Contacts of the strand formed by residues 192 - 197 (chain F) in PDB entry 5JLH
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 GLN 192 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181F ALA* 3.2 21.5 - - + +
184F SER* 2.8 36.7 + - - +
185F MET* 4.2 6.7 - - + +
188F ASP* 5.0 2.8 + - - -
190F GLU* 3.5 17.7 + - - +
191F ASP* 1.3 81.7 + - - +
193F SER* 1.3 63.3 + - - +
473F PHE* 3.4 8.7 + - - +
474F LEU* 3.4 23.3 - - + -
475F GLY 2.8 22.3 + - - -
688F THR* 4.1 2.2 + - - -
689F ASN* 2.7 50.4 + - - +
690F PRO 4.9 1.7 - - - +
691F SER* 5.6 2.0 - - - -
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Residues in contact with SER 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F GLN* 1.3 76.4 + - - +
194F ILE* 1.3 59.8 + - - +
195F LEU* 4.8 4.5 - - - -
265F PHE* 4.5 7.2 - - - -
473F PHE* 5.1 0.2 - - - -
475F GLY 3.2 9.6 - - - -
685F LEU* 3.9 24.4 - - - +
688F THR* 2.4 30.7 + - - +
689F ASN 2.9 5.7 + - - +
690F PRO* 3.2 14.0 - - - +
691F SER* 2.6 35.6 + - - -
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Residues in contact with ILE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F VAL* 4.9 3.8 - - + +
178F THR* 4.7 15.9 - - - +
181F ALA* 4.1 19.5 - - + -
193F SER* 1.3 77.3 - - - +
195F LEU* 1.3 64.5 + - - +
196F CYS* 3.6 13.5 + - - -
211F VAL* 5.8 6.3 - - + -
474F LEU* 3.9 13.5 - - + -
475F GLY 2.7 16.0 + - - +
476F ILE* 4.1 19.7 - - + +
477F LEU 2.7 26.2 + - - +
691F SER* 3.4 25.6 - - - +
693F VAL* 4.2 22.2 - - + -
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Residues in contact with LEU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F SER* 4.8 3.6 - - - -
194F ILE* 1.3 78.4 - - - +
196F CYS* 1.4 63.0 + - - +
197F THR* 5.8 0.9 - - + -
477F LEU* 3.5 35.0 - - + -
502F LEU* 4.7 26.0 - - + +
505F LEU* 4.7 16.6 - - + -
685F LEU* 4.1 16.4 - - + -
690F PRO* 4.7 4.0 - - + -
691F SER 2.6 17.5 + - - +
692F PHE* 3.6 28.2 - - + -
693F VAL* 2.8 31.0 + - - +
694F ARG* 3.7 11.7 + - - +
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Residues in contact with CYS 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F ILE* 3.6 12.3 + - - -
195F LEU* 1.4 76.3 - - - +
197F THR* 1.3 61.1 + - - +
204F LYS* 3.3 32.5 + - + -
208F THR* 4.4 17.5 - - - -
476F ILE* 5.0 4.5 - - - -
477F LEU* 2.9 24.4 + - - +
478F ASP* 4.8 1.6 - - + -
479F ILE* 3.7 12.6 + - - +
693F VAL* 3.6 26.5 - - - +
695F CYS* 4.7 6.1 - - - -
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Residues in contact with THR 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F LEU* 5.8 1.3 - - + -
196F CYS* 1.3 72.6 - - - +
198F GLY* 1.3 69.9 + - - +
199F GLU* 3.2 4.9 + - - +
204F LYS* 3.2 13.7 - - - +
479F ILE* 4.1 3.6 - - + -
481F GLY* 4.9 5.6 - - - -
499F ASN* 5.6 4.9 - - - +
502F LEU* 6.4 2.0 - - + -
693F VAL 3.4 4.2 + - - -
694F ARG* 3.1 62.1 - - - +
695F CYS* 4.0 8.4 + - - +
719F ASN* 4.1 16.8 - - + +
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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
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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