Contacts of the helix formed by residues 3602 - 3612 (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 ASN3602 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3595C GLU 3.8 13.2 + - - +
3596C LEU* 5.3 4.6 - - - +
3598C LYS* 4.2 1.0 - - - +
3599C THR 3.1 23.6 + - - +
3600C PRO* 4.9 3.3 - - - +
3601C VAL* 1.3 74.8 - - - +
3603C LYS* 1.3 69.5 + - - +
3604C LYS 3.8 0.2 - - - -
3605C ASN* 3.3 29.4 + - + +
3606C ILE* 3.5 6.6 + - + +
3655C LYS* 2.4 60.5 + - + +
3656C LEU* 4.0 13.1 - - - +
3657C SER 5.0 1.2 - - - +
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Residues in contact with LYS3603 (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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3601C VAL* 3.3 9.6 - - + +
3602C ASN* 1.3 81.4 - - - +
3604C LYS* 1.3 65.3 + - - +
3605C ASN 3.2 0.2 + - - -
3607C GLU* 2.4 42.6 + - - +
3654C MET 4.4 6.4 + - - -
3655C LYS* 2.6 45.5 + - + +
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Residues in contact with LYS3604 (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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3601C VAL* 3.2 34.0 - - - +
3603C LYS* 1.3 79.5 - - + +
3605C ASN* 1.3 70.3 + - - +
3607C GLU* 2.8 29.9 + - - +
3608C LYS* 3.1 14.4 + - - +
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Residues in contact with ASN3605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3595C GLU* 2.9 41.0 + - + +
3598C LYS* 3.9 11.7 - - - +
3601C VAL 3.1 25.9 + - - +
3602C ASN* 3.3 24.6 + - - +
3603C LYS 3.1 0.4 - - - -
3604C LYS* 1.3 82.2 - - - +
3606C ILE* 1.3 64.6 + - + +
3608C LYS* 4.3 0.9 + - - +
3609C MET* 3.1 28.3 + - - +
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Residues in contact with ILE3606 (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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3592C VAL* 3.4 59.2 - - + +
3595C GLU* 3.4 24.5 - - + -
3596C LEU* 5.3 6.7 - - + -
3602C ASN* 3.5 12.7 + - + +
3605C ASN* 1.3 74.6 - - + +
3607C GLU* 1.3 53.9 + - - +
3608C LYS 3.6 0.4 - - - -
3609C MET* 3.3 6.7 - - - +
3610C TYR* 2.8 77.4 + - + +
3651C LEU* 4.0 0.7 - - + -
3655C LYS* 4.3 14.8 - - + -
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Residues in contact with GLU3607 (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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3603C LYS* 2.4 36.6 + - - +
3604C LYS* 2.8 37.8 + - - +
3606C ILE* 1.3 73.9 - - - +
3608C LYS* 1.3 65.7 + - - +
3610C TYR* 3.0 16.6 + - + +
3611C GLU* 3.0 33.3 + - + +
3655C LYS* 3.5 7.4 - - - +
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Residues in contact with LYS3608 (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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3541C SER 4.8 7.4 - - - +
3542C PHE* 5.1 7.6 - - - +
3604C LYS 3.1 8.8 + - - +
3605C ASN 5.2 0.7 - - - +
3607C GLU* 1.3 80.5 - - - +
3609C MET* 1.3 64.9 + - + +
3611C GLU* 2.6 50.1 + - - +
3612C ARG* 2.9 60.5 + - - +
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Residues in contact with MET3609 (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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3588C TRP* 3.6 9.2 + - + +
3591C ASP* 3.5 25.6 - - + +
3592C VAL* 3.4 45.3 - - + -
3595C GLU* 3.5 24.9 - - + +
3605C ASN 3.1 22.0 - - - +
3606C ILE* 3.3 14.1 - - - +
3608C LYS* 1.3 78.6 - - + +
3610C TYR* 1.3 56.6 + - - +
3612C ARG* 3.6 3.6 + - - +
3613C MET* 2.9 29.7 + - - +
3799C ARG* 5.4 3.4 - - - +
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Residues in contact with TYR3610 (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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3588C TRP* 4.2 11.9 - + - -
3606C ILE* 2.8 45.0 + - + +
3607C GLU* 3.0 10.9 + - - +
3609C MET* 1.3 74.6 - - - +
3611C GLU* 1.3 66.0 + - - +
3613C MET* 2.8 13.5 + - - -
3614C TYR* 2.9 25.9 + + + +
3615C ALA 3.9 0.5 + - - -
3648C GLY 4.6 0.7 - - - -
3651C LEU* 2.2 52.9 + - + +
3652C LEU* 3.3 45.5 - - + -
3655C LYS* 3.4 28.1 + - - +
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Residues in contact with GLU3611 (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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3607C GLU* 3.0 23.9 + - + +
3608C LYS* 2.6 56.7 + - - +
3610C TYR* 1.3 74.1 - - - +
3612C ARG* 1.3 57.8 + - + +
3615C ALA* 2.4 39.1 + - - +
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Residues in contact with ARG3612 (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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3541C SER* 4.0 21.2 + - - +
3542C PHE* 5.8 0.4 - - - +
3608C LYS* 2.9 58.2 + - - +
3609C MET* 3.7 4.5 - - - +
3611C GLU* 1.3 81.2 + - + +
3613C MET* 1.3 53.4 + - - +
3615C ALA* 3.6 7.4 - - + -
3616C ALA* 2.5 36.6 - - - +
3797C THR* 4.4 8.8 + - - -
3798C SER* 3.3 28.7 + - - -
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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