Contacts of the helix formed by residues 404 - 411 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356D TYR* 3.7 53.6 - - + +
360D MET* 4.2 16.2 - - + -
367D ILE* 3.5 23.8 - - + -
369D PHE* 3.9 7.6 - - - -
400D MET* 2.8 19.0 + - - +
401D GLU* 4.1 3.6 - - - +
403D LEU* 1.3 101.9 - - + +
405D ASP* 1.3 66.1 + - - +
406D LYS 3.7 0.7 - - - -
407D ILE* 4.3 13.0 - - + -
408D SER* 2.9 24.4 + - - -
421D ILE* 3.8 15.5 - - + -
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Residues in contact with ASP 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401D GLU* 3.4 15.3 + - - +
402D ARG* 3.2 22.8 - - - +
403D LEU 2.8 2.6 + - - -
404D MET* 1.3 79.3 - - - +
406D LYS* 1.3 91.2 + - + +
408D SER* 3.0 14.1 + - - -
409D PHE* 3.5 5.4 + - - +
25E ARG* 4.3 13.3 + - - -
29E ILE* 5.0 12.6 - - - +
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Residues in contact with LYS 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D ARG* 3.7 10.9 + - - +
403D LEU 4.3 8.0 + - - +
405D ASP* 1.3 105.9 + - + +
407D ILE* 1.3 66.6 + - - +
409D PHE* 2.8 20.3 + - - +
410D SER* 3.3 16.7 + - - +
425D TYR* 4.7 12.1 - - + +
428D ASP* 5.8 1.3 - - - -
429D ALA* 3.7 26.8 + - + +
25E ARG* 5.3 7.6 - - - +
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Residues in contact with ILE 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D MET* 3.6 27.1 - - + -
365D VAL* 5.0 2.9 - - + -
367D ILE* 4.7 5.2 - - + -
404D MET* 3.8 15.8 + - + +
405D ASP 3.4 0.4 - - - -
406D LYS* 1.3 79.7 - - + +
408D SER* 1.3 49.8 + - - +
410D SER* 4.8 2.9 - - - +
411D ALA* 2.6 50.2 + - + +
414D MET* 4.8 11.0 - - + -
419D VAL* 3.5 40.6 - - + -
421D ILE* 4.4 11.9 - - + -
425D TYR* 3.1 33.2 + - + +
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Residues in contact with SER 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TYR* 5.2 5.5 - - - -
360D MET* 4.2 8.3 - - - +
401D GLU* 4.4 11.4 + - - -
404D MET* 2.9 24.1 + - - -
405D ASP* 3.0 6.0 + - - -
406D LYS 2.9 0.4 + - - -
407D ILE* 1.3 76.5 - - - +
409D PHE* 1.3 56.4 + - - +
6E PRO* 4.4 0.7 - - - +
29E ILE* 4.2 15.6 - - - +
33E ASN* 4.0 14.4 + - - -
36E ARG* 2.5 55.6 + - - +
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Residues in contact with PHE 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405D ASP 3.5 2.3 + - - +
406D LYS 2.8 9.1 + - - +
408D SER* 1.3 78.2 - - - +
410D SER* 1.3 76.5 + - - +
411D ALA 3.1 2.2 + - - -
412D SER* 3.4 6.4 + - - -
6E PRO* 3.2 55.6 - - + +
7E ARG* 3.8 33.0 - - + -
10E VAL* 4.1 10.3 - - + -
25E ARG* 3.1 61.5 - - + +
28E ALA* 4.3 3.4 - - + -
29E ILE* 3.6 23.2 - - + +
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Residues in contact with SER 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D LYS* 3.3 15.7 + - - +
407D ILE 4.7 0.2 - - - -
409D PHE* 1.3 82.7 - - - +
411D ALA* 1.3 64.7 + - - +
412D SER* 2.6 8.6 + - - -
413D ASP* 3.0 17.3 + - - +
414D MET* 2.9 44.5 + - - +
25E ARG* 4.6 4.3 + - - -
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Residues in contact with ALA 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D MET* 3.6 24.2 - - - -
363D GLU* 3.4 17.2 - - + +
365D VAL* 3.4 21.2 - - + +
407D ILE* 2.6 29.8 + - + +
409D PHE 3.1 0.8 - - - -
410D SER* 1.3 72.6 - - - +
412D SER* 1.3 62.5 + - - +
414D MET* 3.3 17.3 + - - -
36E ARG* 3.8 13.2 - - - +
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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