Contacts of the helix formed by residues 401 - 407 (chain A) in PDB entry 2D7I
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 TYR 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A TRP* 3.8 28.6 - + + -
398A MET* 2.8 14.6 + - + +
400A GLU* 1.3 99.0 - - - +
402A ALA* 1.3 64.6 + - - +
403A GLU 3.0 2.2 - - - -
404A TYR* 2.9 52.3 + + + +
405A ILE* 3.7 2.4 + - - +
435A PHE* 3.4 25.6 - + + -
436A LYS* 2.9 47.2 + - + +
439A MET* 3.7 27.1 - - + +
440A THR* 4.9 1.7 + - - -
452A PRO* 5.2 7.2 - - + -
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Residues in contact with ALA 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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394A ALA* 3.7 31.0 - - + +
395A GLU* 4.6 4.9 - - - +
398A MET* 3.4 9.5 + - + -
399A ASP 3.3 14.9 + - - +
400A GLU 3.1 0.8 - - - -
401A TYR* 1.3 77.3 - - - +
403A GLU* 1.3 57.8 + - - +
405A ILE* 2.9 34.9 + - - +
406A TYR* 3.4 24.3 + - + +
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Residues in contact with GLU 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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399A ASP 4.6 0.2 + - - -
400A GLU* 3.2 15.7 + - - +
402A ALA* 1.3 80.0 - - - +
404A TYR* 1.3 66.0 + - + +
406A TYR* 2.9 22.8 + - - -
407A GLN* 3.0 38.5 + - - +
413A ARG* 3.0 42.4 + - - -
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Residues in contact with TYR 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A TRP* 3.9 19.7 - + + -
400A GLU* 4.3 7.0 - - + -
401A TYR* 2.9 62.7 + + - +
403A GLU* 1.3 78.4 - - + +
405A ILE* 1.3 58.9 + - - +
407A GLN* 3.6 21.4 + - - +
408A ARG* 3.1 29.4 + - - +
436A LYS* 5.8 1.7 + - - -
452A PRO* 3.5 42.2 - - + +
453A VAL* 3.8 17.1 - - + +
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Residues in contact with ILE 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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290A TRP* 3.7 30.0 - - + +
291A GLU* 5.2 3.8 - - - -
292A MET* 3.9 21.1 - - + -
390A LEU* 5.6 3.1 - - + +
394A ALA* 3.8 16.6 - - + -
398A MET* 3.6 33.2 - - + -
401A TYR 4.1 6.3 - - - +
402A ALA* 2.9 13.1 + - - +
404A TYR* 1.3 77.7 - - - +
406A TYR* 1.3 62.3 + - + +
408A ARG* 3.3 5.5 + - - +
409A ARG* 3.1 25.8 + - + +
412A TYR* 4.0 29.2 - - + -
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Residues in contact with TYR 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LYS* 3.1 27.1 - - + +
394A ALA* 4.1 7.1 - - + +
395A GLU* 3.0 27.9 + - - +
402A ALA* 3.6 33.9 - - + +
403A GLU* 2.9 21.2 + - - +
405A ILE* 1.3 77.8 - - + +
407A GLN* 1.3 59.3 + - - +
408A ARG 3.0 6.8 + - - -
409A ARG 3.7 5.6 - - - +
410A PRO* 3.1 30.1 - - - +
412A TYR* 3.3 35.9 - + + -
413A ARG* 3.3 39.2 + - + +
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Residues in contact with GLN 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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403A GLU* 3.0 41.4 + - - +
404A TYR* 3.6 32.5 - - - +
405A ILE 3.3 0.6 - - - -
406A TYR* 1.3 76.0 - - - +
408A ARG* 1.3 61.1 + - + +
410A PRO* 4.7 5.5 - - - +
413A ARG* 3.8 7.6 - - - +
452A PRO 4.8 2.6 - - - +
453A VAL* 5.1 4.5 - - - +
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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