Contacts of the strand formed by residues 91 - 94 (chain C) in PDB entry 1ESQ
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 VAL 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C LEU* 3.2 26.5 - - + +
64C LEU* 3.9 15.3 - - + -
81C GLY 4.1 4.5 - - - +
84C ALA* 3.4 23.6 - - + -
85C ASN* 3.9 16.3 - - - +
89C VAL 3.4 15.3 - - - +
90C PRO* 1.3 71.4 - - - +
92C ILE* 1.3 67.7 + - - +
115C VAL* 4.1 5.6 - - + -
116C ARG 3.9 10.3 + - - +
117C LEU* 3.6 21.6 - - + +
118C ALA* 2.8 32.0 + - - +
119C ALA 3.7 1.0 + - - -
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Residues in contact with ILE 92 (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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61C ALA* 4.6 0.9 - - + -
62C LEU 2.7 15.7 + - - +
63C VAL* 3.2 9.2 - - + +
64C LEU* 2.7 34.1 + - - +
90C PRO* 3.6 18.4 - - + +
91C VAL* 1.3 81.7 - - - +
93C LEU* 1.3 59.4 + - - +
117C LEU* 4.5 1.8 - - - -
118C ALA* 4.6 1.8 - - + -
119C ALA* 3.6 15.7 - - + +
121C ARG* 5.2 3.4 - - + +
201C THR* 3.2 35.2 - - + +
204C VAL* 4.0 25.1 - - + -
205C GLY* 3.9 19.5 - - - -
208C CYS* 4.2 17.0 - - + -
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Residues in contact with LEU 93 (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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64C LEU* 3.6 19.7 - - + +
66C ILE* 5.1 4.7 - - + -
92C ILE* 1.3 75.7 - - - +
94C ASP* 1.3 75.2 + - - +
95C PRO* 3.5 18.3 - - + +
108C ALA* 4.3 12.1 - - - +
111C ILE* 4.4 20.4 - - + -
112C ILE* 4.0 18.2 - - + -
117C LEU* 3.6 36.7 - - + +
119C ALA 3.1 9.6 + - - +
120C ILE* 3.2 15.4 - - + -
121C ARG 2.9 25.8 + - - -
130C THR* 5.0 0.4 - - + -
201C THR* 4.4 2.4 - - - +
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Residues in contact with ASP 94 (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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64C LEU 2.9 14.3 + - - +
65C ASN* 3.8 10.6 - - + +
66C ILE* 3.7 15.2 + - - +
93C LEU* 1.3 75.7 - - - +
95C PRO* 1.3 53.6 - - - +
96C VAL* 2.7 41.8 + - - +
121C ARG* 3.1 28.0 + - - +
122C GLY* 4.6 1.7 - - - -
126C GLU* 4.8 0.5 - - - +
197C GLY 3.6 4.9 - - - +
198C SER* 3.7 10.2 + - - -
201C THR* 2.6 36.8 + - + +
350C MG 3.8 2.4 - - - -
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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