Contacts of the helix formed by residues 398 - 403 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370F LEU* 3.5 23.6 + - - +
373F THR* 3.3 26.5 - - + +
374F ALA* 3.2 26.0 - - - +
377F VAL* 4.1 8.4 - - + +
397F ASP* 1.3 73.1 - - - +
399F PRO* 1.3 56.4 - - - +
400F ALA* 2.9 3.8 - - + +
401F ILE* 2.6 50.8 + - + +
402F MET* 2.8 14.2 + - - +
419F ASP 3.3 24.2 + - - -
421F LEU 3.4 16.4 - - - +
422F VAL* 4.2 4.9 - - + -
92H THR* 4.0 3.8 + - - +
95H LEU* 5.4 3.3 - - + +
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Residues in contact with PRO 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F PRO* 4.6 12.6 - - + -
397F ASP* 3.1 23.3 - - - +
398F GLN* 1.3 80.2 - - - +
400F ALA* 1.3 61.2 + - - +
402F MET* 4.3 0.2 - - + -
403F SER* 2.9 30.9 + - - +
404F TYR* 3.2 23.4 - - + -
417F ILE* 4.4 11.0 - - + -
421F LEU* 3.6 33.7 - - + +
423F ARG* 4.0 21.1 - - + +
605F PMC 5.9 1.3 - - - +
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Residues in contact with ALA 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370F LEU* 4.7 3.6 - - + -
398F GLN* 2.7 9.0 + - + +
399F PRO* 1.3 75.9 - - - +
401F ILE* 1.3 63.3 + - + +
404F TYR* 3.1 7.2 - - - +
405F TRP* 3.1 29.6 + - + -
412F ARG* 3.8 13.5 - - - +
417F ILE* 3.6 17.5 - - + +
418F MET 3.7 23.9 + - - +
419F ASP* 4.0 15.5 - - - +
421F LEU 5.1 0.2 + - - -
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Residues in contact with ILE 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370F LEU* 3.8 29.2 - - + -
398F GLN* 2.6 45.8 + - + +
400F ALA* 1.3 73.4 - - + +
402F MET* 1.3 64.4 + - - +
403F SER 3.4 1.3 + - - -
405F TRP* 3.3 41.9 + - + +
92H THR* 3.6 20.2 - - + -
95H LEU* 4.0 20.9 - - + -
96H ILE* 3.9 26.7 - - + -
99H LYS* 3.7 10.4 - - + +
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Residues in contact with MET 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385F ILE 4.3 0.7 - - - +
386F ALA* 3.6 12.3 - - - +
387F PRO* 3.5 36.1 - - + -
397F ASP* 3.2 38.1 - - + +
398F GLN 2.8 15.7 + - - +
401F ILE* 1.3 75.0 - - - +
403F SER* 1.3 60.7 + - - +
605F PMC 3.3 9.8 + - - +
89H PHE* 3.4 33.4 - - + -
95H LEU* 3.7 24.9 - - + -
99H LYS* 3.0 23.3 + - - +
107H GLU* 4.2 9.7 - - + +
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Residues in contact with SER 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F ARG* 2.9 31.0 + - - -
399F PRO* 2.9 17.2 + - - +
402F MET* 1.3 76.2 - - - +
404F TYR* 1.3 79.6 + - - +
405F TRP 3.8 0.7 - - - -
406F ASP* 4.5 1.1 - - - -
605F PMC 3.1 48.7 + - - -
99H LYS* 4.6 3.6 - - - +
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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