Contacts of the helix formed by residues 413 - 418 (chain A) in PDB entry 4H3T
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 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A ALA 3.0 17.2 + - - +
410A ALA 3.6 9.4 - - - +
411A GLN 3.2 0.4 - - - -
412A ALA* 1.3 74.7 - - - +
414A GLY* 1.3 63.3 + - - +
415A TYR 3.2 0.4 - - - -
416A VAL* 3.1 9.7 + - + +
417A ALA 3.0 17.5 + - - -
452A LEU* 3.6 29.0 - - + +
456A ILE* 3.9 38.6 - - + -
492A ALA* 3.5 24.2 - - - +
495A LEU* 4.1 13.0 - - + -
496A ALA* 3.8 20.9 - - + +
518A PHE* 3.7 18.4 - - + -
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Residues in contact with GLY 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ALA 3.6 4.9 + - - -
411A GLN* 2.9 14.8 + - - -
413A LEU* 1.3 78.4 - - - +
415A TYR* 1.3 60.9 + - - +
417A ALA* 4.1 2.9 - - - -
418A GLU* 3.1 26.0 + - - +
449A ARG* 3.4 38.8 - - - +
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Residues in contact with TYR 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A GLN* 4.4 6.8 + - + -
412A ALA* 3.3 23.3 + - - +
413A LEU 3.2 0.4 - - - -
414A GLY* 1.3 74.6 - - - +
416A VAL* 1.3 60.3 + - - +
418A GLU* 3.5 32.1 - - - +
419A ALA* 3.7 5.7 + - - +
449A ARG* 6.3 0.2 - - - -
514A GLY* 3.5 34.2 - - - +
517A ARG* 3.5 48.7 - - + -
521A MSE 4.0 28.9 - - + -
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Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU* 3.1 10.8 + - + +
415A TYR* 1.3 76.9 - - - +
417A ALA* 1.3 63.9 + - - +
418A GLU 3.2 0.4 - - - -
419A ALA* 3.1 21.6 + - - +
420A ARG* 4.6 1.2 + - - -
452A LEU* 4.7 1.8 - - + -
496A ALA* 3.9 26.5 - - + +
499A GLU* 3.4 33.5 - - + +
500A LEU* 4.2 14.1 - - + -
503A LEU* 5.5 0.9 - - - +
514A GLY* 4.0 13.7 - - - +
515A GLU* 4.2 6.7 - - - +
518A PHE* 3.9 29.2 - - + -
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Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU 3.0 13.1 + - - +
414A GLY 3.3 7.2 + - - +
416A VAL* 1.3 76.6 - - - +
418A GLU* 1.3 61.5 + - - +
419A ALA 3.5 0.5 + - - -
420A ARG* 3.0 36.2 + - - +
421A TYR* 4.3 1.4 - - - -
448A ALA* 3.6 31.6 - - - +
449A ARG* 3.8 12.1 - - - -
452A LEU* 3.8 18.1 - - + +
499A GLU* 5.1 0.9 - - - -
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A GLY 3.1 17.1 + - - +
415A TYR* 3.5 32.7 - - - +
417A ALA* 1.3 76.0 - - - +
419A ALA* 1.4 62.5 + - - +
420A ARG 3.2 3.4 - - - -
421A TYR* 2.9 24.6 + - - +
422A LEU* 3.2 23.4 + - + +
437A VAL* 3.8 22.1 - - + +
445A ALA* 4.2 10.8 - - + -
449A ARG* 2.8 32.4 + - + +
517A ARG* 4.3 7.3 + - - -
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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