Contacts of the strand formed by residues 96 - 102 (chain R) in PDB entry 1D0G
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 SER 96 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203D ASP 6.1 0.2 - - - -
205D GLN* 3.3 22.4 - - - +
92R ARG* 3.2 21.7 - - - +
93R GLU* 2.7 42.0 + - - +
95R ASP* 1.3 75.8 - - - +
97R PRO* 1.3 57.6 - - - +
98R GLU 3.6 0.7 + - - -
99R MET 3.9 2.4 - - - +
101R ARG* 3.0 39.9 + - - -
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Residues in contact with PRO 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 4.1 27.7 - - + +
148D GLY 5.0 0.9 - - - +
205D GLN* 4.1 1.8 - - - +
207D VAL* 4.9 3.4 - - + -
209D TYR* 3.7 19.5 - - + +
261D THR* 3.8 15.3 - - + -
92R ARG* 3.0 32.9 + - + +
93R GLU 4.0 4.3 - - - +
94R GLU* 3.5 18.8 - - - +
95R ASP 3.4 5.8 - - - +
96R SER* 1.3 85.4 - - - +
98R GLU* 1.3 64.4 + - - +
99R MET 3.7 0.2 - - - -
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Residues in contact with GLU 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A TYR* 2.8 32.6 + - - +
191A ARG* 3.3 31.9 + - - -
239A LEU* 4.3 10.5 - - + -
147D LEU* 5.1 2.9 - - - +
205D GLN* 3.1 11.0 + - - +
207D VAL* 3.7 27.4 - - + -
209D TYR* 3.5 16.1 + - - +
224D LYS* 2.9 41.4 + - - +
226D ALA* 4.1 4.5 - - + -
67R ASP* 4.7 1.0 - - - +
92R ARG* 4.8 4.9 + - - -
97R PRO* 1.3 82.4 - - - +
99R MET* 1.3 61.5 + - + +
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Residues in contact with MET 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ARG* 3.1 38.6 - - + +
192A PHE 4.0 17.9 - - - +
193A GLN* 3.4 32.3 - - - +
237A TYR* 3.7 22.7 - - + -
239A LEU* 3.5 30.1 - - + -
205D GLN* 3.0 28.4 + - - +
67R ASP* 5.4 2.5 - - - +
92R ARG* 4.2 6.3 - - - +
96R SER 3.9 5.9 - - - +
97R PRO 3.7 0.4 - - - -
98R GLU* 1.3 79.7 - - - +
100R CYS* 1.3 75.1 + - - +
101R ARG* 3.4 3.8 + - - +
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Residues in contact with CYS 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLN* 3.9 19.8 + - - +
237A TYR* 4.4 3.8 - - - -
67R ASP* 5.1 3.5 + - - -
69R GLY 3.7 8.5 - - - +
70R GLU* 3.7 20.6 - - - -
86R CYS* 2.0 57.9 - - - -
90R THR* 3.5 16.8 - - - +
91R PHE 3.6 2.5 - - - -
92R ARG* 3.8 4.2 - - - +
99R MET* 1.3 89.3 - - - +
101R ARG* 1.3 58.6 + - - +
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Residues in contact with ARG 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A TYR* 4.0 8.5 - - + -
200D THR* 5.5 3.4 - - - +
201D LYS* 3.0 39.7 + - - +
203D ASP* 3.0 49.9 + - - +
205D GLN* 3.6 7.4 - - - +
90R THR* 3.0 9.2 - - - -
91R PHE* 2.8 63.4 + - + +
93R GLU* 3.7 11.9 + - - -
96R SER* 3.0 40.8 + - - -
99R MET 3.5 11.9 - - - +
100R CYS* 1.3 73.9 - - - +
102R LYS* 1.3 61.4 + - - +
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Residues in contact with LYS 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLN* 6.2 1.6 - - - +
195A GLU* 3.4 28.6 + - - -
236A GLU* 3.8 42.0 + - + +
237A TYR* 6.1 0.2 - - - -
201D LYS* 2.7 28.3 + - - +
89R GLY 4.0 4.0 - - - +
90R THR* 4.5 13.0 - - + -
91R PHE* 4.1 0.4 - - - -
101R ARG* 1.3 73.3 - - - +
103R CYS* 1.3 68.0 + - - +
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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