Contacts of the strand formed by residues 127 - 134 (chain D) in PDB entry 1O94
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 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230C ARG* 5.8 3.1 - - - +
123D TYR* 3.6 3.7 - - - -
124D GLN* 3.0 34.4 + - + +
125D GLY 3.6 0.6 - - - -
126D ASP* 1.3 77.7 - - - +
128D LEU* 1.3 67.0 + - - +
129D VAL* 3.6 9.0 + - + +
144D ASP* 5.2 9.2 - - + +
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Residues in contact with LEU 128 (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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28D LEU* 3.9 22.7 - - + -
89D SER 5.4 0.2 - - - +
90D VAL* 4.1 17.9 - - + -
121D VAL* 4.7 8.3 - - + -
122D GLU 3.7 6.7 - - - +
123D TYR* 3.6 40.2 - - + +
126D ASP 4.1 0.2 + - - -
127D GLU* 1.3 71.2 - - - +
129D VAL* 1.3 59.9 + - - +
130D ALA 4.3 0.4 - - - -
144D ASP* 3.4 26.3 - - - +
145D PHE* 3.8 16.9 + - + -
151D VAL* 3.8 39.5 - - + -
153D LEU* 4.2 12.3 - - + -
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Residues in contact with VAL 129 (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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230C ARG* 3.4 47.1 - - - +
120D ILE* 3.8 1.0 - - - +
121D VAL* 3.4 6.6 - - - -
122D GLU* 2.9 40.8 + - + +
124D GLN* 4.0 14.1 - - + +
127D GLU* 3.9 12.3 - - + +
128D LEU* 1.3 79.9 - - - +
130D ALA* 1.3 63.6 + - - +
131D THR* 5.0 1.5 + - - +
142D GLU* 4.0 23.8 - - + +
143D VAL 3.3 9.2 - - - +
144D ASP* 4.2 6.1 - - + -
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Residues in contact with ALA 130 (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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118D VAL* 4.0 25.6 - - + -
120D ILE 3.3 5.2 - - - -
121D VAL* 4.1 7.6 - - + -
128D LEU* 4.3 0.6 - - + -
129D VAL* 1.3 74.8 - - - +
131D THR* 1.3 63.3 + - - +
142D GLU* 3.3 1.9 - - - -
143D VAL* 2.7 43.2 + - + +
145D PHE* 3.9 27.6 - - + -
153D LEU* 4.3 2.9 - - + -
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Residues in contact with THR 131 (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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233C TYR* 3.9 11.3 + - - +
118D VAL* 3.5 5.8 - - - -
119D TYR* 3.0 29.4 + - + -
120D ILE* 2.8 38.8 + - + +
129D VAL* 5.0 1.9 + - - +
130D ALA* 1.3 77.2 - - - +
132D ARG* 1.3 62.9 + - - +
140D ASN* 3.7 34.8 - - + +
141D VAL 3.2 12.6 - - - +
142D GLU* 3.5 16.7 + - + +
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Residues in contact with ARG 132 (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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125C GLN* 2.9 21.6 + - - +
126C ALA* 3.0 28.7 + - - +
127C TYR* 3.7 25.9 - - - +
115D ALA* 4.6 15.7 - - - -
116D THR* 2.8 50.1 + - - +
117D ASP* 3.8 10.8 - - - +
118D VAL* 4.7 2.9 - - + -
119D TYR* 3.3 18.8 + - - -
131D THR* 1.3 74.2 - - - +
133D GLY* 1.3 73.2 + - - +
140D ASN* 3.5 0.7 - - - -
141D VAL* 2.7 47.4 + - + +
143D VAL* 5.2 11.2 - - + -
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Residues in contact with GLY 133 (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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124C ASP 5.5 0.4 - - - -
125C GLN* 4.4 2.7 - - - +
117D ASP* 4.7 1.2 + - - +
119D TYR* 3.1 21.2 + - - -
132D ARG* 1.3 104.4 + - - +
134D GLY* 1.3 57.9 + - - -
137D GLN* 3.7 23.1 + - - +
139D VAL 3.4 4.5 - - - -
141D VAL* 3.9 5.4 - - - +
156D ARG* 4.8 0.6 - - - +
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Residues in contact with GLY 134 (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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124C ASP 3.8 2.0 - - - -
125C GLN* 3.7 10.3 - - - -
133D GLY* 1.3 74.8 - - - -
135D TYR* 1.3 71.4 + - - +
136D ASN 3.4 1.8 - - - -
137D GLN 3.1 2.6 + - - +
138D LYS 2.9 18.0 + - - -
139D VAL* 3.0 29.5 + - - +
141D VAL* 3.8 7.2 - - - -
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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