Contacts of the strand formed by residues 182 - 186 (chain B) in PDB entry 3SZB
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 HIS 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 3.8 15.1 - - + +
106B VAL 3.7 2.4 + - - -
107B VAL* 3.4 14.7 - - + -
108B LEU 3.0 24.1 + - - -
180B PHE* 3.5 3.0 - - - +
181B ASP* 1.3 79.6 - - - +
183B ILE* 1.3 91.7 + - - +
184B LEU 4.0 0.4 - - - -
204B THR* 3.6 1.7 - - - +
205B PRO* 3.4 37.2 + - + +
206B VAL 4.1 3.4 - - - -
207B THR* 2.8 33.0 + - - -
420B THR* 3.6 25.7 + - + +
421B PHE* 3.8 19.7 - + - -
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.3 31.4 - - + +
110B ILE* 4.3 6.3 - - + -
176B LEU* 3.9 22.2 - - + +
180B PHE* 4.3 10.8 - - + -
182B HIS* 1.3 82.8 - - - +
184B LEU* 1.3 70.1 + - - +
185B TYR 4.5 0.2 - - - +
195B ILE* 3.9 22.7 - - + -
198B ALA 5.5 0.2 - - - -
199B ALA* 4.0 21.8 - - + +
204B THR* 3.9 17.7 - - + +
205B PRO 3.0 6.5 + - - -
206B VAL* 3.2 11.1 - - + +
207B THR 2.9 24.8 + - - +
208B LEU* 5.3 0.2 - - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 5.1 0.2 - - - +
108B LEU 2.9 9.3 + - - +
109B VAL* 3.5 10.3 - - + -
110B ILE* 2.9 28.7 + - - +
119B LEU 5.5 0.4 - - - +
123B PRO* 4.1 23.1 - - + -
182B HIS* 4.0 1.0 - - - -
183B ILE* 1.3 73.9 - - - +
185B TYR* 1.3 65.1 + - - +
186B THR* 3.8 21.5 - - - +
207B THR* 3.3 33.4 - - + +
209B GLU* 4.9 3.6 - - + -
412B TYR* 4.0 23.6 - - + -
420B THR* 5.4 0.2 - - + -
421B PHE* 3.8 34.3 - - + -
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Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 3.6 33.9 - - + -
111B GLY 5.3 0.7 - - - -
183B ILE* 4.1 0.4 - - + -
184B LEU* 1.3 76.0 - - - +
186B THR* 1.3 70.3 + - - +
187B GLY* 3.3 21.4 - - - -
188B SER* 3.1 32.9 + - - -
191B VAL* 3.3 30.0 - - + +
192B GLY* 3.9 8.1 - - - -
195B ILE* 3.9 26.9 - - + -
207B THR 2.9 6.1 + - - +
208B LEU* 3.6 15.7 - - + -
209B GLU* 2.8 27.2 + - - +
210B LEU* 3.7 13.9 - - + -
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE 3.4 11.1 + - - -
111B GLY 4.1 5.0 - - - +
112B THR* 3.4 39.4 - - + -
119B LEU* 4.4 23.4 + - + +
184B LEU* 3.8 14.7 - - - +
185B TYR* 1.3 86.9 - - - +
187B GLY* 1.3 60.9 + - - +
209B GLU* 3.3 24.1 - - + +
243B CYS* 5.8 1.6 - - + -
401B PHE* 6.4 0.4 - - + -
412B TYR* 4.6 7.1 + - - -
1001B I1E 4.8 10.3 - - + -
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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
------------------------------------------------------------
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