Contacts of the helix formed by residues 401 - 405 (chain C) in PDB entry 1N8Y
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 401 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389C LEU* 5.7 1.1 - - + -
391C ILE* 3.9 22.4 - - + -
394C TRP* 4.0 26.7 - - + +
400C ASP* 1.3 70.4 - - - +
402C SER* 1.3 52.5 + - - +
403C VAL 3.2 2.7 - - - -
404C PHE* 2.7 41.1 + - + +
424C LEU* 3.7 38.6 - - + -
427C LEU* 4.7 4.0 - - + -
429C ILE* 4.2 20.6 - - + -
432C LEU* 2.7 29.9 + - + +
433C GLY 4.8 0.9 - - - -
434C LEU* 3.7 26.9 - - + +
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Residues in contact with SER 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C ASP* 2.7 35.6 + - - -
401C LEU* 1.3 75.8 - - - +
403C VAL* 1.3 58.1 + - - +
404C PHE 3.0 0.7 - - - -
405C GLN* 2.9 52.3 + - - +
432C LEU 4.0 0.4 + - - -
433C GLY* 4.5 9.6 + - - -
506C GLN* 4.9 2.8 + - - -
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Residues in contact with VAL 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C PRO 4.9 2.0 - - - +
376C LEU* 3.7 40.4 - - + +
377C GLN* 4.7 11.4 - - + +
379C PHE* 3.5 27.4 - - + +
380C GLU* 3.9 7.5 + - - +
394C TRP* 3.5 31.0 - - + -
398C LEU* 4.3 19.1 - - + -
400C ASP 5.0 0.4 + - - -
401C LEU 3.0 2.4 + - - -
402C SER* 1.3 75.8 - - - +
404C PHE* 1.3 69.6 + - + +
405C GLN 3.4 1.0 + - - -
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Residues in contact with PHE 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C LEU* 3.8 21.1 - - + -
355C PHE* 3.6 30.7 - + - -
379C PHE* 3.8 29.4 - + + -
382C LEU* 4.1 16.6 - - + -
385C ILE* 5.3 0.2 - - + -
389C LEU* 4.0 22.9 - - + -
391C ILE* 4.2 5.6 - - + -
394C TRP* 3.8 25.6 - + - -
401C LEU* 2.7 29.7 + - + +
403C VAL* 1.3 73.5 - - + +
405C GLN* 1.3 62.2 + - - +
406C ASN 3.2 3.8 - - - -
407C LEU* 3.1 33.3 + - + +
434C LEU* 3.9 21.7 - - + +
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Residues in contact with GLN 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C GLU* 6.2 1.1 - - - +
401C LEU 4.0 0.2 + - - -
402C SER* 2.9 37.2 + - - +
403C VAL 3.4 2.0 + - - +
404C PHE* 1.3 75.2 - - - +
406C ASN* 1.3 59.1 + - - +
407C LEU 3.5 0.2 - - - -
433C GLY 4.2 17.0 - - - +
435C ARG* 2.8 53.0 + - - +
436C SER* 2.7 36.1 + - - -
506C GLN* 4.8 6.3 - - - +
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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