Contacts of the strand formed by residues 498 - 506 (chain C) in PDB entry 3SV1
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 TYR 498 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384C LEU* 3.4 3.4 - - - +
385C SER* 2.7 49.1 + - - +
386C GLU 4.1 5.2 - - - +
387C ARG* 3.7 38.1 - - + +
473C ARG* 5.8 7.4 - - + -
496C LYS 3.4 34.5 - - - -
497C GLN* 1.3 76.9 - - + +
499C LYS* 1.3 59.2 + - - +
500C MET* 3.3 12.2 + - + -
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Residues in contact with LYS 499 (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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382C GLN* 3.3 37.3 + - + +
383C LEU 3.4 7.4 - - - +
384C LEU* 4.4 15.3 - - + -
473C ARG 4.1 1.1 - - - -
474C ARG* 3.2 51.6 + - + +
497C GLN 3.6 5.8 + - - +
498C TYR* 1.3 68.4 - - - +
500C MET* 1.3 61.1 + - - +
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Residues in contact with MET 500 (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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382C GLN* 3.1 14.4 - - - +
383C LEU* 2.6 45.6 + - + -
385C SER* 3.6 21.5 - - - +
394C ARG* 5.0 2.5 - - - +
459C SER* 3.0 29.4 - - - +
471C MET* 3.2 35.7 - - + -
472C ALA 3.0 33.2 - - - +
473C ARG* 3.1 25.6 - - + +
474C ARG* 4.9 0.2 - - - -
498C TYR* 4.2 8.3 - - + +
499C LYS* 1.3 76.5 - - - +
501C ILE* 1.3 61.8 + - - +
502C CYS* 5.6 0.2 - - - -
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Residues in contact with ILE 501 (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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380C SER* 3.5 25.1 - - - +
381C THR 3.4 21.5 - - - +
382C GLN* 4.1 12.8 - - + +
453C HIS* 4.7 4.3 - - + -
470C LEU 3.7 0.7 - - - +
471C MET* 2.8 24.1 - - - -
472C ALA* 3.0 31.1 + - + +
474C ARG* 4.1 25.6 - - + +
500C MET* 1.3 79.4 - - - +
502C CYS* 1.3 62.5 + - - +
503C HIS* 3.6 26.5 + - + +
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Residues in contact with CYS 502 (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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380C SER* 3.1 26.9 - - - -
381C THR* 2.7 19.9 + - + +
383C LEU* 4.4 17.0 - - - -
397C GLN 4.8 0.9 - - - -
398C ALA* 5.2 2.5 - - - -
401C ALA* 3.7 33.7 - - + -
469C VAL* 3.9 13.9 - - + -
470C LEU 3.3 3.4 - - - -
471C MET* 3.5 31.6 - - - -
501C ILE* 1.3 72.5 - - - +
503C HIS* 1.3 61.9 + - - +
504C VAL* 3.5 4.3 + - + +
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Residues in contact with HIS 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TYR* 4.2 1.8 - - + -
380C SER* 2.4 30.0 + - - -
441C VAL* 6.3 0.7 - - + -
451C MET* 3.4 41.9 - - + +
453C HIS* 3.2 33.9 + + - -
468C VAL 3.6 1.9 - - - +
469C VAL* 3.4 5.0 - - - -
470C LEU* 2.8 58.6 + - + +
472C ALA 5.6 1.1 - - - -
501C ILE* 3.6 27.4 - - + +
502C CYS* 1.3 69.9 - - - +
504C VAL* 1.3 62.2 + - - +
505C PHE* 3.5 14.5 - - + -
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Residues in contact with VAL 504 (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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377C TYR* 3.3 17.5 - - - -
378C LEU* 3.4 26.1 + - + -
379C GLY 3.0 12.9 + - - +
401C ALA 4.5 1.1 - - - +
402C VAL* 4.0 36.1 - - + +
405C VAL* 3.2 37.2 - - + -
406C LYS* 5.8 3.4 - - + -
467C ILE* 4.3 5.8 - - + -
468C VAL 3.6 2.2 - - - +
469C VAL* 4.3 7.6 - - + +
502C CYS* 3.9 6.3 - - + +
503C HIS* 1.3 73.5 - - - +
505C PHE* 1.3 77.2 + - - +
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Residues in contact with PHE 505 (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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375C ALA* 4.6 4.5 - - + -
376C ASN 2.9 25.1 - - - +
377C TYR* 3.2 33.9 - + + -
378C LEU* 3.4 7.2 - - - +
430C VAL* 3.9 8.3 - - + -
432C LEU* 4.1 20.0 - - + -
441C VAL* 3.9 33.9 - - + -
451C MET* 5.2 0.7 - - - -
467C ILE* 3.1 13.0 - - - +
468C VAL* 2.7 54.7 + - + +
470C LEU* 3.6 13.9 - - + -
503C HIS* 3.5 29.4 - + + -
504C VAL* 1.3 77.0 - - - +
506C GLU* 1.3 62.6 + - - +
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Residues in contact with GLU 506 (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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375C ALA* 3.1 2.5 - - - +
376C ASN* 2.8 61.0 + - + +
378C LEU* 4.1 14.0 - - + +
427C LEU* 3.7 12.0 - - - +
466C ASN* 2.9 31.2 + - - +
467C ILE* 4.9 5.2 - - + -
505C PHE* 1.3 78.2 - - - +
507C SER* 1.3 64.0 + - - +
508C GLU* 4.8 10.4 - - - +
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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