Contacts of the strand formed by residues 192 - 197 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181G ALA* 3.2 22.3 - - + +
184G SER* 2.8 37.3 + - - +
185G MET* 4.2 7.8 - - + +
188G ASP* 5.0 3.4 + - - -
190G GLU* 3.5 17.1 + - - +
191G ASP* 1.3 81.7 + - - +
193G SER* 1.3 65.7 + - - +
473G PHE* 3.4 8.5 + - - +
474G LEU* 3.4 22.7 - - + -
475G GLY 2.8 22.5 + - - -
688G THR* 4.1 1.7 - - - -
689G ASN* 2.7 51.2 + - - +
690G PRO 4.9 1.7 - - - +
691G SER* 5.6 2.0 - - - -
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Residues in contact with SER 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G GLN* 1.3 76.3 + - - +
194G ILE* 1.3 59.7 + - - +
195G LEU* 4.1 5.2 - - - -
265G PHE* 4.4 7.3 - - - -
473G PHE* 5.1 0.2 - - - -
475G GLY 3.2 9.4 - - - -
685G LEU* 3.9 24.4 - - - +
688G THR* 2.4 30.3 + - - +
689G ASN 2.9 6.1 + - - +
690G PRO* 3.3 13.8 - - - -
691G SER* 2.6 36.9 + - - -
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Residues in contact with ILE 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G VAL* 4.9 3.8 - - + +
178G THR* 4.7 16.6 - - - +
181G ALA* 4.1 18.8 - - + -
193G SER* 1.3 76.3 - - - +
195G LEU* 1.3 62.5 + - - +
196G CYS* 3.6 13.4 + - - -
211G VAL* 5.8 6.5 - - + -
474G LEU* 3.9 14.1 - - + -
475G GLY 2.7 17.5 + - - +
476G ILE* 4.0 18.6 - - + +
477G LEU 2.7 28.4 + - - +
691G SER* 3.4 25.8 - - - +
693G VAL* 4.2 22.7 - - + -
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Residues in contact with LEU 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G SER* 4.8 3.6 - - - -
194G ILE* 1.3 77.9 - - - +
196G CYS* 1.4 61.8 + - - +
197G THR* 4.1 1.1 - - + -
477G LEU* 3.5 35.7 - - + -
502G LEU* 4.7 25.8 - - + +
505G LEU* 4.7 15.7 - - + -
685G LEU* 4.1 16.8 - - + -
690G PRO* 4.7 4.5 - - + -
691G SER 2.6 18.8 + - - +
692G PHE* 3.6 27.7 - - + -
693G VAL* 2.8 30.8 + - - +
694G ARG* 3.7 11.9 + - - +
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Residues in contact with CYS 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G ILE* 3.6 13.9 + - - -
195G LEU* 1.4 76.3 - - - +
197G THR* 1.3 61.6 + - - +
204G LYS* 3.3 32.2 + - + -
208G THR* 4.4 16.4 - - - -
476G ILE* 5.0 4.5 - - - -
477G LEU* 2.9 22.7 + - - +
478G ASP* 4.8 2.0 - - + -
479G ILE* 3.7 12.5 + - - +
693G VAL* 3.6 26.2 - - - +
695G CYS* 4.7 6.3 - - - -
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Residues in contact with THR 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G LEU* 5.6 1.1 - - + -
196G CYS* 1.3 72.7 - - - +
198G GLY* 1.3 70.3 + - - +
199G GLU* 3.2 4.7 + - - +
204G LYS* 3.1 13.5 - - - +
479G ILE* 4.1 3.6 - - + -
481G GLY* 4.9 7.0 - - - -
499G ASN* 5.7 5.4 - - - +
502G LEU* 6.4 1.8 - - + -
693G VAL 3.4 3.6 + - - -
694G ARG* 3.1 62.4 - - - +
695G CYS* 4.0 8.8 + - - +
719G ASN* 4.1 17.0 - - + +
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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