Contacts of the helix formed by residues 488 - 495 (chain C) in PDB entry 3F7F
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 THR 488 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485C LYS* 4.1 7.9 - - - +
487C ASN* 1.3 78.4 - - - +
489C THR* 1.3 68.3 + - - +
490C VAL* 3.8 6.1 + - - +
491C GLU* 2.8 42.3 + - - +
492C ASN* 3.1 16.2 + - - -
622C LEU* 4.3 12.8 - - + +
699C ILE* 3.9 33.2 - - + -
703C ASP* 4.7 6.7 - - - +
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Residues in contact with THR 489 (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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488C THR* 1.3 73.0 - - - +
490C VAL* 1.3 66.4 + - - +
492C ASN* 2.9 23.0 + - - +
493C TRP* 3.2 50.1 + - + +
590C GLN* 4.0 21.0 + - - +
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Residues in contact with VAL 490 (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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488C THR* 3.4 7.6 - - - +
489C THR* 1.3 75.5 - - - +
491C GLU* 1.3 63.2 - - + +
493C TRP* 3.2 21.6 + - + +
494C PHE* 3.1 20.8 + - - +
586C LEU* 5.2 2.9 - - + -
590C GLN* 3.5 41.7 - - + +
591C MET* 5.1 1.3 - - + +
622C LEU* 5.2 3.8 - - + -
625C ILE* 4.4 7.9 - - + -
626C HIS* 4.7 17.5 - - + +
629C ILE* 3.5 31.7 - - + +
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Residues in contact with GLU 491 (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 LYS* 2.6 30.8 + - - -
487C ASN* 3.2 15.1 - - + -
488C THR* 2.8 42.4 + - - +
489C THR 3.1 0.4 - - - -
490C VAL* 1.3 75.8 - - - +
492C ASN* 1.3 57.9 + - - +
494C PHE* 2.9 5.2 + - - +
495C TYR* 2.9 36.2 + - + -
618C SER 5.0 0.7 - - - +
621C GLN* 2.8 31.0 + - - +
622C LEU* 4.0 24.7 - - + +
625C ILE* 4.1 19.5 - - + -
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Residues in contact with ASN 492 (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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2C ALA 3.3 21.0 - - - +
3C CYS* 3.8 8.4 + - - +
343C ASN* 4.0 23.6 + - - +
487C ASN* 3.4 26.0 + - - +
488C THR 3.1 20.7 + - - -
489C THR* 2.9 11.8 + - + +
491C GLU* 1.3 77.0 - - - +
493C TRP* 1.3 65.7 + - + +
496C ASN* 2.8 35.3 + - - +
500C GLU* 4.6 6.3 - - - +
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Residues in contact with TRP 493 (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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489C THR* 3.2 35.8 + - + +
490C VAL* 3.6 21.3 - - + +
491C GLU 3.2 1.0 - - - -
492C ASN* 1.3 79.1 - - + +
494C PHE* 1.3 64.0 + - - +
496C ASN 3.2 1.2 + - - -
497C MET* 3.2 32.6 + - + +
500C GLU* 4.0 13.3 + - - -
504C SER* 3.7 19.8 + - - +
506C LEU* 3.2 38.1 - - + -
507C PHE* 3.4 42.8 - + + +
510C LEU* 3.4 28.7 - - + -
585C ASP* 5.1 0.7 - - - -
586C LEU* 4.9 1.1 - - + -
590C GLN* 3.8 20.9 - - + -
629C ILE* 6.2 0.4 - - + -
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Residues in contact with PHE 494 (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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386C LEU* 4.1 24.0 - - + -
389C LEU* 6.2 0.4 - - + -
390C GLN* 5.4 5.6 - - + -
395C LEU* 6.2 3.4 - - + -
490C VAL 3.1 9.8 + - - +
491C GLU 2.9 8.4 + - - +
493C TRP* 1.3 82.3 - - - +
495C TYR* 1.3 84.2 + + - +
496C ASN 3.3 3.6 + - - -
497C MET* 3.7 21.1 + - + +
624C SER 5.9 0.4 - - - -
625C ILE* 3.5 51.6 - - + -
628C ARG* 3.6 46.0 + - + -
629C ILE* 5.8 4.9 - - + +
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Residues in contact with TYR 495 (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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2C ALA* 4.8 3.8 - - + +
5C SER* 3.6 22.0 - - - -
6C ARG 5.3 0.9 + - - -
382C VAL* 3.4 37.9 - - + +
384C LYS 5.3 0.5 + - - -
386C LEU* 3.6 19.6 + - + +
389C LEU* 4.3 12.8 - - + -
487C ASN* 3.8 19.1 - - - +
491C GLU* 2.9 27.6 + - + +
493C TRP 3.4 0.2 - - - -
494C PHE* 1.3 92.5 - + - +
496C ASN* 1.3 77.4 + - - +
497C MET 3.9 0.4 - - - -
499C SER* 4.9 0.5 + - - -
621C GLN* 2.6 32.9 + - - +
625C ILE* 4.2 9.4 - - + -
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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