Contacts of the helix formed by residues 398 - 403 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F THR* 3.8 7.8 + - - +
95F LEU* 5.5 4.3 - - + +
370H LEU* 3.5 22.4 + - - +
373H THR* 3.2 34.2 - - + +
374H ALA* 3.4 20.5 - - - +
377H VAL* 4.2 7.2 - - + +
397H ASP* 1.3 74.6 - - - +
399H PRO* 1.3 55.2 - - - -
400H ALA* 3.0 4.0 - - + +
401H ILE* 2.7 51.1 + - + +
402H MET* 2.7 18.9 + - - +
419H ASP 3.3 15.5 + - - +
421H LEU 3.6 15.0 - - - +
422H VAL* 4.2 3.6 - - + -
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Residues in contact with PRO 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212H PRO* 4.5 9.2 - - + -
397H ASP* 3.3 21.5 - - - +
398H GLN* 1.3 82.0 - - - +
400H ALA* 1.3 61.7 + - - +
402H MET* 4.3 0.4 - - + -
403H SER* 2.9 30.3 + - - +
404H TYR* 3.2 22.5 - - + -
417H ILE* 4.3 15.3 - - + -
421H LEU* 3.7 33.7 - - + +
423H ARG* 4.1 21.8 - - + +
607H PMC 6.0 0.2 - - - +
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Residues in contact with ALA 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370H LEU* 4.8 2.7 - - + -
398H GLN* 2.8 4.2 + - + +
399H PRO* 1.3 78.7 - - - +
401H ILE* 1.3 63.2 + - + +
404H TYR* 3.3 5.8 - - - +
405H TRP* 3.1 29.8 + - - -
412H ARG* 3.7 10.1 - - - +
417H ILE* 3.5 17.2 - - + +
418H MET 3.5 25.0 + - - +
419H ASP* 3.9 21.8 - - - +
421H LEU 5.5 0.2 - - - +
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Residues in contact with ILE 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F THR* 3.6 27.6 - - + -
95F LEU* 3.8 27.1 - - + -
96F ILE* 4.0 18.6 - - + -
99F LYS* 3.8 12.0 - - + +
370H LEU* 3.6 39.0 - - + -
398H GLN* 2.7 28.6 + - + +
400H ALA* 1.3 72.7 - - - +
402H MET* 1.3 63.5 + - - +
403H SER 3.4 0.6 + - - -
405H TRP* 3.3 42.9 + - + +
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Residues in contact with MET 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F PHE* 3.5 29.2 - - + -
95F LEU* 4.0 22.2 - - + -
99F LYS* 2.8 25.0 + - - +
107F GLU* 4.2 10.6 - - + +
385H ILE 4.6 0.7 - - - +
386H ALA* 3.7 8.3 - - - +
387H PRO* 3.4 48.2 - - + -
397H ASP* 3.2 36.1 - - + +
398H GLN 2.7 16.1 + - - +
401H ILE* 1.3 74.4 - - - +
403H SER* 1.3 63.1 + - - +
607H PMC 3.4 9.4 + - - +
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Residues in contact with SER 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F LYS* 4.6 3.6 - - - +
164H ARG* 2.9 30.9 + - - -
399H PRO* 2.9 15.7 + - - +
402H MET* 1.3 77.1 - - - +
404H TYR* 1.3 81.2 + - - +
405H TRP 3.8 0.7 - - - -
406H ASP* 4.5 1.1 - - - -
607H PMC 2.9 49.0 + - - -
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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