Contacts of the strand formed by residues 49 - 54 (chain I) in PDB entry 1C9T
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 GLU 49 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ALA* 3.5 10.7 - - - +
28I CYS* 5.1 1.8 - - - +
29I SER* 4.7 9.4 + - - +
32I HIS* 3.5 27.6 + - + +
41I PHE* 3.7 29.7 + - + +
42I LYS 3.2 9.0 - - - +
43I LYS* 4.0 17.6 - - + +
47I GLY 4.5 2.7 - - - +
48I CYS* 1.3 77.3 - - - +
50I TYR* 1.3 63.7 + - - +
51I ALA 3.4 2.3 + - - -
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Residues in contact with TYR 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLY* 4.1 4.9 - - - -
18I ALA* 3.7 23.6 - - + -
32I HIS* 3.2 8.2 + - - -
41I PHE* 3.3 13.3 - - - +
42I LYS* 2.6 56.0 + - + +
43I LYS 4.1 1.1 - - - -
44I ASP* 3.6 32.8 - - + +
49I GLU* 1.3 70.5 - - - +
51I ALA* 1.3 67.6 + - - +
52I CYS 3.2 0.9 + - - +
53I ILE* 3.6 25.6 - - + -
57L ALA* 3.6 9.5 + - + +
58L PRO* 2.6 51.8 + - + -
59L GLN* 4.5 2.9 - - - -
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Residues in contact with ALA 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASN 5.9 2.5 - - - +
99C LEU* 5.8 2.2 - - + -
18I ALA* 5.1 0.6 - - - +
29I SER* 5.5 3.6 + - - +
31I LEU* 3.4 34.3 - - + +
32I HIS* 2.7 38.1 - - - +
33I CYS 3.4 1.5 + - - +
41I PHE* 3.0 8.3 - - - -
49I GLU 3.4 3.8 + - - -
50I TYR* 1.3 69.4 - - - +
52I CYS* 1.3 61.4 + - + +
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Residues in contact with CYS 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C HIS* 3.6 27.1 - - - -
94C TYR* 5.6 0.9 - - - +
96C SER 5.2 5.4 - - - +
99C LEU* 4.7 14.4 - - + -
33I CYS* 2.0 49.4 - - + -
35I VAL* 3.8 4.0 - - - -
41I PHE* 3.6 2.7 - - - -
50I TYR 3.3 0.2 - - - -
51I ALA* 1.3 79.6 - - + +
53I ILE* 1.3 68.6 + - - +
54I CYS* 6.1 0.2 - - - -
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Residues in contact with ILE 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PHE* 3.2 15.4 - - - +
42I LYS* 2.7 53.7 + - + -
50I TYR* 3.6 20.6 + - + +
52I CYS* 1.3 82.8 - - - +
54I CYS* 1.3 58.5 + - - +
39L HIS* 4.6 8.7 - - + +
56L ASP* 3.8 13.7 - - + +
57L ALA* 3.4 27.1 - - + -
58L PRO* 3.5 17.9 - - + -
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Residues in contact with CYS 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 5.8 1.8 - - - -
60C LYS* 6.0 4.5 - - - -
35I VAL* 5.1 9.9 - - - -
36I LYS 4.8 1.3 - - - -
37I CYS* 2.0 56.1 - - + -
38I GLU 5.3 0.9 - - - +
40I GLY 3.5 4.0 - - - -
41I PHE* 5.1 0.7 - - - -
42I LYS* 3.5 18.5 - - - -
53I ILE* 1.3 77.9 - - - +
55I ALA* 1.3 69.3 + - - +
56I ASP* 3.7 4.2 + - - +
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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
------------------------------------------------------------
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