Contacts of the helix formed by residues 398 - 405 (chain K) in PDB entry 1I43
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 398 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92I THR* 4.0 6.2 + - - +
95I LEU* 5.5 3.5 - - + +
370K LEU* 3.5 23.4 + - - +
373K THR* 3.4 24.9 - - + +
374K ALA* 3.3 21.2 - - - +
377K VAL* 4.3 7.0 - - + +
397K ASP* 1.3 73.6 - - - +
399K PRO* 1.3 57.9 - - - -
400K ALA* 2.9 4.3 - - + +
401K ILE* 2.5 54.6 + - + +
402K MET* 2.8 12.8 + - - +
419K ASP* 3.3 23.0 + - - +
421K LEU 3.5 15.7 - - - +
422K VAL* 4.1 5.6 - - + -
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Residues in contact with PRO 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K PRO* 4.6 11.9 - - + -
397K ASP* 3.1 25.1 - - - +
398K GLN* 1.3 80.5 - - - +
400K ALA* 1.3 64.8 + - - +
402K MET* 4.2 8.7 - - + -
403K SER* 2.9 23.9 + - - +
404K TYR* 3.2 21.9 + - + -
417K ILE* 4.5 6.3 - - + -
421K LEU* 3.8 36.8 - - + +
423K ARG* 3.9 20.2 - - + +
610K PMC 5.8 1.3 - - - +
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Residues in contact with ALA 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370K LEU* 4.9 2.9 - - + -
398K GLN* 2.7 8.8 + - + +
399K PRO* 1.3 76.5 - - - +
401K ILE* 1.3 63.5 + - + +
404K TYR* 3.2 5.9 - - - +
405K TRP* 3.0 29.6 + - - -
412K ARG* 4.0 13.9 - - - +
417K ILE* 3.6 17.7 - - + +
418K MET 3.7 24.1 + - - +
419K ASP* 4.0 15.7 - - - +
421K LEU 5.2 0.6 + - - +
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Residues in contact with ILE 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I THR* 3.5 20.9 - - + -
95I LEU* 3.9 25.1 - - + -
96I ILE* 4.0 22.0 - - + -
99I LYS* 3.9 9.2 - - + +
370K LEU* 3.7 31.4 - - + -
374K ALA* 5.1 0.2 - - + -
398K GLN* 2.5 45.4 + - + +
400K ALA* 1.3 72.1 - - - +
402K MET* 1.3 65.5 + - - +
405K TRP* 3.4 37.6 - - + +
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Residues in contact with MET 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I PHE* 3.5 28.7 - - + -
95I LEU* 4.0 21.5 - - + -
99I LYS* 2.6 32.7 + - - +
107I GLU* 4.4 10.3 - - - +
385K ILE 4.5 0.7 - - - +
386K ALA* 3.5 9.9 - - - +
387K PRO* 3.3 45.1 - - + -
397K ASP* 3.0 38.1 - - + +
398K GLN 2.8 16.5 + - - +
399K PRO* 4.2 0.2 - - + -
401K ILE* 1.3 73.3 - - - +
403K SER* 1.3 59.4 + - - +
610K PMC 3.5 7.8 + - - +
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Residues in contact with SER 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I LYS* 4.6 2.9 - - - +
164K ARG* 2.8 30.5 + - - -
399K PRO* 2.9 14.3 + - - +
402K MET* 1.3 74.0 - - - +
404K TYR* 1.3 78.5 + - - +
405K TRP 3.8 1.1 - - - -
406K ASP* 4.4 1.3 - - - -
610K PMC 2.9 52.3 + - - -
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Residues in contact with TYR 404 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162K CYS 5.2 2.9 + - - -
164K ARG* 3.4 39.2 + - + +
211K ASN* 5.4 8.5 + - - -
212K PRO* 5.6 3.0 - - + +
399K PRO* 3.2 23.4 + - + -
400K ALA* 3.2 12.3 - - - +
403K SER* 1.3 94.2 - - - +
405K TRP* 1.3 66.3 + - - +
406K ASP* 3.0 9.6 - - - -
407K LEU* 3.0 31.7 + - + +
412K ARG* 3.4 28.9 + - + +
415K TYR* 5.8 6.5 - + + -
417K ILE* 3.9 36.8 - - + +
610K PMC 5.7 0.4 - - - -
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Residues in contact with TRP 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ILE* 4.1 20.1 - - + +
99I LYS* 3.7 35.8 - - + +
100I GLU* 3.2 32.7 + - + +
370K LEU* 4.4 26.5 - - + -
400K ALA 3.0 13.1 + - - -
401K ILE* 3.4 41.0 + - + +
403K SER 3.8 0.8 - - - -
404K TYR* 1.3 78.3 - - - +
406K ASP* 1.3 60.2 + - - +
407K LEU 3.1 8.5 + - - +
412K ARG* 3.6 31.0 + - - +
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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