Contacts of the strand formed by residues 230 - 236 (chain C) in PDB entry 2J1Y
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 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C GLN* 3.3 1.8 - - - -
145C LEU* 2.7 62.9 + - + +
220C TYR* 3.9 5.2 + - - -
221C GLU* 2.6 43.5 + - + +
222C PRO* 3.4 1.9 - - - +
223C PRO* 3.3 19.4 - - - +
229C CYS* 1.3 72.6 - - - +
231C THR* 1.3 71.2 + - - +
232C ILE* 4.9 4.5 - - + -
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Residues in contact with THR 231 (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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142C PRO* 4.1 13.7 - - + -
143C VAL 3.5 7.4 - - - +
144C GLN* 3.8 18.0 + - + +
229C CYS* 4.1 7.1 + - - -
230C THR* 1.3 81.1 - - - +
232C ILE* 1.3 70.8 + - - +
233C HIS* 3.7 29.9 + - + +
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Residues in contact with ILE 232 (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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141C CYS 3.4 2.3 - - - +
142C PRO* 3.7 1.2 - - - +
143C VAL* 2.9 36.9 + - - +
145C LEU* 3.9 21.1 - - + -
157C VAL* 3.8 24.0 - - + -
197C VAL* 4.4 14.6 - - + -
200C ASN* 6.2 1.6 - - - +
218C VAL* 3.8 21.5 - - + -
230C THR* 4.9 5.4 - - + -
231C THR* 1.3 78.6 - - - +
233C HIS* 1.3 69.9 + - - +
234C TYR* 3.5 46.6 + - + +
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Residues in contact with HIS 233 (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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140C THR* 3.4 32.3 - - + +
141C CYS 3.6 2.7 - - - -
142C PRO* 4.0 11.7 - - + +
197C VAL* 3.5 6.8 - - - +
198C GLU* 2.8 54.7 + - + +
199C GLY* 6.0 0.6 - - - -
231C THR* 3.7 26.0 + - + +
232C ILE* 1.3 74.5 - - - +
234C TYR* 1.3 60.3 + - - +
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Residues in contact with TYR 234 (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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141C CYS* 2.8 43.6 + - + +
143C VAL* 3.7 32.3 - - + -
145C LEU* 6.1 0.2 - - + -
157C VAL* 4.3 10.2 + - - +
158C ARG 4.8 0.2 - - - -
159C ALA* 3.6 31.1 + - + +
195C ILE* 3.6 15.0 - - + -
196C ARG 3.2 13.5 - - - -
197C VAL* 3.6 23.2 - - + +
216C VAL* 4.3 1.6 + - + -
218C VAL* 5.3 0.9 - - - +
232C ILE* 3.5 39.3 - - + +
233C HIS* 1.3 72.1 - - - +
235C ASN* 1.3 69.5 + - - +
236C TYR* 4.5 15.9 - - + -
253C THR* 6.2 0.7 - - + -
255C ILE* 3.8 17.7 - - + +
270C PHE* 5.7 0.7 - + - -
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Residues in contact with ASN 235 (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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138C ALA* 3.4 18.1 + - - +
139C LYS 3.2 17.3 + - - -
194C LEU 3.5 3.5 - - - +
195C ILE* 3.6 3.3 - - - +
196C ARG* 2.8 42.4 + - + +
198C GLU* 3.0 42.7 + - - +
234C TYR* 1.3 87.4 + - - +
236C TYR* 1.3 64.2 + - - +
237C MET* 3.9 16.3 + - - +
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Residues in contact with TYR 236 (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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133C LEU* 4.4 6.1 - - + -
135C CYS* 3.8 9.0 - - - -
136C GLN 5.4 0.8 + - - +
137C LEU* 3.7 3.8 - - - +
138C ALA* 2.8 25.9 + - - +
139C LYS 4.7 1.6 + - - +
141C CYS* 3.8 31.4 - - + -
194C LEU* 3.6 16.8 - - + -
195C ILE* 3.8 27.6 - - + -
234C TYR* 4.5 16.3 - - + +
235C ASN* 1.3 74.4 - - - +
237C MET* 1.3 63.2 + - - +
238C CYS 3.5 3.4 + - - +
251C ILE* 5.0 2.0 - - + -
253C THR* 2.7 33.5 + - - +
270C PHE* 3.4 19.8 - - - -
272C VAL* 3.8 21.5 - - + -
274C VAL* 3.5 23.8 - - + -
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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