Contacts of the strand formed by residues 164 - 170 (chain D) in PDB entry 1B06
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 PRO 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D TYR* 3.3 23.0 - - - -
140D TYR* 3.3 31.8 + - + +
142D ASN* 4.2 9.2 - - - +
162D GLU 3.6 5.4 - - - +
163D LEU* 1.3 84.5 - - - +
165D VAL* 1.3 66.0 + - - +
166D ILE* 4.2 3.6 - - + +
207D TYR* 3.5 56.5 - - + +
162F GLU* 3.5 13.0 - - + +
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Residues in contact with VAL 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LEU* 4.8 12.1 - - + -
86D ILE* 4.0 26.0 - - + -
137D VAL* 3.6 29.6 - - + -
138D LEU 3.9 3.6 - - - -
139D TYR* 4.0 14.4 - - + -
159D HIS* 5.9 0.7 - - - +
164D PRO* 1.3 72.0 - - - +
166D ILE* 1.3 65.7 + - - +
167D LEU 3.8 10.1 - - - +
168D ILE* 4.0 15.0 - - + -
203D ARG* 3.4 22.9 + - - +
161F ALA* 5.0 2.7 - - + -
162F GLU* 2.8 28.8 + - + +
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Residues in contact with ILE 166 (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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90D ASN* 3.4 15.9 - - - +
105D LEU* 4.4 20.4 - - + -
138D LEU* 2.8 26.1 + - + +
139D TYR 4.2 1.6 - - - +
140D TYR* 3.8 32.1 - - + +
147D LEU* 4.7 5.4 - - + -
164D PRO* 4.4 8.7 - - + +
165D VAL* 1.3 83.1 - - - +
167D LEU* 1.3 60.4 + - + +
200D ALA* 3.6 36.4 - - + +
203D ARG* 4.0 11.3 - - + +
204D LEU* 3.7 33.0 - - + +
207D TYR* 5.3 0.2 - - + -
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Residues in contact with LEU 167 (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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90D ASN* 3.4 20.9 - - - +
119D PHE* 4.2 15.3 - - + -
123D PHE* 4.0 21.1 - - + -
137D VAL* 3.4 5.2 - - - +
138D LEU* 2.9 39.1 + - + -
165D VAL* 4.1 0.9 - - - -
166D ILE* 1.3 81.6 - - + +
168D ILE* 1.3 66.6 + - - +
191D TRP* 3.9 24.0 - - + -
192D TRP* 4.5 2.2 - - + -
195D VAL* 3.5 29.2 - - + -
197D TRP* 4.0 28.7 - - + -
200D ALA* 5.1 1.6 - - + -
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Residues in contact with ILE 168 (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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83D LEU* 4.1 25.1 - - + +
86D ILE* 3.9 22.0 - - + -
87D TYR* 3.9 27.5 - - + -
90D ASN* 3.0 18.1 + - - +
91D MET* 5.8 0.2 - - - +
135D TRP* 3.5 32.8 - - + -
136D THR 3.5 11.9 - - - +
137D VAL* 3.8 19.3 - - + -
165D VAL* 4.0 9.9 - - + -
167D LEU* 1.3 77.7 - - - +
169D VAL* 1.3 67.1 + - - +
191D TRP* 3.5 13.7 + - - -
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Residues in contact with VAL 169 (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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87D TYR* 4.4 1.6 - - - -
123D PHE* 3.4 35.9 - - + -
135D TRP* 3.3 11.7 - - - +
136D THR* 3.1 32.0 + - - +
168D ILE* 1.3 73.4 - - - +
170D ASP* 1.3 63.5 + - - +
171D GLU* 3.6 3.7 + - + +
187D TYR* 4.0 10.5 - - + +
188D LEU* 4.1 21.5 - - + -
191D TRP* 3.4 50.0 - - + +
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Residues in contact with ASP 170 (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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33D HIS* 2.9 11.8 + - - -
84D HIS* 3.3 2.6 + - - -
87D TYR* 3.6 27.4 - - + +
134D GLY 3.8 0.7 - - - +
135D TRP* 3.3 28.6 - - + -
169D VAL* 1.3 71.4 - - - +
171D GLU* 1.3 68.9 + - - +
172D PHE* 3.0 22.4 + - - +
175D ALA* 3.8 11.7 - - + +
187D TYR* 2.8 29.8 + - - -
325D FE 1.9 33.6 - - - -
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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