Contacts of the helix formed by residues 398 - 403 (chain B) in PDB entry 5Y7G
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 CYS 398 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B PHE* 2.9 41.6 + - + +
395B GLY 3.9 2.0 - - - -
397B LEU* 1.3 79.0 - - - +
399B TRP* 1.3 65.5 + - - +
400B GLU 3.1 3.4 - - - -
401B ALA* 2.8 14.2 + - + -
402B ILE* 3.0 15.0 + - + +
434B PHE* 3.8 27.6 - - + -
437B CYS* 3.7 23.6 - - + -
438B LEU* 4.1 16.8 - - - -
491B PHE* 5.5 0.2 - - - -
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Residues in contact with TRP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B GLU* 3.7 6.7 + - + -
395B GLY 3.2 23.6 + - - -
396B LEU* 3.4 20.0 - - + +
397B LEU 3.3 2.8 - - - -
398B CYS* 1.3 75.6 - - - +
400B GLU* 1.3 69.0 + - + +
402B ILE* 3.2 6.0 + - + -
403B PHE* 3.1 57.6 + + + +
453B ARG* 3.7 15.7 - - + +
457B LYS* 3.4 54.6 - - + +
460B LEU* 4.0 26.9 - - + -
462B SER* 3.8 15.9 - - - -
465B VAL* 3.5 26.2 - - + -
467B TRP* 4.3 11.9 - + - -
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B CYS 3.1 1.2 - - - -
399B TRP* 1.3 84.3 - - + +
401B ALA* 1.3 59.5 + - - +
403B PHE* 4.0 1.9 - - - -
404B ALA* 3.3 17.0 + - - +
433B LEU* 3.3 21.1 - - + +
437B CYS* 4.3 9.2 - - - -
453B ARG* 2.4 48.9 + - - +
457B LYS* 6.1 0.9 - - - -
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B CYS* 2.8 15.7 + - + +
400B GLU* 1.3 73.3 - - - +
402B ILE* 1.3 59.5 + - - +
404B ALA* 3.6 4.2 + - - +
430B ARG* 2.7 35.2 + - + +
433B LEU* 3.9 26.7 - - + +
434B PHE* 3.5 42.0 - - + -
437B CYS* 4.3 1.8 - - - -
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B PHE* 4.0 8.7 - - + -
395B GLY* 4.0 21.3 - - - +
398B CYS* 3.0 14.3 + - + +
399B TRP* 3.8 6.7 - - + +
401B ALA* 1.3 79.6 - - - +
403B PHE* 1.3 76.1 + - + +
404B ALA 3.3 1.3 + - - -
410B PHE* 3.9 1.7 - - - -
418B PRO* 3.3 41.2 - - + +
421B LEU* 5.4 1.1 - - + -
426B PHE* 4.6 10.3 - - + -
430B ARG* 3.9 2.8 + - - -
434B PHE* 4.5 12.8 - - + -
463B PRO* 4.8 13.5 - - + -
464B PHE* 3.5 34.3 - - + -
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B GLU* 3.8 30.1 - - + +
203B VAL* 3.6 23.2 - - + +
399B TRP* 3.1 65.8 + + + +
400B GLU* 4.0 3.1 - - - -
402B ILE* 1.3 89.7 - - + +
404B ALA* 1.3 65.9 + - - +
405B ALA* 3.7 0.7 + - - +
410B PHE* 3.8 26.0 - + - -
415B HIS 4.3 6.5 - - - -
416B SER 3.5 26.5 - - - -
417B ALA* 4.7 2.5 - - - -
418B PRO* 5.0 0.2 - - + -
461B GLN 4.0 11.0 - - - -
462B SER* 4.3 5.2 - - - -
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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