Contacts of the strand formed by residues 196 - 202 (chain C) in PDB entry 3IU3
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 TYR 196 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C LEU* 4.1 28.5 - - + -
156C TRP* 4.4 6.3 - + + -
157C ASN* 3.6 4.0 - - - -
161C LEU* 3.6 27.1 - - + -
184C VAL* 5.0 0.9 - - + -
186C VAL* 3.2 45.6 - - + +
187C PRO* 5.3 0.2 - - - +
190C SER* 3.7 18.4 + - - -
191C LEU* 4.6 12.3 - - + -
194C GLN* 3.5 43.7 - - + +
195C THR* 1.3 78.4 - - - +
197C ILE* 1.3 59.3 + - - +
212C ARG* 3.5 4.3 - - - +
213C VAL* 2.8 46.8 + - - +
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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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156C TRP* 3.4 7.0 - - - -
157C ASN* 2.7 47.5 + - - +
195C THR* 4.7 12.3 - - + -
196C TYR* 1.3 79.2 - - - +
198C CYS* 1.3 65.2 + - - +
199C ASN* 3.8 16.2 - - - +
210C ASP* 4.1 16.6 - - + +
211C LYS 3.4 9.6 - - - +
212C ARG* 3.8 25.6 - - + +
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Residues in contact with CYS 198 (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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123C VAL* 4.0 4.7 - - - -
142C CYS* 2.0 50.0 - - + -
154C VAL* 4.3 5.4 - - + -
155C SER 3.5 5.4 - - - +
156C TRP* 3.6 26.8 - - + -
197C ILE* 1.3 72.7 - - - +
199C ASN* 1.3 59.9 + - - +
200C VAL* 3.8 16.2 - - - -
209C VAL 3.7 0.9 - - - +
210C ASP* 3.5 4.7 - - - -
211C LYS* 3.0 30.5 + - - -
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Residues in contact with ASN 199 (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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153C THR* 3.2 7.8 - - - +
154C VAL* 3.2 1.4 - - - -
155C SER* 2.6 63.0 + - - +
156C TRP 3.8 0.2 - - - +
157C ASN 3.9 0.6 - - - +
158C SER* 2.9 40.7 + - - +
197C ILE* 3.8 10.8 - - - +
198C CYS* 1.3 73.9 - - - +
200C VAL* 1.3 60.7 + - - +
201C ASN* 3.9 8.4 + - - +
208C LYS* 6.0 1.3 - - + -
209C VAL 4.2 2.5 - - - -
210C ASP* 3.1 24.4 - - - +
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Residues in contact with VAL 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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121C PRO* 4.3 11.0 - - + -
123C VAL* 3.8 28.7 - - + -
144C VAL* 3.7 37.2 - - + -
152C VAL* 4.6 7.4 - - + -
153C THR 3.3 5.4 - - - +
154C VAL* 4.4 6.3 - - + -
198C CYS* 3.8 23.1 - - - -
199C ASN* 1.3 74.1 - - - +
201C ASN* 1.3 63.8 + - - +
202C HIS 4.2 0.2 + - - -
207C THR* 4.6 0.9 - - + +
208C LYS* 3.2 8.3 - - - +
209C VAL* 3.1 37.6 + - + +
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Residues in contact with ASN 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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151C PRO 4.4 0.3 - - - +
152C VAL* 3.4 8.7 - - - +
153C THR* 2.7 58.4 + - + +
199C ASN* 3.9 8.2 + - - +
200C VAL* 1.3 75.5 - - - +
202C HIS* 1.3 59.7 + - - +
203C LYS* 4.0 23.7 - - + +
207C THR 3.9 3.6 + - - -
208C LYS* 3.4 34.0 - - - +
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Residues in contact with HIS 202 (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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119C LYS 3.5 12.6 + - - -
121C PRO* 3.8 21.4 - - + +
147C TYR* 3.8 3.8 - + - -
148C PHE 3.3 26.9 - - - -
149C PRO 2.6 24.3 + - - -
151C PRO 3.2 25.5 + - - -
152C VAL* 3.6 16.2 - - + -
200C VAL 4.2 0.2 + - - -
201C ASN* 1.3 73.8 - - - +
203C LYS* 1.3 66.4 + - - +
204C PRO* 3.8 17.6 - - + +
205C SER* 2.6 32.5 + - - +
207C THR* 3.0 34.6 + - + +
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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