Contacts of the strand formed by residues 192 - 197 (chain A) in PDB entry 4TR8
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 192 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A SER* 4.1 28.7 + - - -
126A LEU* 4.1 24.8 - - + +
160A LEU 4.0 0.6 - - - +
161A GLU* 3.3 6.2 - - - +
162A VAL* 2.8 45.5 + - + +
188A SER* 3.2 23.0 + - - -
190A ASP* 3.2 31.7 + - + -
191A ARG* 1.4 73.0 - - - +
193A GLN* 1.3 60.2 - - - +
194A VAL* 6.2 0.4 - - + -
219A LEU* 4.5 11.2 - - + -
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A LEU* 3.6 26.3 - - + +
160A LEU 3.6 4.7 - - - -
161A GLU* 2.7 31.0 + - + +
191A ARG* 4.0 21.0 - - + +
192A HIS* 1.3 78.3 - - - +
194A VAL* 1.3 68.4 + - - +
195A ILE* 5.9 0.4 - - + -
241A LYS* 5.7 0.5 - - - -
242A PHE* 4.4 20.3 + - - +
243A PRO 5.6 0.8 + - - -
245A TYR* 4.5 4.6 - - - -
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A MET 3.6 0.9 - - - +
159A LEU* 3.4 4.6 - - - +
160A LEU* 2.9 51.2 + - + +
192A HIS* 6.2 0.4 - - + -
193A GLN* 1.3 80.5 - - - +
195A ILE* 1.3 63.1 + - - +
196A VAL* 4.3 9.0 - - + -
219A LEU* 3.9 39.5 - - + -
220A GLY 4.1 11.2 - - - +
224A ILE* 4.6 1.8 - - + -
237A LEU* 3.7 36.6 - - + -
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A TYR* 3.7 29.6 - - + +
157A GLY* 4.3 3.8 - - - -
158A MET 3.5 20.2 - - - +
159A LEU* 4.7 2.5 - - + -
193A GLN* 5.9 0.4 - - + -
194A VAL* 1.3 76.4 - - - +
196A VAL* 1.3 60.8 + - - +
237A LEU* 3.4 9.6 - - - +
238A VAL* 2.8 57.6 + - + +
240A GLY* 3.5 23.6 - - - +
241A LYS 4.0 1.1 - - - -
242A PHE* 3.5 45.1 - - + +
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY* 3.1 1.9 - - - -
158A MET* 2.9 33.0 + - - +
160A LEU* 4.1 17.3 - - + -
194A VAL* 4.3 4.5 - - + -
195A ILE* 1.3 73.9 - - - +
197A PRO* 1.4 75.8 - - + +
200A GLY 4.2 1.8 - - - -
201A ILE* 3.7 50.4 - - + +
204A LEU* 5.9 0.4 - - + -
224A ILE* 3.9 29.4 - - + -
233A PHE* 5.3 2.5 - - + -
235A SER* 4.2 11.4 - - - +
237A LEU* 4.3 5.6 - - + -
238A VAL* 4.3 0.4 - - - -
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Residues in contact with PRO 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.7 33.4 - - + +
156A ASN 3.7 8.3 - - - +
195A ILE 3.8 5.6 - - - +
196A VAL* 1.4 80.4 - - + +
198A ARG* 1.3 66.5 + - - +
199A LYS 3.3 1.1 - - - +
200A GLY* 3.1 2.9 + - - -
201A ILE* 2.9 20.4 + - - +
235A SER* 3.8 8.7 - - - +
236A LYS* 3.1 30.1 - - + +
237A LEU 4.4 2.0 - - - +
238A VAL* 3.7 21.0 - - + +
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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