Contacts of the helix formed by residues 519 - 528 (chain C) in PDB entry 5VSW
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 ASN 519 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517C GLN* 3.5 2.8 - - - +
518C ASN* 1.3 83.8 + - + +
520C PRO* 1.3 72.0 - - - +
521C LEU* 2.9 32.9 + - - +
522C SER* 2.7 37.6 + - - -
523C GLU* 2.9 18.3 + - - +
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Residues in contact with PRO 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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519C ASN* 1.3 91.2 - - - +
521C LEU* 1.3 56.1 + - - +
523C GLU* 4.0 12.1 - - + +
524C ILE* 3.2 28.4 + - - +
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Residues in contact with LEU 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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519C ASN* 2.9 16.8 + - - +
520C PRO* 1.3 77.9 - - - +
522C SER* 1.3 62.2 + - - +
524C ILE* 3.8 16.6 - - + -
525C THR* 2.8 53.3 + - + +
562C GLU* 5.0 5.8 - - - +
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Residues in contact with SER 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C ASP* 2.5 49.2 + - - +
518C ASN* 3.3 9.6 + - - -
519C ASN* 2.7 31.6 + - - +
521C LEU* 1.3 77.5 - - - +
523C GLU* 1.3 60.4 + - - -
525C THR* 3.6 8.8 - - - +
526C HIS* 3.1 24.9 + - - +
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Residues in contact with GLU 523 (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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515C MET* 3.7 25.5 - - + +
516C ASP 3.8 3.4 - - - -
517C GLN* 3.4 30.2 + - + +
519C ASN 2.9 18.5 + - - +
520C PRO* 4.0 11.2 - - - +
522C SER* 1.3 76.6 - - - +
524C ILE* 1.3 62.4 + - - +
526C HIS* 3.0 5.8 + - - +
527C LYS* 3.0 56.0 + - - +
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Residues in contact with ILE 524 (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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27C LEU* 3.8 39.3 - - + -
28C LEU* 3.8 24.0 - - + -
520C PRO 3.2 15.5 + - - +
521C LEU* 3.6 25.8 - - + +
523C GLU* 1.3 79.6 - - - +
525C THR* 1.3 64.5 + - - +
527C LYS* 4.3 5.7 - - - +
528C ARG* 3.3 36.3 + - - +
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Residues in contact with THR 525 (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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516C ASP* 5.8 2.0 - - - +
521C LEU* 2.8 31.5 + - + +
522C SER* 3.6 13.2 - - - +
524C ILE* 1.3 76.7 - - - +
526C HIS* 1.3 63.5 + - + +
528C ARG* 2.8 25.9 - - - +
529C ARG* 3.7 29.2 + - - +
562C GLU* 3.0 35.0 + - - +
574C SER* 4.2 4.1 + - - -
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Residues in contact with HIS 526 (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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144C VAL* 3.5 33.3 - - + +
146C VAL* 3.9 9.8 - - + +
513C GLN* 3.0 48.0 + - + +
514C PHE 3.8 7.2 - - - -
515C MET* 3.9 1.9 - - + -
516C ASP* 3.1 37.7 + - + +
522C SER 3.1 16.9 + - - +
523C GLU* 3.0 7.3 + - - +
525C THR* 1.3 80.6 - - + +
527C LYS* 1.3 66.2 + - - +
529C ARG* 3.1 29.7 + - + +
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Residues in contact with LYS 527 (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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28C LEU* 3.5 29.1 - - + +
30C ILE* 5.3 3.6 - - - +
31C GLN* 3.6 28.0 - - + +
133C ASN* 3.1 38.2 + - - +
134C GLY* 4.4 5.6 - - - +
135C THR* 3.5 21.7 - - - +
144C VAL* 3.9 24.9 - - + +
145C ILE 5.3 0.5 - - - +
146C VAL* 5.8 0.2 - - - -
147C SER* 4.8 6.2 + - - -
515C MET* 3.8 13.7 - - - -
523C GLU* 3.0 43.3 + - - +
524C ILE* 4.3 1.9 - - - +
526C HIS* 1.3 75.5 - - - +
528C ARG* 1.3 58.5 + - - +
529C ARG 3.4 5.2 + - - +
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Residues in contact with ARG 528 (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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26C TYR 4.6 1.2 + - - -
27C LEU* 2.5 71.5 + - - +
28C LEU* 5.1 1.1 - - + -
30C ILE* 4.6 9.8 - - + +
524C ILE* 3.3 25.8 + - + +
525C THR* 2.8 16.1 - - - +
526C HIS 3.2 0.4 - - - -
527C LYS* 1.3 75.5 - - + +
529C ARG* 1.3 60.4 + - - +
574C SER* 3.3 16.8 + - - +
575C LEU* 3.3 42.7 + - + +
576C SER 2.5 36.2 + - - -
577C VAL* 3.3 16.2 + - - +
579C ALA 5.6 0.6 + - - -
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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