Contacts of the helix formed by residues 401 - 411 (chain A) in PDB entry 2JI8
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 ALA 401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLY* 1.3 70.2 - - - -
402A ASN* 1.3 66.9 + - - +
403A ALA 3.3 0.4 - - - +
404A LEU* 3.2 1.9 + - - +
405A ASP* 3.1 33.0 + - - -
483A TYR* 3.5 31.0 - - + -
553A SER* 4.0 13.9 - - - -
554A GLY* 4.6 0.9 - - - -
1566A TPP 3.2 29.6 + - - +
1569A FYN 4.2 7.9 - - - -
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Residues in contact with ASN 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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377A TYR* 3.5 17.2 - - + -
401A ALA* 1.3 83.3 - - - +
403A ALA* 1.3 57.9 + - - +
405A ASP* 4.6 1.1 - - - +
406A ASN* 2.7 49.7 + - - +
483A TYR* 3.5 12.5 + - - +
550A GLY* 3.3 7.5 - - - -
551A VAL* 2.8 54.6 + - - +
554A GLY* 4.0 7.4 - - - -
1566A TPP 2.7 31.3 + - - +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.8 8.3 - - + -
381A LEU* 5.1 0.9 - - - -
398A ASN* 3.0 10.0 + - - -
399A GLU 3.9 4.3 - - - +
400A GLY* 4.5 1.8 - - - -
401A ALA 3.3 0.6 - - - -
402A ASN* 1.3 76.2 - - - +
404A LEU* 1.3 57.2 + - - +
407A THR* 2.6 29.3 + - - -
449A VAL* 3.9 1.9 - - + +
450A GLU 4.2 0.7 - - - -
451A GLY* 3.6 36.8 - - - +
477A MET* 4.0 19.3 - - + -
1566A TPP 3.2 10.3 + - - +
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Residues in contact with LEU 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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398A ASN* 3.4 23.6 - - - +
399A GLU* 4.0 3.4 - - - -
400A GLY* 3.3 24.3 - - - +
401A ALA 3.2 3.1 + - - +
402A ASN 3.2 0.4 - - - -
403A ALA* 1.3 77.6 - - - +
405A ASP* 1.3 64.4 + - - +
406A ASN 3.3 0.2 - - - -
407A THR 3.3 0.9 + - - -
408A ARG* 2.9 45.8 + - - +
419A ARG* 3.6 21.8 - - - +
421A ASP* 3.7 22.0 - - + +
422A SER* 4.2 8.5 - - - +
1569A FYN 3.6 40.4 - - - +
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Residues in contact with ASP 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ALA* 3.1 14.5 + - - +
402A ASN* 4.5 3.1 - - - +
404A LEU* 1.3 82.9 - - - +
406A ASN* 1.3 63.9 + - - +
408A ARG* 3.1 33.2 + - - +
409A MET* 3.3 22.9 + - - +
553A SER 3.7 4.5 - - - +
554A GLY* 3.3 8.6 - - - -
555A ARG* 2.5 49.5 + - + +
556A ILE 4.2 0.7 + - - -
1569A FYN 4.0 18.7 + - - +
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Residues in contact with ASN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.7 22.2 - - + +
378A SER* 5.4 2.1 + - - -
381A LEU* 3.8 17.3 - - + -
402A ASN* 2.7 46.3 + - - +
405A ASP* 1.3 77.3 - - - +
407A THR* 1.3 59.4 + - - +
409A MET* 3.5 20.4 + - - +
410A ILE* 3.0 40.5 + - + +
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Residues in contact with THR 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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381A LEU* 3.4 12.3 - - - +
396A LEU* 4.1 10.5 - - + -
398A ASN* 3.2 20.9 - - - +
403A ALA 2.6 26.7 + - - -
404A LEU 3.3 1.6 + - - -
406A ASN* 1.3 75.6 - - - +
408A ARG* 1.3 59.6 + - - +
411A VAL* 2.8 54.1 + - + +
419A ARG* 3.8 8.5 + - - +
449A VAL* 3.3 21.0 - - + +
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Residues in contact with ARG 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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248A GLY* 3.8 23.7 - - - +
251A LYS* 2.8 50.1 + - + +
404A LEU* 2.9 23.7 + - - +
405A ASP* 3.1 35.3 + - - +
407A THR* 1.3 76.3 - - - +
409A MET* 1.3 58.9 + - - +
411A VAL 4.2 0.2 - - - +
419A ARG* 3.4 26.6 - - - +
421A ASP* 5.1 2.4 + - - -
555A ARG* 4.3 0.2 - - - +
1569A FYN 2.9 82.0 + - - +
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Residues in contact with MET 409 (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 LYS* 4.9 0.7 + - - -
362A LEU* 3.8 27.6 - - + -
365A LYS* 6.2 1.8 - - + +
378A SER* 5.5 1.8 - - - +
405A ASP 3.3 14.6 + - - +
406A ASN* 3.6 25.1 - - - +
407A THR 3.2 0.2 - - - -
408A ARG* 1.3 82.9 - - - +
410A ILE* 1.3 70.1 + - + +
412A ASP* 4.4 4.0 - - - +
555A ARG* 5.7 1.8 - - - -
1569A FYN 3.4 90.0 + - + +
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Residues in contact with ILE 410 (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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362A LEU* 4.0 17.2 - - + +
366A MET* 3.6 25.6 - - + -
377A TYR 3.6 24.2 - - - +
378A SER* 3.8 19.3 - - - +
381A LEU* 3.8 28.9 - - + +
385A ARG* 3.5 20.1 + - + -
406A ASN* 3.0 24.6 + - + +
407A THR 4.6 0.2 - - - +
409A MET* 1.3 99.0 - - + +
411A VAL* 1.3 59.9 + - - +
412A ASP* 3.2 12.6 + - - +
1569A FYN 5.6 0.3 + - - -
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Residues in contact with VAL 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LYS* 3.4 23.2 - - - -
381A LEU* 4.1 19.7 - - + +
384A VAL* 3.9 23.1 - - + +
385A ARG* 4.1 5.8 - - - +
388A MET* 3.8 33.2 - - + -
396A LEU* 4.3 7.9 - - + -
407A THR* 2.8 44.3 + - + +
410A ILE* 1.3 68.6 - - - +
412A ASP* 1.3 62.0 + - - +
413A MET* 3.7 15.2 + - - +
419A ARG* 5.4 1.3 + - - +
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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