Contacts of the helix formed by residues 397 - 408 (chain E) in PDB entry 3IKM
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 GLN 397 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393E LEU* 4.3 8.3 - - + +
394E GLU* 2.8 43.9 + - + +
395E LEU 3.2 2.8 + - - -
396E ARG* 1.3 76.3 - - - +
398E VAL* 1.3 62.8 + - + +
399E CYS* 3.0 7.7 + - - -
400E GLN* 3.6 14.0 + - - +
401E GLY* 3.9 4.2 + - - -
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Residues in contact with VAL 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E GLU 5.9 0.4 - - - +
395E LEU 5.4 1.3 - - - +
397E GLN* 1.3 77.0 - - + +
399E CYS* 1.3 61.3 + - - +
400E GLN 3.2 0.4 - - - -
401E GLY* 3.0 12.7 - - - +
402E LEU* 2.5 67.2 + - + +
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Residues in contact with CYS 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388E GLY* 5.0 8.1 - - - +
395E LEU* 2.6 39.0 - - - -
396E ARG* 3.4 15.3 - - - -
397E GLN 3.0 0.8 - - - +
398E VAL* 1.3 81.8 - - - +
400E GLN* 1.3 53.0 + - - +
402E LEU* 3.5 8.2 - - - +
403E PHE* 2.4 38.1 + - - +
413E VAL* 5.2 0.7 - - - +
415E PRO* 5.6 0.4 - - + -
417E TYR* 3.6 25.6 - - + -
443E VAL* 6.1 4.7 - - - -
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Residues in contact with GLN 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E ARG 6.2 0.4 - - - +
397E GLN 3.6 9.7 + - - +
398E VAL 3.2 0.2 - - - -
399E CYS* 1.3 74.6 - - - +
401E GLY* 1.3 54.7 + - - +
402E LEU 2.4 4.0 + - - -
403E PHE* 2.3 41.0 + - + -
404E ASN* 2.5 35.3 + - - +
417E TYR* 3.3 27.4 + - + +
121F PHE* 4.5 21.5 - - - +
122F ARG* 5.8 2.9 - - - +
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Residues in contact with GLY 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E GLN 3.9 2.0 + - - -
398E VAL* 2.9 21.7 + - - -
400E GLN* 1.3 78.7 - - - +
402E LEU* 1.3 58.2 + - - +
404E ASN* 4.4 4.2 - - - +
405E GLU* 2.8 28.8 + - - +
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Residues in contact with LEU 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398E VAL* 2.5 46.5 + - + +
399E CYS* 3.5 5.6 - - - +
400E GLN 2.4 5.4 + - - -
401E GLY* 1.3 72.9 - - - -
403E PHE* 1.3 68.6 + - - +
404E ASN 3.1 0.4 - - - -
405E GLU* 2.7 32.3 + - - +
406E LEU* 2.8 23.2 - - + +
413E VAL* 6.2 0.2 - - + -
443E VAL* 5.7 9.4 - - + -
468E ILE* 3.3 43.7 - - + -
471E LEU* 6.3 0.2 - - + -
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Residues in contact with PHE 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E CYS 2.4 23.3 + - - +
400E GLN* 2.3 22.4 + - + +
402E LEU* 1.3 72.5 - - - +
404E ASN* 1.3 79.9 + - - +
406E LEU* 3.1 5.5 - - - +
407E LEU* 3.3 40.6 + - + +
412E SER* 5.6 0.2 - - - -
413E VAL* 2.8 80.8 - - + +
415E PRO* 4.6 13.9 - - + -
417E TYR* 4.2 13.0 - - - -
120F VAL 3.6 18.6 - - - -
121F PHE 4.2 11.2 - - - -
122F ARG* 5.8 1.1 - - - -
124F GLN* 5.8 5.2 - - - -
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Residues in contact with ASN 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400E GLN* 2.5 56.5 + - - +
401E GLY* 3.8 3.5 + - - +
403E PHE* 1.3 84.7 - - - +
405E GLU* 1.3 54.0 + - - +
406E LEU 2.4 18.8 + - - -
407E LEU* 2.5 30.3 + - + +
408E GLU* 2.7 20.7 + - + -
120F VAL* 5.3 7.7 + - - +
121F PHE 5.8 1.0 + - - -
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Residues in contact with GLU 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E GLY 2.8 25.1 + - - +
402E LEU* 2.7 30.4 + - - +
404E ASN* 1.3 73.4 - - - +
406E LEU* 1.3 54.0 + - + +
408E GLU* 3.9 12.5 - - + +
409E ASN* 2.6 34.6 + - - +
468E ILE* 4.7 4.9 - - - +
469E SER* 5.2 5.5 - - - +
472E LYS* 4.7 20.9 + - + +
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Residues in contact with LEU 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E LEU* 6.0 2.5 - - + -
402E LEU* 2.8 40.0 + - + +
403E PHE 3.1 0.2 - - - +
404E ASN 2.4 13.5 + - - -
405E GLU* 1.3 75.6 - - + +
407E LEU* 1.3 66.0 + - - +
408E GLU 3.1 1.1 - - - -
409E ASN* 3.0 19.1 + - - +
410E GLY 3.2 7.1 + - - -
411E ILE* 3.2 26.2 + - + +
413E VAL* 3.0 32.1 - - + -
471E LEU* 4.9 18.2 - - + -
472E LYS* 5.1 10.3 - - - -
475E LEU* 3.6 31.4 - - + -
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Residues in contact with LEU 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E PHE* 3.3 38.8 - - + +
404E ASN* 2.5 21.0 + - - +
406E LEU* 1.3 65.1 - - - +
408E GLU* 1.3 52.3 - - - +
409E ASN 2.4 19.6 + - - -
410E GLY* 2.7 12.9 + - - -
411E ILE 2.6 37.0 + - - +
412E SER* 2.9 27.4 - - - +
413E VAL 3.4 9.9 - - - +
120F VAL* 4.3 21.8 - - + +
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Residues in contact with GLU 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E ASN* 2.7 29.0 + - + +
405E GLU* 3.9 11.0 - - + +
406E LEU 3.1 0.2 - - - -
407E LEU* 1.3 69.6 - - + +
409E ASN* 1.3 70.9 + - - +
484F ASN* 5.6 5.4 + - - +
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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