Contacts of the helix formed by residues 476 - 480 (chain P) in PDB entry 1E33
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 GLN 476 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85P MET 4.1 13.6 + - - +
86P GLY* 3.0 16.2 + - - +
87P MET* 4.1 11.0 - - + -
92P LEU* 5.0 1.8 - - + -
98P GLY* 3.3 13.8 + - - -
99P GLY 3.0 44.4 + - - +
101P PRO* 4.4 12.6 - - + +
134P PHE* 4.9 0.2 - - - -
474P PRO* 3.3 10.7 + - - +
475P SER* 1.3 68.9 - - - +
477P VAL* 1.3 67.8 + - + +
479P ARG* 2.8 60.3 + - - +
480P GLY 5.5 0.2 - - - +
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Residues in contact with VAL 477 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P THR* 5.7 2.2 - - + -
87P MET* 5.1 3.4 - - + -
88P TYR 3.8 18.9 + - - +
89P PRO* 3.3 35.7 - - + +
90P GLY* 4.8 1.6 - - - +
91P VAL* 4.3 17.9 - - - +
92P LEU* 3.8 26.5 - - + -
96P SER* 5.5 4.3 + - - +
475P SER* 3.2 2.6 + - - -
476P GLN* 1.3 82.3 - - + +
478P ALA* 1.3 59.2 + - - +
479P ARG 3.2 1.4 + - - -
480P GLY* 3.6 10.4 + - - +
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Residues in contact with ALA 478 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P PRO* 5.4 4.5 - - + -
475P SER* 3.0 25.2 + - - +
476P GLN 3.2 0.4 - - - -
477P VAL* 1.3 74.4 - - - +
479P ARG* 1.3 61.4 + - - +
480P GLY* 2.9 7.9 + - - +
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Residues in contact with ARG 479 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97P ARG* 2.6 62.8 + - + +
98P GLY* 3.9 7.0 - - - +
134P PHE* 4.2 13.3 - - - -
475P SER 3.8 8.3 + - - +
476P GLN* 2.8 62.1 + - - +
478P ALA* 1.3 77.2 - - - +
480P GLY* 1.3 51.5 + - - +
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Residues in contact with GLY 480 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96P SER* 3.6 5.9 + - - -
97P ARG* 2.7 38.2 + - - +
98P GLY 4.5 0.7 + - - -
476P GLN 4.5 0.4 + - - +
477P VAL 3.6 10.3 + - - +
478P ALA 2.9 7.4 - - - -
479P ARG* 1.3 79.9 - - - +
481P GLU* 1.3 61.6 + - - -
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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