Contacts of the helix formed by residues 404 - 411 (chain F) in PDB entry 1G3I
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 MET 404 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F TYR* 3.6 55.2 - - + -
360F MET* 4.1 16.4 - - + -
367F ILE* 3.3 25.4 - - + -
369F PHE* 3.9 7.9 - - - -
400F MET* 2.7 24.1 + - + +
401F GLU* 4.2 6.0 - - - +
403F LEU* 1.3 97.3 - - + +
405F ASP* 1.3 66.6 + - - +
406F LYS 3.7 0.2 - - - -
407F ILE* 4.4 13.4 - - + +
408F SER* 3.1 23.0 + - - -
421F ILE* 3.7 17.0 - - + -
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Residues in contact with ASP 405 (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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25A ARG* 4.2 15.9 + - - -
29A ILE* 5.1 13.6 - - - +
401F GLU* 3.7 13.0 + - - +
402F ARG* 3.2 24.6 + - - +
403F LEU 2.6 6.5 + - - -
404F MET* 1.3 78.8 - - - +
406F LYS* 1.3 88.5 + - - +
408F SER* 2.9 14.8 + - - -
409F PHE* 3.5 4.3 + - - +
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Residues in contact with LYS 406 (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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25A ARG* 5.4 7.2 - - - +
402F ARG* 3.7 5.1 + - - +
403F LEU 4.2 7.4 + - - +
405F ASP* 1.3 103.8 + - + +
407F ILE* 1.3 67.7 + - + +
409F PHE* 2.7 20.8 + - - +
410F SER* 3.3 16.1 + - - +
425F TYR* 4.8 11.4 - - + +
428F ASP* 5.6 2.0 - - - +
429F ALA* 3.6 34.0 + - + +
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Residues in contact with ILE 407 (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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360F MET* 3.5 28.0 - - + -
365F VAL* 5.1 2.7 - - + -
367F ILE* 4.6 3.8 - - + -
403F LEU 5.5 1.6 - - - +
404F MET* 4.4 15.6 - - + +
405F ASP 3.4 0.4 - - - -
406F LYS* 1.3 76.5 - - + +
408F SER* 1.3 55.1 + - - +
410F SER* 4.7 3.1 - - - +
411F ALA* 2.6 45.7 + - + +
414F MET* 4.9 11.7 - - + -
419F VAL* 3.7 30.3 - - + -
421F ILE* 4.1 13.7 - - + -
425F TYR* 2.9 43.1 - - + +
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Residues in contact with SER 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 4.2 2.3 - - - +
29A ILE* 4.6 17.2 - - - +
33A ASN* 3.8 13.5 + - - -
36A ARG* 2.5 55.0 + - - +
356F TYR* 5.5 5.1 - - - -
360F MET* 4.2 8.9 - - - +
401F GLU* 4.4 10.3 + - - -
404F MET* 3.1 20.8 + - - -
405F ASP* 2.9 8.1 + - - -
406F LYS 2.8 2.8 + - - -
407F ILE* 1.3 75.3 - - - +
409F PHE* 1.3 56.3 + - - +
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Residues in contact with PHE 409 (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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6A PRO* 3.0 66.7 - - + +
7A ARG* 3.7 30.1 - - + -
10A VAL* 4.2 9.6 - - + -
25A ARG* 2.9 60.6 - - + +
28A ALA* 4.6 1.6 - - + -
29A ILE* 3.7 21.0 - - + +
405F ASP 3.5 2.6 + - - +
406F LYS 2.7 16.1 + - - +
408F SER* 1.3 74.2 - - - +
410F SER* 1.3 67.7 + - - +
411F ALA 3.6 0.3 + - - -
412F SER* 3.7 6.8 + - - -
413F ASP* 5.9 0.2 - - - -
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Residues in contact with SER 410 (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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25A ARG* 5.0 2.3 + - - -
406F LYS* 3.3 15.2 + - - +
407F ILE 4.4 0.2 - - - -
409F PHE* 1.3 80.5 - - - +
411F ALA* 1.3 65.0 + - - +
412F SER 2.6 7.8 + - - -
413F ASP* 2.9 16.9 + - - +
414F MET* 2.9 46.9 + - - +
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Residues in contact with ALA 411 (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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36A ARG* 3.9 11.7 - - - +
360F MET* 3.6 25.6 - - - -
363F GLU* 3.2 26.7 - - + +
365F VAL* 3.5 16.1 - - + +
407F ILE* 2.6 29.2 + - + +
409F PHE 3.3 0.6 - - - -
410F SER* 1.3 72.1 - - - +
412F SER* 1.3 61.9 + - - +
414F MET* 3.5 16.6 + - - -
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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