Contacts of the helix formed by residues 748 - 755 (chain C) in PDB entry 3V53
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 ALA 748 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746C PRO* 4.6 0.8 - - - +
747C THR* 1.3 83.6 + - - +
749C LYS* 1.3 65.7 + - - +
750C PRO* 3.3 10.6 - - + -
751C GLU* 3.4 10.3 + - + +
752C LEU* 2.9 24.1 + - - +
824C VAL* 5.1 0.4 - - - -
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Residues in contact with LYS 749 (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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747C THR 4.0 2.0 + - - -
748C ALA* 1.3 70.2 - - - +
750C PRO* 1.4 74.5 - - + +
752C LEU* 4.3 4.7 - - - -
753C PHE* 2.9 55.5 + - + +
805C GLN* 3.2 33.0 + - - +
808C LEU* 4.3 3.3 - - + +
820C GLU* 3.7 37.4 + - + +
824C VAL* 4.7 15.2 - - + +
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Residues in contact with PRO 750 (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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748C ALA* 3.6 11.4 - - + -
749C LYS* 1.4 100.3 - - + +
751C GLU* 1.3 62.0 + - - +
753C PHE* 3.4 4.6 + - + +
754C ALA* 3.2 20.1 + - - +
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Residues in contact with GLU 751 (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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746C PRO* 4.0 26.8 - - + +
747C THR 5.3 0.9 + - - -
748C ALA* 3.4 12.7 + - + +
750C PRO* 1.3 75.7 - - - +
752C LEU* 1.3 68.4 + - - +
754C ALA* 2.9 19.0 + - + +
755C TYR* 3.2 10.0 + - - +
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Residues in contact with LEU 752 (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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745C ILE* 4.1 0.7 - - + -
746C PRO* 3.4 36.1 - - + +
747C THR 5.4 0.2 - - - +
748C ALA 2.9 18.0 + - - +
749C LYS* 3.6 3.1 - - - +
751C GLU* 1.3 76.0 - - - +
753C PHE* 1.3 62.7 + - + +
755C TYR* 3.0 26.2 + - - +
824C VAL* 3.4 49.1 - - + +
827C TRP* 3.7 22.8 - - + -
828C ARG* 3.9 12.6 - - + +
831C ILE* 3.5 27.1 - - + -
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Residues in contact with PHE 753 (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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749C LYS* 2.9 42.6 + - + +
750C PRO* 3.8 4.7 - - + +
752C LEU* 1.3 93.2 - - + +
754C ALA* 1.3 59.6 + - - +
755C TYR 3.4 3.5 + - - +
804C PRO* 3.6 39.2 - - + +
805C GLN* 3.4 47.6 - - + -
808C LEU* 3.7 24.7 - - + -
820C GLU 5.7 0.2 - - - -
823C ILE* 3.9 20.2 - - + -
824C VAL* 4.6 5.2 - - + -
827C TRP* 4.5 4.6 + + + -
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Residues in contact with ALA 754 (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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750C PRO 3.2 11.2 + - - +
751C GLU* 2.9 14.5 + - + +
753C PHE* 1.3 79.2 - - - +
755C TYR* 1.3 63.5 + - - +
756C PRO* 3.4 4.7 - - - +
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Residues in contact with TYR 755 (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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744C LYS* 4.2 26.3 - - + +
746C PRO* 4.2 17.0 - - + -
751C GLU 3.2 5.4 + - - +
752C LEU* 3.0 20.6 + - - +
753C PHE 3.4 3.1 - - - +
754C ALA* 1.3 77.3 - - - +
756C PRO* 1.3 83.6 - - + +
757C LEU* 2.8 33.2 + - + +
827C TRP* 4.9 4.4 + - + -
831C ILE* 3.6 38.5 - - + +
835C GLU* 3.5 31.5 + - - +
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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