ASP* 5.8 3.8 - - + +
627C ILE* 4.5 15.3 - - + -
629C ALA* 4.2 23.8 - - + -
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Residues in contact with ASN 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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548B ARG* 2.5 44.6 + - - +
473C SER* 2.8 20.9 - - - +
474C VAL* 4.1 3.2 - - - +
476C VAL* 1.3 78.2 - - - +
478C ALA* 1.3 57.4 + - - +
480C LEU* 4.5 0.9 - - - -
481C LEU* 2.9 36.8 + - + +
503C GLU 3.7 13.8 + - - +
504C LEU* 4.5 2.6 - - - +
507C TYR* 2.8 33.4 + - - +
696C VAL* 3.5 21.3 - - + -
701C VAL* 4.7 1.3 - - + -
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Residues in contact with ALA 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C PHE* 3.7 24.0 - - + -
442C ALA 4.3 9.4 - - - +
443C LEU* 5.3 2.9 - - - +
474C VAL 3.4 19.6 + - - +
475C GLY* 4.2 9.4 - - - +
476C VAL 3.2 0.6 - - - -
477C ASN* 1.3 79.6 - - - +
479C MET* 1.3 58.2 + - + +
481C LEU* 3.5 0.4 + - - -
482C SER* 2.9 32.4 + - - -
694C ALA* 4.3 13.0 - - + +
696C VAL* 3.7 8.9 - - + +
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Residues in contact with MET 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C LEU* 3.5 32.3 - - + +
442C ALA 5.3 1.6 - - - +
443C LEU* 3.6 25.4 - - + -
462C LEU* 3.5 33.0 - - + -
464C VAL* 4.1 9.6 - - + -
475C GLY* 3.1 22.2 - - - +
476C VAL* 3.2 13.7 + - + +
478C ALA* 1.3 77.5 - - + +
480C LEU* 1.3 60.0 + - + +
482C SER* 3.1 8.1 + - - -
483C ILE* 3.0 31.6 + - - +
627C ILE* 4.5 17.9 - - + -
650C ILE* 3.7 10.3 - - + -
652C PHE* 5.7 2.9 - - + -
678C MET* 5.9 0.9 - - + -
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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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476C VAL* 2.9 24.4 + - + +
477C ASN 4.0 2.0 - - - +
479C MET* 1.3 77.7 - - + +
481C LEU* 1.3 59.5 + - - +
483C ILE* 3.1 11.7 + - + +
484C LEU* 2.9 34.4 + - + +
494C LEU* 3.8 28.3 - - + -
496C MET* 4.1 6.7 - - + -
504C LEU* 3.7 19.1 - - + -
507C TYR* 3.4 38.1 - - + +
591C VAL* 4.7 2.9 - - + -
593C VAL* 3.7 31.9 - - + -
627C ILE* 6.2 0.2 - - + -
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Residues in contact with LEU 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C LEU* 4.2 13.2 - - + -
423C PHE* 4.0 12.1 - - + -
477C ASN 2.9 28.6 + - - +
478C ALA* 3.9 3.1 - - - +
480C LEU* 1.3 73.4 - - - +
482C SER* 1.3 64.9 + - - +
484C LEU* 4.0 8.9 - - + +
485C PHE* 3.1 33.0 + - + +
507C TYR* 3.2 24.7 - - + +
696C VAL* 3.8 23.3 - - + -
700C GLU 4.3 1.3 - - - +
701C VAL* 3.8 26.7 - - + -
704C VAL* 4.1 31.2 - - + -
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Residues in contact with SER 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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423C PHE* 3.6 6.8 - - - -
427C LEU* 5.2 0.2 - - - -
432C TYR* 3.1 28.0 + - - -
440C PRO* 3.3 31.9 - - - +
441C LEU* 4.0 1.1 - - - -
442C ALA* 3.0 37.1 + - - +
478C ALA 2.9 17.9 + - - -
479C MET 3.3 8.3 - - - -
481C LEU* 1.3 75.9 - - - +
483C ILE* 1.3 61.4 + - - +
486C LYS* 4.0 4.0 + - - +
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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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438C THR 4.9 0.2 - - - +
439C VAL* 3.6 34.1 - - + -
440C PRO* 3.5 20.2 - - - +
441C LEU* 4.1 8.1 - - + -
456C LEU* 4.7 4.3 - - + -
479C MET 3.0 15.8 + - - +
480C LEU* 3.1 17.9 + - + +
482C SER* 1.3 77.6 - - - +
484C LEU* 1.3 65.9 + - + +
486C LYS 3.5 0.2 + - - -
487C SER* 3.2 27.1 + - - +
492C ALA* 4.3 23.6 - - + +
494C LEU* 4.3 25.4 - - + -
512C HIS* 5.6 1.8 - - + -
591C VAL* 4.9 4.3 - - + -
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Residues in contact with LEU 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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315C LEU* 3.3 14.4 - - - +
316C PRO* 4.4 1.4 - - + +
480C LEU* 2.9 25.4 + - + +
481C LEU* 3.3 17.7 + - + +
483C ILE* 1.3 78.6 - - + +
485C PHE* 1.3 58.9 + - + +
486C LYS 3.0 6.2 + - - -
487C SER 3.4 6.6 - - - +
494C LEU* 3.9 19.1 - - + -
496C MET* 6.1 0.2 - - + -
507C TYR* 4.9 13.7 - - + -
510C ILE* 4.0 12.3 - - + -
512C HIS* 3.3 35.0 - - + +
704C VAL* 4.1 27.4 - - + +
705C VAL* 5.1 7.0 - - + +
708C TRP* 4.4 18.1 - - + +
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Residues in contact with PHE 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 3.5 20.0 - - - +
316C PRO* 3.5 32.0 - - + +
317C PRO 4.8 6.1 - - - -
318C LEU* 3.7 17.0 - - + +
320C LEU* 4.8 6.7 - - + -
321C LEU* 3.6 34.5 - - + -
423C PHE* 4.4 4.9 - + - -
427C LEU* 3.4 21.1 - - + -
432C TYR* 3.9 14.1 + - + +
481C LEU* 3.1 20.9 + - + +
483C ILE 3.5 0.4 - - - -
484C LEU* 1.3 77.0 - - - +
486C LYS* 1.3 58.1 + - - +
704C VAL* 3.4 47.3 - - + -
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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