Contacts of the helix formed by residues 400 - 408 (chain A) in PDB entry 4JYI
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 PRO 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A TRP* 4.2 3.8 - - + +
222A SER* 3.9 26.5 - - - +
223A GLU* 4.9 1.8 - - - +
226A THR* 3.4 27.8 - - + +
398A SER 4.5 1.6 - - - +
399A MET* 1.3 87.5 - - + +
401A PRO* 1.3 71.6 - - + +
402A LEU 3.2 1.6 - - - +
403A ILE* 3.0 37.1 + - + +
404A GLN 3.0 10.2 + - - -
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Residues in contact with PRO 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A MET 3.3 2.2 - - - +
400A PRO* 1.3 87.0 - - + +
402A LEU* 1.3 57.3 + - + +
404A GLN* 3.3 18.5 + - - +
405A GLU* 2.9 28.8 + - - +
630G HIS* 3.9 6.6 + - + +
632G ILE* 3.5 24.5 - - + -
701G FLC 3.6 23.6 - - + +
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Residues in contact with LEU 402 (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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226A THR* 3.9 24.0 - - + +
229A ILE* 3.7 29.2 - - + -
230A ILE* 3.8 17.5 - - + -
400A PRO* 3.2 1.4 + - - +
401A PRO* 1.3 81.0 - - - +
403A ILE* 1.3 58.1 + - + +
405A GLU* 3.3 12.5 + - - +
406A MET* 3.0 49.6 + - - +
632G ILE* 3.8 29.5 - - + +
633G LEU* 4.4 6.3 - - + +
636G LEU* 3.7 24.5 - - + -
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Residues in contact with ILE 403 (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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218A TRP* 5.1 0.2 - - + -
222A SER* 3.7 29.6 - - - +
225A ALA* 4.2 4.9 - - + -
226A THR* 3.8 9.9 - - - +
229A ILE* 4.0 17.7 - - + -
399A MET* 3.8 24.0 - - + -
400A PRO* 3.0 27.6 + - + +
402A LEU* 1.3 73.8 - - - +
404A GLN* 1.3 66.1 + - - +
406A MET* 3.3 6.1 + - - +
407A MET* 3.1 33.3 + - + +
501A JYI 3.6 36.3 - - + -
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Residues in contact with GLN 404 (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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392A LYS* 6.5 1.3 - - + -
398A SER* 3.7 16.7 + - - -
399A MET* 2.7 38.6 - - + +
400A PRO 3.0 7.9 + - - +
401A PRO* 3.4 14.3 - - - +
403A ILE* 1.3 78.0 - - - +
405A GLU* 1.3 63.2 + - - +
407A MET* 3.4 3.8 + - - +
408A GLU* 3.4 24.2 + - + +
630G HIS* 3.2 31.2 + - - +
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Residues in contact with GLU 405 (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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251A ILE* 5.8 0.2 - - - +
255A LYS* 3.2 40.3 + - - +
401A PRO 2.9 15.8 + - - +
402A LEU* 3.6 6.5 - - + +
403A ILE 3.2 0.2 - - - -
404A GLN* 1.3 78.2 - - - +
406A MET* 1.3 62.8 + - - +
408A GLU* 3.4 11.5 - - - +
630G HIS* 3.4 46.0 - - + +
632G ILE* 3.6 8.3 + - - +
633G LEU* 3.0 47.5 + - + +
634G HIS* 4.3 11.1 + - - -
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Residues in contact with MET 406 (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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229A ILE* 4.1 23.3 - - + -
233A VAL* 5.8 0.9 - - + -
254A LEU* 3.5 40.8 - - + +
255A LYS* 3.8 26.3 - - + +
258A CYS* 3.6 27.8 - - + -
402A LEU* 3.0 30.9 + - - +
403A ILE* 3.3 4.9 + - - +
405A GLU* 1.3 77.2 - - - +
407A MET* 1.3 68.9 + - + +
408A GLU 3.0 12.5 + - - +
633G LEU* 3.8 32.8 - - + -
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Residues in contact with MET 407 (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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255A LYS 4.8 6.1 - - - +
258A CYS* 4.7 17.0 - - + -
259A LEU* 4.8 22.2 - - + -
262A LEU* 6.4 0.2 - - + -
385A ALA* 5.2 7.0 - - + -
388A VAL* 3.8 45.5 - - + -
389A ILE* 5.3 11.1 - - + +
399A MET* 5.7 0.4 - - - -
403A ILE* 3.1 26.8 + - + +
404A GLN* 3.4 4.9 + - - +
406A MET* 1.3 86.1 - - + +
408A GLU* 1.3 63.0 + - - +
501A JYI 5.2 7.4 - - + -
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Residues in contact with GLU 408 (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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255A LYS* 4.0 20.7 + - - +
404A GLN* 3.4 15.8 + - + +
405A GLU* 3.4 18.6 - - - +
406A MET 3.0 8.4 + - - +
407A MET* 1.3 82.5 - - - +
630G HIS* 3.9 24.2 + - - +
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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