Contacts of the strand formed by residues 196 - 201 (chain C) in PDB entry 1RJF
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 THR 196 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C PHE* 4.5 1.0 - - - -
100C GLN* 2.7 42.2 + - + +
102C VAL* 3.8 18.8 - - + -
194C ILE 3.0 7.3 + - - -
195C PRO* 1.3 69.8 - - - +
197C ILE* 1.3 63.2 + - - +
198C VAL* 3.5 12.9 + - + +
223C PHE* 3.4 39.3 - - + -
225C HIS 3.2 9.4 + - - -
226C GLY* 3.2 6.4 - - - -
227C LEU 3.2 18.9 + - - -
328C TRP* 4.6 1.3 - - - -
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Residues in contact with ILE 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ILE* 4.1 18.8 - - + +
92C PHE* 3.5 41.1 - - + -
93C LEU* 3.7 26.2 - - + -
99C VAL* 3.9 11.9 - - + -
100C GLN 3.2 5.9 + - - -
101C VAL* 3.4 15.5 - - + +
102C VAL 3.2 22.2 + - - -
195C PRO 4.3 0.4 + - - -
196C THR* 1.3 69.8 - - - +
198C VAL* 1.3 61.9 + - - +
199C ILE* 4.2 11.4 - - + -
227C LEU* 3.4 11.4 - - + +
229C ILE* 3.8 28.0 - - + -
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Residues in contact with VAL 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL* 3.9 13.2 - - + +
104C LEU* 3.4 31.9 - - + -
196C THR* 3.5 21.7 + - + +
197C ILE* 1.3 73.7 - - - +
199C ILE* 1.3 63.7 + - - +
219C ILE* 3.7 24.7 - - + -
223C PHE* 5.0 0.7 - - + -
227C LEU 3.1 7.9 + - - +
228C TRP* 3.4 34.9 - - + +
229C ILE 3.1 25.8 + - - +
328C TRP* 4.9 6.3 - - + -
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Residues in contact with ILE 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE* 4.7 9.0 - - + -
89C ILE* 3.9 24.9 - - + -
101C VAL* 3.8 25.6 - - + -
102C VAL 3.4 5.7 + - - +
103C ASN* 3.9 20.9 - - - +
104C LEU* 3.1 32.3 + - - +
111C ARG* 4.3 15.3 - - - +
124C TYR* 4.0 14.8 - - + +
197C ILE* 4.2 10.8 - - + -
198C VAL* 1.3 80.5 - - - +
200C SER* 1.3 64.1 + - - +
201C GLU* 4.0 16.8 - - + +
229C ILE* 3.5 13.5 - - + +
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Residues in contact with SER 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LEU* 3.8 6.7 - - - -
199C ILE* 1.3 77.6 - - - +
201C GLU* 1.3 62.1 + - - +
202C CYS 3.5 0.7 + - - -
203C LEU* 4.1 23.5 + - - -
204C LEU* 3.6 14.3 - - - +
228C TRP* 3.4 16.3 + - - -
229C ILE 3.2 5.4 + - - -
230C SER* 2.7 28.6 + - - -
231C TYR 3.4 21.0 + - - +
232C ASP* 4.8 1.2 - - - +
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 5.1 11.1 - - - -
81C ARG* 3.1 45.0 + - - +
82C THR* 5.5 1.2 + - - -
85C ILE* 4.0 22.6 - - + +
103C ASN* 5.1 3.6 + - - +
104C LEU 4.1 5.7 + - - -
105C GLY 3.6 17.7 - - - +
106C CYS 5.3 2.4 - - - +
109C ASP* 3.5 14.0 - - - +
111C ARG* 3.3 21.8 + - - -
199C ILE* 4.0 12.3 - - + +
200C SER* 1.3 70.4 - - - +
202C CYS* 1.3 73.1 + - - +
203C LEU* 3.4 0.9 + - - +
231C TYR* 4.3 7.4 - - + -
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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