Contacts of the strand formed by residues 43 - 47 (chain C) in PDB entry 1GXD
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 ILE 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C GLU* 4.2 14.1 - - - +
29C VAL* 2.6 29.6 - - + -
42C ARG* 1.3 73.5 - - - +
44C GLN* 1.3 62.8 + - - +
45C TYR* 3.9 26.5 - - + +
64C TYR* 3.1 7.4 - - - +
65C THR* 2.8 43.3 + - + +
66C ALA 3.5 19.3 - - - +
67C PRO* 3.4 21.1 - - + +
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Residues in contact with GLN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLU* 3.0 8.7 - - - +
27C LYS* 2.3 91.3 + - + +
28C GLU 5.0 2.4 + - - -
29C VAL* 3.9 0.8 - - - +
30C ASP* 5.1 9.1 - - - +
42C ARG 4.5 2.2 + - - +
43C ILE* 1.3 77.5 - - - +
45C TYR* 1.3 59.2 - - - +
62C PHE* 4.1 5.1 - - + -
63C ILE 3.0 4.5 - - - +
64C TYR* 2.6 52.1 + - + -
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Residues in contact with TYR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA* 3.7 23.1 - - + -
26C GLU* 4.1 16.4 - - + +
27C LYS 3.8 1.1 - - - +
43C ILE* 3.9 19.5 - - + +
44C GLN* 1.3 75.4 - - - +
46C GLU* 1.3 55.3 + - - +
47C ILE* 3.8 9.2 - - + -
62C PHE* 2.7 21.0 - - - +
63C ILE* 2.5 61.5 + - + -
65C THR* 3.5 27.7 - - + +
74C VAL 3.4 1.1 + - - -
75C SER* 3.3 12.5 + - - -
76C LEU* 3.2 60.9 + - + -
78C VAL* 4.9 2.2 - - + -
98C ILE* 4.3 1.1 - - + -
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LYS 3.2 2.8 - - - +
23C ALA* 3.2 2.0 - - - +
24C VAL* 2.7 48.8 + - + +
25C SER* 1.9 60.6 + - - +
27C LYS* 3.9 8.8 + - + +
45C TYR* 1.3 69.7 - - - +
47C ILE* 1.3 61.1 + - - +
61C GLU 4.6 0.2 - - - +
62C PHE* 3.2 30.0 - - + -
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 3.6 22.7 - - + -
22C LYS 2.8 19.3 - - - +
24C VAL* 4.9 3.6 - - - -
45C TYR* 3.5 13.7 - - + +
46C GLU* 1.3 80.4 - - - +
48C LYS* 1.3 60.2 + - - +
49C GLN* 3.7 11.2 + - + +
60C ILE* 2.7 34.6 - - + +
61C GLU* 2.8 34.7 + - - +
62C PHE 3.8 2.5 - - - +
63C ILE* 2.9 37.0 - - + -
76C LEU* 6.3 0.7 - - + -
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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