Contacts of the helix formed by residues 3442 - 3448 (chain C) in PDB entry 5Y3R
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 TYR3442 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3386C SER* 5.7 7.0 - - - -
3387C GLU* 4.8 6.8 + - + +
3390C GLN* 3.2 41.6 + - - +
3416C LEU* 5.8 4.9 - - + -
3419C PHE* 6.5 2.0 - + - -
3420C CYS* 3.9 24.5 - - - -
3438C GLU* 2.8 66.0 + - + +
3439C LEU* 4.6 2.2 - - - +
3441C ALA* 1.3 82.5 - - + +
3443C PRO* 1.4 53.5 - - + +
3444C ALA 2.6 17.8 + - - -
3445C LEU* 2.6 33.4 + - + +
3446C VAL* 3.9 3.7 + - + +
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Residues in contact with PRO3443 (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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3420C CYS* 5.0 9.2 - - + -
3439C LEU* 2.9 32.8 - - + +
3440C GLN* 3.5 0.7 - - + -
3441C ALA 3.5 2.9 - - - -
3442C TYR* 1.4 83.1 - - + +
3444C ALA* 1.3 62.0 + - - +
3445C LEU 3.2 0.2 - - - -
3446C VAL* 3.3 12.7 - - + +
3447C VAL* 3.0 32.7 + - + +
3464C LYS* 4.0 21.1 - - - +
3468C LEU* 4.6 9.4 - - + -
3474C ARG* 3.1 27.6 - - - +
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Residues in contact with ALA3444 (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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3441C ALA 3.5 12.3 - - - +
3442C TYR 2.6 3.2 + - - -
3443C PRO* 1.3 77.2 - - - +
3445C LEU* 1.3 67.6 + - + +
3447C VAL* 3.1 19.8 - - - +
3448C GLU* 4.0 7.4 + - - +
3475C TYR* 3.4 29.5 - - + +
3478C GLU* 3.0 30.6 - - - +
3482C LEU* 5.2 1.6 - - - +
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Residues in contact with LEU3445 (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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3390C GLN* 4.3 21.1 - - - +
3393C GLU* 5.5 8.3 - - - +
3394C GLU* 5.6 4.0 - - - +
3416C LEU* 5.8 4.5 - - + -
3441C ALA 5.3 1.1 - - - +
3442C TYR* 2.6 27.0 + - + +
3444C ALA* 1.3 78.2 - - + +
3446C VAL* 1.3 66.9 + - + +
3448C GLU* 3.2 17.1 + - - +
3449C LYS* 2.7 33.0 + - - +
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Residues in contact with VAL3446 (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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3413C TYR* 3.9 10.2 - - + +
3416C LEU* 4.0 16.4 - - + -
3417C ALA* 3.4 47.5 - - + +
3420C CYS* 5.1 5.6 - - + -
3442C TYR* 5.0 2.5 - - + +
3443C PRO* 3.3 23.3 - - + +
3445C LEU* 1.3 78.3 - - + +
3447C VAL* 1.3 71.1 + - - +
3448C GLU 3.2 0.5 + - - -
3449C LYS* 3.2 26.9 + - - +
3450C MET* 3.8 5.9 - - - +
3464C LYS* 4.3 12.6 - - - +
3465C PHE* 4.1 2.5 - - + -
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Residues in contact with VAL3447 (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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3443C PRO 3.0 10.1 + - - +
3444C ALA* 3.1 22.7 - - - +
3446C VAL* 1.3 76.3 - - - +
3448C GLU* 1.3 63.3 + - + +
3449C LYS 2.9 6.9 + - - -
3450C MET* 3.2 20.6 - - - +
3464C LYS* 3.0 31.4 - - - +
3465C PHE* 3.2 28.8 - - + -
3468C LEU* 3.4 13.2 - - + -
3478C GLU* 6.1 2.2 - - + -
3479C THR* 6.1 0.7 - - - -
3482C LEU* 5.8 4.5 - - + -
3483C MET* 4.0 24.9 - - + +
3486C GLU* 4.8 0.3 - - - +
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Residues in contact with GLU3448 (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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3444C ALA 4.3 5.7 - - - +
3445C LEU* 3.2 13.4 + - - +
3446C VAL 3.2 1.6 - - - -
3447C VAL* 1.3 80.4 - - + +
3449C LYS* 1.3 59.7 + - + +
3450C MET* 2.8 11.1 + - - +
3451C LEU* 3.4 28.1 + - + +
3482C LEU* 3.2 58.8 - - + +
3483C MET* 5.9 1.3 - - - -
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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