Contacts of the helix formed by residues 452 - 465 (chain E) in PDB entry 5MG3
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 PHE 452 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449E THR 4.9 6.0 + - - +
450E VAL* 4.2 3.0 - - - +
451E ALA* 1.4 72.3 - - - +
453E ALA* 1.3 70.7 + - - +
454E ARG 3.5 1.9 - - - +
455E GLU* 3.4 5.1 + - - +
456E ALA* 3.2 20.9 + - + +
326Y ILE* 3.8 31.2 - - + -
329Y CYS* 3.8 26.5 - - + -
330Y PHE* 3.7 48.7 - + + -
378Y ALA 3.3 28.3 - - - -
379Y LEU* 3.4 23.0 - - + +
383Y PHE* 4.4 13.2 - + - -
443Y ARG* 4.2 13.2 - - + -
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Residues in contact with ALA 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E PHE* 1.3 84.2 - - - +
454E ARG* 1.3 62.6 + - - +
456E ALA* 3.4 9.4 + - - +
457E ARG* 3.2 47.7 + - - +
326Y ILE* 4.2 26.3 - - + +
383Y PHE* 3.9 8.1 - - + -
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Residues in contact with ARG 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E PHE 3.5 1.4 - - - +
453E ALA* 1.3 78.5 - - - +
455E GLU* 1.3 78.0 + - - +
456E ALA 3.5 0.3 + - - -
457E ARG* 3.5 29.9 + - + +
458E THR* 3.6 9.9 + - - -
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Residues in contact with GLU 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ALA* 4.1 34.8 - - + +
452E PHE 3.5 6.1 - - - +
454E ARG* 1.3 93.7 - - - +
456E ALA* 1.3 55.4 + - - +
458E THR* 3.8 7.3 + - - +
459E GLU* 3.0 26.7 + - - +
379Y LEU* 3.5 26.6 - - + +
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Residues in contact with ALA 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E PHE* 3.2 15.2 + - + +
453E ALA 3.4 10.8 - - - +
455E GLU* 1.3 74.9 - - - +
457E ARG* 1.3 54.9 + - - +
459E GLU* 3.4 1.8 + - - +
460E VAL* 3.0 33.8 + - - +
379Y LEU* 3.5 33.1 - - + +
383Y PHE* 3.7 26.2 - - + -
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Residues in contact with ARG 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E ALA* 3.2 41.0 + - - +
454E ARG* 3.5 18.6 - - + +
456E ALA* 1.3 74.1 - - - +
458E THR* 1.4 54.9 + - - +
460E VAL* 3.4 4.8 + - - +
461E ARG* 2.9 29.4 + - - +
322Y ALA 5.4 5.5 + - - -
323Y SER* 5.8 4.2 - - - +
383Y PHE* 3.7 25.6 - - + -
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Residues in contact with THR 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E ARG* 3.6 9.5 + - - +
455E GLU* 4.2 8.3 - - - +
456E ALA 3.5 0.2 - - - -
457E ARG* 1.4 72.6 - - - +
459E GLU* 1.3 65.0 + - - +
461E ARG* 3.8 6.2 - - - +
462E LYS* 3.1 40.5 + - + +
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Residues in contact with GLU 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455E GLU 3.0 19.7 + - - +
456E ALA 3.4 7.6 + - - +
458E THR* 1.3 75.9 - - - +
460E VAL* 1.3 56.7 - - - +
462E LYS* 3.5 4.9 + - - +
463E VAL* 3.0 31.6 + - + +
372Y ARG* 2.8 39.4 + - - +
377Y GLY 6.1 0.5 - - - -
379Y LEU* 3.8 22.2 + - + +
380Y TYR* 3.6 29.2 + - + +
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Residues in contact with VAL 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456E ALA 3.0 18.3 + - - +
457E ARG* 3.4 5.8 + - - +
459E GLU* 1.3 70.6 - - - +
461E ARG* 1.4 64.3 + - - +
463E VAL* 3.2 2.3 + - - +
464E ILE* 3.0 44.9 + - + +
379Y LEU 4.6 0.2 - - - +
380Y TYR* 3.7 30.7 - - + +
383Y PHE* 3.7 26.2 - - + -
384Y ILE* 4.3 13.7 - - + +
387Y ILE* 4.2 17.9 - - + -
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Residues in contact with ARG 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457E ARG 2.9 21.2 + - - +
458E THR* 3.8 9.2 - - - +
459E GLU 3.5 0.2 - - - -
460E VAL* 1.4 74.0 - - - +
462E LYS* 1.3 69.7 + - + +
464E ILE* 3.5 37.8 + - - +
465E TRP* 3.0 28.3 + - + +
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Residues in contact with LYS 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E THR* 3.1 33.1 + - + +
459E GLU* 3.9 5.2 - - - +
461E ARG* 1.3 88.0 - - + +
463E VAL* 1.4 62.0 + - - +
465E TRP* 3.8 29.9 - - + +
466E PRO* 3.4 18.9 - - - +
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Residues in contact with VAL 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E GLU* 3.0 23.6 + - + +
460E VAL 3.2 1.5 + - - +
462E LYS* 1.4 73.0 - - - +
464E ILE* 1.3 65.7 + - - +
466E PRO* 3.6 4.2 - - - +
467E THR* 4.8 0.3 - - - +
469E GLN* 5.0 0.2 + - - -
242Y ARG* 2.8 43.4 + - - +
368Y LYS 6.3 0.2 - - - -
369Y VAL* 3.9 18.8 - - + -
372Y ARG* 4.0 27.1 - - - +
380Y TYR* 3.8 41.1 - - + +
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Residues in contact with ILE 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460E VAL* 3.0 38.2 + - + +
461E ARG* 3.5 38.8 - - - +
463E VAL* 1.3 79.3 - - + +
465E TRP* 1.4 63.0 + - - +
466E PRO 3.6 0.7 - - - -
467E THR* 3.1 21.0 + - - +
469E GLN* 3.1 40.5 + - + +
380Y TYR* 6.0 0.9 - - + -
384Y ILE* 4.7 11.0 - - + -
387Y ILE* 4.5 13.7 - - + -
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Residues in contact with TRP 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461E ARG* 3.0 20.8 + - + +
462E LYS* 3.8 31.4 - - + +
463E VAL 3.4 0.2 - - - -
464E ILE* 1.4 76.4 - - - +
466E PRO* 1.4 89.5 - - + +
467E THR 2.9 9.8 + - - +
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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