Contacts of the helix formed by residues 394 - 405 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B VAL* 3.5 13.7 - - - +
392B ALA* 3.5 1.7 - - - +
393B ARG* 1.3 87.1 - - - +
395B TYR* 1.3 66.0 + - - +
396B GLU* 3.2 9.0 + - - +
397B GLU* 2.8 37.6 + - - +
398B ALA* 3.0 22.5 + - - +
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Residues in contact with TYR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ILE* 5.9 1.6 - - + -
255B MSE 3.9 37.9 - - + +
288B VAL* 3.9 3.6 - - - +
394B ASN* 1.3 73.9 - - - +
396B GLU* 1.3 85.3 + - + +
398B ALA* 3.1 8.1 + - - +
399B LEU* 2.9 34.7 + - + +
413B ILE* 4.4 3.8 - - + -
420B ALA* 3.9 23.1 - - + -
423B ASP* 2.7 29.3 + - + +
424B PHE* 3.0 43.3 + + + -
427B ARG* 3.8 5.4 + - - -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B ASN* 3.2 7.6 + - - +
395B TYR* 1.3 87.1 - - + +
397B GLU* 1.3 67.5 + - - +
399B LEU* 3.5 5.8 + - - +
400B SER* 3.1 23.7 + - - -
427B ARG* 2.8 44.0 + - - -
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ARG 4.3 3.1 - - - +
392B ALA* 3.4 12.7 - - + -
393B ARG* 2.7 62.1 + - - +
394B ASN* 2.8 28.3 + - - +
396B GLU* 1.3 71.4 - - - +
398B ALA* 1.3 61.6 + - - +
400B SER* 2.8 23.3 + - - +
401B LEU* 3.5 14.7 + - + +
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ILE* 3.8 18.4 - - + +
286B VAL* 3.8 15.9 - - + -
288B VAL* 3.8 24.2 - - + -
392B ALA* 3.8 9.8 - - + +
394B ASN 3.0 13.6 + - - +
395B TYR* 3.1 8.9 + - + +
397B GLU* 1.3 75.8 - - - +
399B LEU* 1.3 63.4 + - - +
401B LEU* 3.3 6.9 + - - +
402B PRO* 3.1 20.3 - - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B TYR* 2.9 28.8 + - + +
396B GLU* 4.0 7.0 - - - +
398B ALA* 1.3 76.9 - - - +
400B SER* 1.3 62.8 + - - +
401B LEU 3.2 1.0 + - - -
402B PRO* 3.4 4.2 - - - +
403B MSE 3.2 41.9 + - + +
424B PHE* 3.5 41.0 - - + +
427B ARG* 3.4 47.8 - - - +
428B ILE* 3.8 17.7 - - + +
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Residues in contact with SER 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B GLU 3.1 13.9 + - - -
397B GLU* 2.8 23.8 + - - +
399B LEU* 1.3 78.4 - - - +
401B LEU* 1.3 59.1 + - - +
403B MSE 3.7 9.2 - - - -
404B LYS* 2.9 47.9 + - - +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B HIS* 3.9 5.8 - - + -
286B VAL* 3.7 30.5 - - + -
373B PRO* 3.6 28.7 - - + -
378B TYR* 3.4 29.6 + - + +
390B VAL* 3.7 24.0 - - + -
392B ALA* 4.6 5.6 - - + -
397B GLU* 3.7 18.8 - - + +
398B ALA* 3.3 1.7 + - - +
399B LEU 3.1 1.2 - - - -
400B SER* 1.3 80.3 + - - +
402B PRO* 1.4 74.4 - - + +
403B MSE 3.1 0.5 + - - -
404B LYS* 4.0 1.5 - - - +
405B HIS* 3.2 15.4 + - - +
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Residues in contact with PRO 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B HIS* 3.8 27.8 - - + +
253B ILE* 3.9 19.5 - - + -
398B ALA 3.1 24.0 - - - +
399B LEU 3.4 9.0 - - - +
401B LEU* 1.4 83.3 - - + +
403B MSE 1.3 54.8 + - - +
405B HIS* 3.4 7.4 + - + +
411B VAL* 3.9 12.1 - - + -
424B PHE* 4.3 3.8 - - + -
428B ILE* 3.8 11.0 - - + -
430B ILE* 3.7 25.4 - - + +
452B LYS* 2.8 22.9 + - - -
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Residues in contact with MSE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B LEU* 3.2 49.8 + - + +
400B SER* 3.7 9.6 - - - +
401B LEU 3.0 0.6 - - - -
402B PRO* 1.3 78.1 - - - +
404B LYS* 1.3 61.5 + - + +
405B HIS 4.0 0.3 - - - +
427B ARG* 3.4 35.2 - - + +
428B ILE* 3.5 4.2 - - + +
429B ASN* 3.0 67.1 + - - +
452B LYS* 3.2 8.0 + - - +
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Residues in contact with LYS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B SER* 2.9 32.3 + - - +
401B LEU* 4.2 1.6 - - - +
403B MSE 1.3 78.4 - - + +
405B HIS* 1.3 66.3 + - - +
406B GLU 3.5 0.9 + - - -
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Residues in contact with HIS 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B LYS* 3.5 20.6 - - + +
251B HIS* 3.9 17.3 - + + -
378B TYR* 3.1 52.5 + + - -
379B LYS* 3.6 19.1 + - + -
401B LEU 3.2 11.6 + - - +
402B PRO* 3.7 11.9 - - + +
403B MSE 3.3 1.6 - - - -
404B LYS* 1.3 79.8 - - - +
406B GLU* 1.3 77.7 + - + +
407B TYR* 3.1 33.2 + + - +
452B LYS* 2.8 29.5 + - - +
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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