Contacts of the strand formed by residues 59 - 63 (chain C) in PDB entry 2I6A
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 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP 3.4 0.4 - - - +
19C ILE* 3.3 3.6 - - - -
20C SER* 2.7 32.1 + - - +
57C LYS 4.9 4.0 - - - +
58C VAL* 1.3 91.1 - - - +
60C TYR* 1.3 68.1 + - - +
61C HIS* 3.6 18.6 + - - +
333C ARG 4.5 0.9 - - - +
334C THR* 3.2 14.4 + - + +
335C GLY* 2.4 37.0 + - - -
336C CYS* 4.0 2.0 + - - -
337C THR* 2.6 38.3 + - - +
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Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.6 15.5 - - + -
18C ASP 3.2 4.7 - - - +
19C ILE* 3.8 29.8 - - + -
53C VAL* 3.8 17.9 - - + +
58C VAL* 3.6 31.2 - - + +
59C GLU* 1.3 83.3 - - - +
61C HIS* 1.3 77.3 + - - +
94C LYS* 5.9 4.3 - - - -
95C PHE* 4.2 25.4 - + - -
98C ILE* 6.3 1.8 - - + -
337C THR* 5.0 4.5 + - - +
340C GLU* 5.1 11.9 - - - +
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Residues in contact with HIS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.6 6.2 - - - +
18C ASP* 2.6 39.6 + - - +
20C SER* 4.3 7.2 - - - -
59C GLU* 3.6 23.5 + - + +
60C TYR* 1.3 93.8 + - - +
62C ALA* 1.3 62.4 + - - +
332C ARG* 3.3 54.3 + - + +
333C ARG 4.2 14.7 + - - -
336C CYS* 5.6 5.6 - - + -
337C THR* 4.1 18.6 - - + -
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.8 4.4 - - + +
61C HIS* 1.3 72.5 - - - +
63C GLY* 1.3 57.8 + - - +
67C GLN* 5.2 0.4 - - - +
68C ASN* 3.6 9.0 - - - +
71C LYS* 3.4 28.1 + - - +
98C ILE* 5.6 1.5 - - + +
99C LEU* 3.6 26.5 - - + -
102C LYS* 4.0 21.6 - - + +
332C ARG* 3.8 11.3 + - - -
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Residues in contact with GLY 63 (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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16C LEU 2.6 21.3 + - - +
18C ASP* 3.6 19.3 - - - -
61C HIS 3.2 1.4 + - - -
62C ALA* 1.3 74.9 - - - +
64C GLY* 1.3 63.7 + - - +
67C GLN* 2.6 34.5 + - - +
68C ASN* 3.4 8.9 - - - +
500C 5I5 3.6 1.8 - - - -
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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