Contacts of the strand formed by residues 94 - 99 (chain F) in PDB entry 2I9B
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 94 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F TYR 3.5 3.7 + - - +
93F LEU* 1.3 76.8 - - - +
95F CYS* 1.3 62.8 + - - +
112F SER* 3.5 19.8 + - - +
113F LEU 3.3 8.1 - - - +
114F GLN* 3.9 19.5 + - - +
122F CYS* 3.9 1.9 - - - -
174F THR* 3.8 21.2 + - + +
175F LYS* 2.8 53.3 + - + +
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Residues in contact with CYS 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F LEU* 4.1 1.6 - - - -
94F GLU* 1.3 75.0 - - - +
96F ILE* 1.3 70.0 + - - +
112F SER* 3.5 5.9 + - - -
113F LEU* 2.8 36.5 + - + +
115F CYS* 3.5 26.0 - - - -
122F CYS* 2.0 59.0 - - + -
146F GLY* 3.9 8.5 - - - +
147F CYS* 4.0 2.2 - - - -
175F LYS* 4.2 3.8 - - - +
177F ASN* 3.9 2.9 - - - +
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Residues in contact with ILE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F CYS* 1.3 76.6 - - - +
97F SER* 1.3 65.7 + - - +
110F HIS* 3.5 37.0 - - + +
111F GLN 3.5 15.0 - - - +
112F SER* 5.6 2.7 - - - +
145F ARG* 3.7 9.5 - - - +
146F GLY 3.6 4.0 + - - -
175F LYS* 3.8 35.9 - - + +
177F ASN* 2.9 42.9 + - - +
178F GLU* 3.5 31.2 - - + +
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Residues in contact with SER 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F TYR* 3.4 3.5 - - - -
58F ARG* 2.8 35.7 + - - +
96F ILE* 1.3 78.0 - - - +
98F CYS* 1.3 65.9 - - - +
110F HIS* 3.6 2.0 - - - +
111F GLN* 3.1 35.7 + - - +
112F SER 4.6 0.4 - - - -
113F LEU* 3.8 25.1 - - - +
145F ARG* 2.7 20.3 + - - -
146F GLY* 3.9 1.6 - - - -
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Residues in contact with CYS 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F TYR* 4.0 7.9 - - - +
58F ARG 3.4 14.6 - - - -
97F SER* 1.3 80.5 + - - +
99F GLY* 1.3 59.5 + - - +
104F SER* 3.3 12.6 - - - +
105F CYS* 2.0 50.7 - - - +
110F HIS* 3.8 24.5 - - + -
111F GLN* 5.9 0.4 - - - +
144F LEU* 3.5 1.4 - - - -
145F ARG* 2.8 46.2 + - - +
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Residues in contact with GLY 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F TYR* 4.7 1.1 - - - -
58F ARG 4.2 2.8 + - - -
59F THR* 4.3 11.6 + - - -
98F CYS* 1.3 73.8 - - - +
100F SER* 1.3 62.4 + - - -
101F SER* 3.3 6.0 + - - -
102F ASP* 3.6 1.0 - - - +
104F SER* 2.8 32.6 + - - -
105F CYS* 3.2 8.3 + - - -
143F HIS 3.5 9.6 - - - -
144F LEU* 4.0 9.2 - - - -
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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