Contacts of the strand formed by residues 196 - 200 (chain B) in PDB entry 1EQB
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 TYR 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.0 55.3 - - + +
110B LEU* 5.0 1.3 - - + -
168B LYS* 3.1 31.5 + - + +
169B MET* 3.3 17.3 - - + +
170B ILE* 2.7 34.7 + - - +
190B ALA* 4.5 0.9 - - - -
194B GLY 5.8 1.1 - - - -
195B ALA* 1.3 76.7 - - - +
197B LEU* 1.3 60.9 + - - +
221B HIS* 3.6 30.3 - + + +
248B LEU* 5.3 7.8 - - + +
251B LYS* 5.7 2.3 + - - -
132C PRO* 5.3 9.8 - - + +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 3.5 23.1 - - + +
172B GLY 4.6 0.4 - - - +
183B TRP* 3.8 10.1 - - + +
186B MET* 3.9 27.1 - - + +
187B ARG* 3.5 31.4 - - + +
190B ALA* 4.2 10.3 - - + -
196B TYR* 1.3 73.2 - - - +
198B PHE* 1.3 58.7 + - - +
199B VAL* 4.0 19.3 - - + -
219B HIS* 3.6 16.2 - - + +
220B ALA* 3.3 14.9 - - + +
221B HIS* 2.7 42.5 + - + +
222B VAL 3.6 3.3 + - - -
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Residues in contact with PHE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASN* 3.3 31.9 - - + -
105B VAL* 3.9 25.4 - - + -
106B TYR* 4.5 15.5 - + - -
109B LEU* 5.7 0.9 - - + -
129B HIS* 5.4 1.6 - + - -
169B MET* 3.8 32.1 - - + -
170B ILE 2.9 9.0 + - - +
171B ILE* 3.2 32.2 - - + +
172B GLY 2.8 24.5 + - - +
196B TYR* 3.6 1.0 + - + -
197B LEU* 1.3 72.4 - - - +
199B VAL* 1.3 72.3 + - - +
200B ASP* 4.4 5.6 - - + -
222B VAL* 3.5 14.8 - - + +
223B VAL 4.6 0.2 - - - -
224B THR* 3.2 32.3 - - + -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLY* 3.0 11.2 - - - +
183B TRP* 3.7 35.0 - - + -
197B LEU* 4.0 16.1 + - + -
198B PHE* 1.3 80.9 - - - +
200B ASP* 1.3 67.3 + - - +
201B MET* 4.2 1.8 - - + +
216B PRO* 3.7 29.4 - - + -
220B ALA* 3.8 23.6 - - + -
222B VAL 3.0 8.1 + - - +
223B VAL* 3.1 9.9 - - + +
224B THR 2.9 23.6 + - - -
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Residues in contact with ASP 200 (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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102B ASN* 2.9 19.4 + - - +
129B HIS* 3.0 22.7 + - + +
171B ILE* 5.1 0.4 - - + -
172B GLY 2.8 8.9 + - - +
173B GLY* 3.4 18.4 - - - -
174B PHE 4.0 4.5 + - - +
183B TRP* 5.6 0.2 - - - -
198B PHE* 4.2 7.2 + - + -
199B VAL* 1.3 70.8 - - - +
201B MET* 1.3 58.2 + - - +
202B ALA* 3.2 17.5 + - - +
224B THR* 3.5 23.6 + - - +
225B THR* 4.5 0.5 - - - -
2291B PLP 2.5 37.8 + - - +
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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
------------------------------------------------------------
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