Contacts of the helix formed by residues 495 - 501 (chain A) in PDB entry 3V98
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 GLY 495 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A TYR* 3.3 1.3 - - - +
494A GLU* 1.3 80.2 - - - +
496A ASP* 1.3 65.7 + - - -
497A GLN* 3.3 3.6 - - - -
498A VAL* 3.3 17.1 + - - +
499A VAL* 3.5 14.0 + - - +
532A ARG* 3.8 16.6 - - - +
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Residues in contact with ASP 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A GLY* 1.3 68.6 - - - -
497A GLN* 1.3 65.8 + - - +
499A VAL* 3.1 5.8 + - - +
500A GLU* 2.9 20.1 + - - +
530A LYS 3.5 18.7 - - - +
531A SER* 3.4 20.2 - - - +
532A ARG* 2.9 30.4 + - - +
533A GLU 4.6 0.3 + - - -
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Residues in contact with GLN 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A GLY* 3.3 1.5 - - - -
496A ASP* 1.3 78.4 - - - +
498A VAL* 1.3 61.0 + - + +
500A GLU* 3.2 23.3 + - - +
501A GLU* 2.8 69.3 + - - +
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Residues in contact with VAL 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.8 19.3 - - + -
120A ARG* 3.8 31.6 - - - +
493A TYR* 3.7 18.0 - - + -
494A GLU* 3.9 21.8 - - + +
495A GLY* 3.6 15.0 - - - +
496A ASP 3.2 0.4 - - - -
497A GLN* 1.3 79.4 - - + +
499A VAL* 1.3 62.1 + - - +
501A GLU* 3.5 10.4 + - - +
502A ASP* 3.2 21.8 + - - +
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Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A TYR* 3.5 28.9 - - + -
495A GLY 3.7 12.3 - - - +
496A ASP 3.1 7.3 + - - +
498A VAL* 1.3 76.5 - - - +
500A GLU* 1.3 62.5 + - - +
501A GLU 3.2 0.9 + - - -
502A ASP* 3.2 12.0 + - - +
505A LEU* 3.7 17.4 - - + +
506A GLN* 3.0 15.6 + - - -
529A VAL* 3.6 20.0 - - + +
531A SER 3.7 20.9 - - - +
532A ARG* 3.8 24.7 - - + +
535A LEU* 4.3 7.2 - - + -
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASP 2.9 12.9 + - - +
497A GLN* 3.6 25.0 - - - +
499A VAL* 1.3 77.6 - - - +
501A GLU* 1.3 63.8 + - + +
506A GLN* 3.4 18.9 + - - +
529A VAL 3.7 11.2 - - - -
530A LYS* 3.9 46.5 + - + +
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Residues in contact with GLU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A GLN* 2.8 60.4 + - + +
498A VAL* 3.9 8.1 - - - +
499A VAL 3.2 0.4 - - - -
500A GLU* 1.3 80.4 - - + +
502A ASP* 1.3 60.0 + - - +
503A PRO* 3.1 16.0 - - - +
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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