Contacts of the strand formed by residues 119 - 123 (chain D) in PDB entry 2IB8
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 CYS 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C ASN 4.8 0.2 - - - +
124C LYS* 3.4 21.0 - - - +
88D GLU* 5.8 0.2 - - - -
89D ALA* 3.3 6.5 - - - -
90D TYR* 5.3 0.4 - - - -
104D THR* 3.7 6.7 - - + -
105D ARG* 3.6 48.5 - - + +
108D VAL* 3.6 29.2 - - - -
117D THR 3.4 17.7 - - - -
118D PRO* 1.3 74.4 - - - +
120D THR* 1.3 65.8 + - - +
2003D CL 3.4 10.4 - - + +
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ILE* 3.9 25.4 - - + -
123C ASN 3.8 10.5 - - - +
124C LYS* 3.7 8.0 - - + +
131C LYS* 3.4 28.0 - - + -
135C MET* 4.3 3.1 - - + -
88D GLU* 4.7 0.7 + - - -
89D ALA 3.1 6.3 + - - -
90D TYR* 3.3 21.7 - - - +
91D MET 3.2 23.4 + - - -
104D THR* 3.2 5.6 + - - +
119D CYS* 1.3 79.1 + - - +
121D THR* 1.3 63.1 + - - +
122D ILE* 3.8 20.0 + - + +
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Residues in contact with THR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C THR 4.2 0.7 - - - +
122C ILE* 3.9 1.2 - - - -
123C ASN* 2.9 48.7 + - - +
91D MET 3.4 3.8 - - - +
93D ASN* 3.6 28.0 - - + +
96D GLN* 3.5 25.6 + - - +
102D ALA* 4.5 1.6 - - - -
103D PRO* 3.8 14.7 - - + +
104D THR* 2.8 32.2 + - - +
120D THR* 1.3 71.7 - - - +
122D ILE* 1.3 66.8 + - - +
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C THR* 3.7 20.0 - - + -
121C THR 4.1 1.1 - - - -
122C ILE* 4.1 8.5 - - + -
135C MET* 3.9 19.7 - - + -
90D TYR* 4.3 7.2 - - + -
91D MET 2.8 14.8 + - - +
92D GLY* 3.3 7.8 - - - -
93D ASN 3.0 27.8 + - - +
96D GLN* 4.7 0.2 - - - -
120D THR* 3.8 30.7 - - + +
121D THR* 1.3 75.3 - - - +
123D ASN* 1.3 64.5 + - - +
124D LYS 4.1 2.0 - - - +
128D SER* 3.6 15.7 - - - +
131D LYS* 4.4 7.9 - - + -
132D ALA* 4.3 17.0 - - + +
135D MET* 3.9 14.6 - - - -
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Residues in contact with ASN 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C GLN* 3.0 30.3 + - - +
102C ALA* 5.3 3.5 - - - +
103C PRO* 4.2 17.9 - - - +
120C THR* 3.8 2.5 - - - -
121C THR* 3.0 46.8 + - - +
93D ASN 4.1 1.6 - - - +
94D VAL* 3.8 25.7 + - - +
96D GLN* 4.0 8.5 - - - +
122D ILE* 1.3 74.7 - - - +
124D LYS* 1.3 58.1 + - - +
125D VAL* 2.9 31.9 + - - +
128D SER* 3.4 3.2 + - - -
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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