Contacts of the strand formed by residues 193 - 199 (chain I) in PDB entry 5G04
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 PHE 193 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188I TYR* 2.9 7.8 - - - -
189I ALA* 2.5 45.1 + - + +
192I MET* 1.3 77.5 - - - +
194I LYS* 1.3 85.0 + - - +
195I ILE* 3.6 27.6 - - + -
252I ALA* 4.7 4.3 - - - -
255I PHE* 3.9 37.7 - + + -
256I THR* 3.3 28.3 - - - +
259I SER* 5.0 5.6 - - - -
537I LEU* 3.6 47.3 - - + -
540I PRO* 5.1 5.2 - - + -
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Residues in contact with LYS 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I GLU* 2.9 25.7 + - + +
187I LEU 3.4 6.5 - - - +
188I TYR* 3.8 28.7 + - + +
193I PHE* 1.3 96.6 - - + +
195I ILE* 1.3 58.0 + - - +
196I ALA 3.6 21.1 - - - +
197I ARG* 3.2 25.1 - - - +
537I LEU* 4.8 2.2 - - + +
538I GLN* 4.0 28.0 + - - +
541I ALA* 3.6 22.9 - - + +
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Residues in contact with ILE 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I LEU* 6.4 0.2 - - + -
175I ILE* 5.0 11.4 - - + -
187I LEU* 2.8 29.0 + - + +
188I TYR 4.9 0.2 - - - -
189I ALA* 4.3 18.2 - - + +
193I PHE* 3.5 24.7 + - + -
194I LYS* 1.3 73.8 - - - +
196I ALA* 1.4 64.2 + - + +
241I LEU* 4.9 7.6 - - + -
248I VAL* 3.8 21.8 - - + -
251I MET* 3.3 35.4 - - + -
252I ALA* 4.6 7.9 - - + -
540I PRO* 5.3 2.0 - - + -
541I ALA* 3.7 6.2 - - - +
544I ILE* 3.3 25.9 - - + +
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Residues in contact with ALA 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I ILE 4.6 0.4 - - - -
186I GLU* 3.4 2.6 - - - -
187I LEU* 2.9 51.6 + - + -
194I LYS* 3.4 7.5 + - - +
195I ILE* 1.4 83.1 - - + +
197I ARG* 1.3 63.2 + - - +
198I VAL* 5.2 0.2 - - + -
241I LEU* 5.5 0.4 - - + -
541I ALA* 3.7 13.9 - - - +
544I ILE* 3.8 19.7 - - + -
545I GLY 4.6 1.8 - - - +
548I MET* 4.1 8.1 - - + -
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Residues in contact with ARG 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I GLU* 3.3 24.3 + - - +
184I PHE* 3.4 14.5 - - + -
185I ILE 3.3 6.7 - - - -
186I GLU* 2.1 54.4 + - + +
194I LYS* 3.2 25.9 - - + +
196I ALA* 1.3 74.9 - - - +
198I VAL* 1.3 69.0 + - - +
199I THR* 4.3 17.6 + - + +
538I GLN* 4.5 6.3 + - - -
541I ALA* 3.3 12.9 + - + +
542I ASP* 4.4 19.8 + - - +
545I GLY* 2.9 22.4 - - - -
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Residues in contact with VAL 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I PHE* 2.9 23.0 - - - +
185I ILE* 2.8 36.7 + - + +
187I LEU* 4.7 9.6 - - + -
196I ALA* 5.2 0.2 - - + -
197I ARG* 1.3 79.0 - - - +
199I THR* 1.3 73.5 + - - +
201I ILE* 4.9 2.0 - - + -
217I LEU* 4.9 1.6 - - + -
236I LEU* 3.8 26.2 - - + -
545I GLY* 4.3 8.5 - - - +
548I MET* 3.7 41.7 - - + +
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Residues in contact with THR 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I GLY 3.9 6.5 - - - +
184I PHE* 4.1 15.5 - - + -
197I ARG* 4.3 17.5 - - + +
198I VAL* 1.3 88.8 - - - +
200I GLY* 1.3 67.0 + - - +
201I ILE* 3.1 10.4 + - - +
545I GLY 5.3 1.0 + - - -
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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