Contacts of the helix formed by residues 649 - 655 (chain C) in PDB entry 4YZ9
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 LEU 649 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648C THR* 1.3 73.2 - - - +
650C GLN* 1.3 57.5 + - - +
652C TYR* 3.3 14.5 + - + -
653C VAL* 3.0 29.0 + - + +
668C LEU* 3.6 40.4 - - + -
672C THR* 5.5 0.2 - - - +
691C PRO* 3.4 22.6 + - + +
694C ILE* 2.7 33.8 + - + +
696C ILE* 4.2 4.6 - - + +
763C VAL* 3.4 32.8 - - + -
766C TYR* 4.8 0.4 - - + -
767C VAL* 3.8 21.1 - - + -
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Residues in contact with GLN 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C THR* 3.0 11.8 + - - +
649C LEU* 1.3 75.3 - - - +
651C GLU* 1.3 66.3 + - - +
653C VAL 3.6 0.2 + - - -
654C GLU* 3.0 48.7 + - - +
691C PRO* 3.8 12.2 + - + +
692C HIS* 3.0 38.2 + - + -
766C TYR* 3.4 23.0 + - - +
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Residues in contact with GLU 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647C ALA* 4.1 18.5 - - + +
648C THR* 2.5 46.0 + - - +
650C GLN* 1.3 76.2 - - - +
652C TYR* 1.3 58.3 + - - +
654C GLU* 5.0 1.6 - - - -
655C GLN* 2.6 61.6 + - + +
660C HIS* 3.9 3.6 - - + -
714C LEU* 4.2 13.6 - - - +
715C CYS 4.5 8.7 - - - +
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Residues in contact with TYR 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C THR 3.1 5.0 + - - +
649C LEU* 3.3 26.4 + - + +
651C GLU* 1.3 78.8 - - - +
653C VAL* 1.3 70.1 + - + +
655C GLN 3.8 9.9 - - - +
660C HIS* 3.6 40.7 + + + -
661C LEU 5.1 0.2 - - - -
663C LEU* 2.8 35.6 + - + -
664C GLU 3.4 1.2 - - - -
665C PRO* 3.3 34.8 - - + +
668C LEU* 3.7 28.7 - - + -
696C ILE* 4.3 14.6 - - + -
767C VAL* 4.9 6.1 - - + -
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Residues in contact with VAL 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C LEU* 3.0 21.4 + - + +
652C TYR* 1.3 85.9 - - + +
654C GLU* 1.3 62.4 + - + +
655C GLN 3.6 4.5 + - - +
766C TYR* 3.5 31.2 - - + +
767C VAL* 4.1 23.8 - - + +
770C GLU* 3.7 15.8 - - - +
771C GLY* 3.4 34.3 - - - +
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Residues in contact with GLU 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650C GLN* 3.0 43.3 + - - +
651C GLU* 3.5 1.1 - - - -
653C VAL* 1.3 79.6 - - + +
655C GLN* 1.3 63.5 + - - +
658C PHE* 4.2 13.8 - - - -
766C TYR* 3.3 21.1 + - + +
771C GLY* 5.5 5.3 - - - +
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Residues in contact with GLN 655 (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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651C GLU* 2.6 51.1 + - + +
652C TYR 3.8 10.4 - - - +
653C VAL 3.4 4.4 - - - +
654C GLU* 1.3 77.1 - - - +
658C PHE* 3.1 73.7 + - - +
660C HIS* 3.3 26.0 - - + +
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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