Contacts of the helix formed by residues 394 - 405 (chain A) in PDB entry 4IYM
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 ASN 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A VAL* 3.5 15.6 - - - +
392A ALA* 3.5 1.4 - - - +
393A ARG* 1.3 86.1 - - - +
395A TYR* 1.3 58.2 + - - +
396A GLU* 3.4 9.0 + - - +
397A GLU* 2.8 36.8 + - - +
398A ALA* 3.0 29.5 + - - +
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Residues in contact with TYR 395 (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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253A ILE* 5.8 0.9 - - + -
255A MSE 3.8 35.4 - - + -
288A VAL* 3.8 6.8 - - - +
394A ASN* 1.3 76.9 - - - +
396A GLU* 1.3 77.7 + - + +
398A ALA* 3.3 8.7 + - + +
399A LEU* 2.9 35.1 + - + +
413A ILE* 4.2 5.8 - - + -
420A ALA* 3.6 19.0 + - + -
423A ASP* 2.8 29.1 + - + -
424A PHE* 2.9 47.2 + + + -
427A ARG* 4.0 2.9 - - - -
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Residues in contact with GLU 396 (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 ASN* 3.4 8.5 + - - +
395A TYR* 1.3 87.0 - - + +
397A GLU* 1.3 65.7 + - - +
399A LEU* 3.4 6.7 + - - +
400A SER* 3.0 24.1 + - - -
427A ARG* 2.9 44.7 + - - -
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Residues in contact with GLU 397 (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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391A ARG 3.9 5.2 - - - +
392A ALA* 3.4 10.6 - - + -
393A ARG* 2.7 63.8 + - - +
394A ASN* 2.8 28.3 + - - +
396A GLU* 1.3 73.6 - - - +
398A ALA* 1.3 62.9 + - - +
400A SER* 2.6 25.7 + - - +
401A LEU* 3.5 14.5 + - + +
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Residues in contact with ALA 398 (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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253A ILE* 3.9 19.2 - - + +
286A VAL* 3.7 13.5 - - + -
288A VAL* 3.8 16.4 - - + -
392A ALA* 3.7 19.7 - - + -
394A ASN 3.0 17.3 + - - +
395A TYR* 3.5 6.1 - - + +
397A GLU* 1.3 76.9 - - - +
399A LEU* 1.3 61.5 + - - +
401A LEU* 3.4 7.4 + - - +
402A PRO* 3.1 19.9 - - - +
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Residues in contact with LEU 399 (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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395A TYR* 2.9 27.3 + - + +
396A GLU* 3.7 9.2 - - - +
398A ALA* 1.3 75.5 - - - +
400A SER* 1.3 62.9 + - - +
401A LEU 3.2 1.0 + - - -
402A PRO* 3.3 5.0 - - - +
403A MSE 3.3 33.3 + - + +
424A PHE* 3.5 43.9 - - + +
427A ARG* 3.5 46.0 - - + +
428A ILE* 3.7 22.0 - - + -
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Residues in contact with SER 400 (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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396A GLU 3.0 13.0 + - - -
397A GLU* 2.6 26.0 + - - +
399A LEU* 1.3 77.5 - - - +
401A LEU* 1.3 58.5 + - - +
403A MSE 3.8 9.4 - - - -
404A LYS* 2.9 50.6 + - - +
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Residues in contact with LEU 401 (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 HIS* 4.0 7.0 - - + -
286A VAL* 3.9 27.1 - - + -
373A PRO* 3.7 28.3 - - + -
378A TYR* 3.4 33.0 + - + +
390A VAL* 3.8 27.1 - - + -
392A ALA* 4.6 5.6 - - + -
397A GLU* 3.9 18.2 - - + +
398A ALA* 3.4 3.3 + - - +
399A LEU 3.2 1.4 - - - -
400A SER* 1.3 80.0 + - - +
402A PRO* 1.4 74.6 - - + +
404A LYS* 3.9 2.7 - - - +
405A HIS* 3.2 17.5 + - - +
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Residues in contact with PRO 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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251A HIS* 3.7 30.2 - - + +
253A ILE* 4.0 18.4 - - + -
398A ALA 3.1 18.8 - - - +
399A LEU 3.3 12.1 - - - +
401A LEU* 1.4 85.2 - - + +
403A MSE 1.3 48.4 + - - +
404A LYS 3.4 0.3 + - - -
405A HIS* 3.4 7.3 + - + +
411A VAL* 4.0 9.2 - - + -
424A PHE* 4.4 2.7 - - + -
428A ILE* 3.8 12.1 - - + -
429A ASN* 3.8 0.7 - - - +
430A ILE* 3.7 25.1 - - + +
452A LYS* 2.7 30.7 + - - -
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Residues in contact with MSE 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 LEU* 3.3 48.0 + - + +
400A SER* 3.6 10.5 - - - +
401A LEU 3.2 0.6 - - - -
402A PRO* 1.3 75.7 - - - +
404A LYS* 1.3 62.0 + - + +
405A HIS 4.1 0.3 - - - +
427A ARG* 3.6 31.2 - - + +
428A ILE* 3.5 3.1 - - + +
429A ASN* 2.9 68.8 + - - +
452A LYS* 3.1 8.5 + - - +
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Residues in contact with LYS 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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400A SER* 2.9 32.7 + - - +
401A LEU* 4.1 2.9 - - - +
403A MSE 1.3 79.0 - - + +
405A HIS* 1.3 65.1 + - - +
406A GLU* 3.7 1.0 + - - -
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Residues in contact with HIS 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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249A LYS* 3.5 10.4 - - + +
251A HIS* 4.0 13.9 - + + -
378A TYR* 3.1 52.9 + + - -
379A LYS* 3.6 16.3 + - - -
401A LEU 3.2 13.8 + - - +
402A PRO* 3.4 13.0 + - + +
404A LYS* 1.3 78.7 - - - +
406A GLU* 1.3 69.8 + - + +
407A TYR* 3.1 54.6 + + - +
452A LYS* 2.7 28.9 + - - +
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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