Contacts of the helix formed by residues 404 - 411 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E TYR* 3.7 56.5 - - + +
360E MET* 4.0 18.6 - - + -
367E ILE* 3.5 24.0 - - + -
369E PHE* 4.0 6.1 - - - -
400E MET* 2.8 13.2 + - + +
401E GLU* 4.0 4.5 - - - +
403E LEU* 1.3 100.4 - - + +
405E ASP* 1.3 68.9 + - - +
406E LYS 3.7 0.4 - - - -
407E ILE* 4.3 14.8 - - + -
408E SER* 2.9 23.3 + - - -
421E ILE* 3.6 18.4 - - - -
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Residues in contact with ASP 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E GLU* 3.4 14.1 + - - +
402E ARG* 3.1 23.4 - - - +
403E LEU 2.7 6.3 + - - -
404E MET* 1.3 78.1 - - - +
406E LYS* 1.3 91.4 + - + +
408E SER* 2.9 14.8 + - - -
409E PHE* 3.5 4.0 + - - +
25F ARG* 4.6 10.4 + - - -
29F ILE* 5.2 11.8 - - - +
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Residues in contact with LYS 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E ARG* 3.8 8.3 + - - +
403E LEU 4.4 7.0 - - - +
404E MET 3.7 0.2 - - - -
405E ASP* 1.3 107.6 + - + +
407E ILE* 1.3 72.3 + - + +
409E PHE* 2.8 20.1 + - - +
410E SER* 3.2 16.8 + - - +
425E TYR* 4.9 7.0 - - + +
428E ASP* 5.9 1.3 - - - +
429E ALA* 3.9 26.5 + - + +
25F ARG* 5.0 8.7 - - - +
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Residues in contact with ILE 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E MET* 3.5 28.0 - - + -
365E VAL* 5.2 1.3 - - + -
367E ILE* 4.5 0.9 - - + -
403E LEU* 5.3 1.1 - - + +
404E MET* 4.0 20.4 - - + +
405E ASP 3.3 0.2 - - - -
406E LYS* 1.3 75.6 - - + +
408E SER* 1.3 59.1 + - - +
409E PHE 2.9 0.2 + - - -
410E SER* 4.7 3.6 - - - +
411E ALA* 2.5 42.0 + - + +
414E MET* 4.8 11.9 - - + -
419E VAL* 3.6 37.7 - - + -
421E ILE* 4.3 13.5 - - + -
425E TYR* 2.8 36.6 - - + +
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Residues in contact with SER 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E TYR* 5.3 6.0 - - - -
360E MET* 4.2 10.1 - - - +
401E GLU* 4.4 11.7 + - - -
404E MET* 2.9 23.2 + - - -
405E ASP* 2.9 8.3 + - - -
407E ILE* 1.3 76.1 - - - +
409E PHE* 1.3 52.6 + - - +
6F PRO* 4.3 0.5 - - - +
29F ILE* 4.2 16.2 - - - +
33F ASN* 4.1 13.5 + - - -
36F ARG* 2.4 59.4 + - - +
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Residues in contact with PHE 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E ASP 3.5 2.1 + - - +
406E LYS 2.8 10.4 + - - +
408E SER* 1.3 78.0 - - - +
410E SER* 1.3 68.7 + - - +
411E ALA 3.2 1.9 + - - -
412E SER* 3.5 5.7 + - - -
6F PRO* 3.1 59.5 - - + +
7F ARG* 4.0 21.4 - - + +
10F VAL* 3.9 18.2 - - + -
25F ARG* 2.8 68.9 - - + +
28F ALA* 4.1 4.9 - - + -
29F ILE* 3.4 20.6 - - + +
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Residues in contact with SER 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E LYS* 3.2 16.2 + - - +
409E PHE* 1.3 81.3 - - - +
411E ALA* 1.3 53.1 + - - +
412E SER 2.5 19.0 + - - -
413E ASP* 3.0 24.9 + - - +
414E MET* 3.0 34.0 + - - +
25F ARG* 4.4 5.5 + - - -
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Residues in contact with ALA 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E MET* 3.7 24.9 - - - -
363E GLU* 2.9 24.3 - - + +
365E VAL* 3.4 23.1 - - + +
407E ILE* 2.5 26.3 + - + +
409E PHE 3.2 0.2 - - - -
410E SER* 1.3 71.2 - - - +
412E SER* 1.3 60.3 + - - +
414E MET* 3.7 14.3 + - - -
36F ARG* 4.0 12.6 - - - +
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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