Contacts of the strand formed by residues 188 - 192 (chain B) in PDB entry 4L1X
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 CYS 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 4.4 5.4 - - + -
113B LEU* 3.8 17.9 - - - -
115B LEU* 3.6 32.3 - - - -
164B GLY* 4.3 0.8 - - - -
165B VAL* 3.1 30.9 + - - +
186B PRO* 3.3 6.0 - - - +
187B VAL* 1.3 84.3 - - + +
189B ASN* 1.3 61.4 + - - +
190B GLN* 4.8 1.6 - - - -
211B ILE* 3.5 7.4 - - - -
212B VAL* 2.9 18.6 - - + +
214B VAL* 4.0 18.6 - - + -
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Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 3.2 18.7 - - + +
167B ASN 3.6 5.4 + - - -
168B PHE* 2.9 43.7 + - - -
173B LEU* 3.8 17.8 - - + +
188B CYS* 1.3 73.7 - - - +
190B GLN* 1.3 60.6 + - - +
191B VAL* 3.6 12.8 + - - +
202B LEU* 3.9 11.5 - - - +
206B CYS* 4.2 17.0 - - - -
211B ILE* 3.6 3.7 - - + +
212B VAL 2.9 7.1 + - - -
213B LEU* 3.5 9.4 - - + +
214B VAL 3.2 17.1 + - - +
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Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 6.0 0.4 + - - -
50B ASP* 2.9 25.7 + - - -
82B THR* 4.8 0.8 - - - +
84B LYS* 3.4 14.5 + - - +
113B LEU* 6.0 1.0 - - - +
115B LEU* 3.7 14.5 - - + +
165B VAL 2.9 8.3 + - - -
166B SER* 2.6 32.1 + - - +
167B ASN 2.9 13.9 + - - -
188B CYS* 4.2 1.9 - - - -
189B ASN* 1.3 69.9 - - - +
191B VAL* 1.3 59.2 + - - +
214B VAL* 3.2 33.0 - - + +
216B TYR* 3.9 8.9 - - + -
268B LEU* 3.7 16.8 - - + +
401B NAP 3.0 35.8 + - - -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASN* 3.9 15.9 - - - +
168B PHE 4.0 4.7 - - - +
189B ASN* 3.6 27.1 - - - +
190B GLN* 1.3 79.8 - - - +
192B GLU* 1.3 67.4 + - - +
193B CYS 3.4 0.9 + - - -
199B GLN* 3.6 23.3 - - - +
202B LEU* 4.2 5.6 - - + -
213B LEU* 3.8 36.1 - - + -
214B VAL 2.9 9.6 + - - +
215B ALA* 3.4 1.7 - - - -
216B TYR* 2.9 31.5 + - - -
304B ARG* 6.2 0.2 - - - +
319B PHE* 5.9 4.3 - - + -
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Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASN* 4.8 0.6 + - - -
191B VAL* 1.3 72.9 - - - +
193B CYS* 1.3 63.3 + - - +
194B HIS* 2.8 31.0 + - + +
197B PHE* 4.2 5.1 - - + +
199B GLN* 2.9 27.5 + - - +
216B TYR* 3.3 32.1 + - + +
217B SER* 4.2 7.4 - - - -
304B ARG* 3.4 27.1 - - - +
305B TYR* 2.7 31.6 + - - -
306B LEU* 2.8 31.8 + - - +
319B PHE* 6.4 0.2 - - + -
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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
------------------------------------------------------------
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