Contacts of the strand formed by residues 227 - 232 (chain C) in PDB entry 1T4P
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 ILE 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C HIS* 4.6 0.9 - - - -
119C CYS* 3.7 17.7 - - - +
121C ILE* 4.3 22.4 - - + -
216C PHE* 4.2 23.1 - - + -
219C LEU* 6.2 0.2 - - + -
220C LEU* 4.3 13.2 - - + -
225C ARG 4.0 7.6 - - - +
226C PRO* 1.3 77.3 - - - +
228C HIS* 1.3 70.9 + - - +
229C LEU* 4.2 4.0 - - + +
264C ILE* 4.7 11.0 - - + -
267C THR* 3.9 22.0 - - - +
269C LEU* 3.0 21.8 + - + +
270C LEU* 3.7 9.4 - - + +
271C SER* 3.0 23.7 + - - -
272C GLY 3.2 7.3 + - - +
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Residues in contact with HIS 228 (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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94C SER* 5.4 2.2 - - - -
107C SER* 3.2 26.9 - - - -
108C ILE* 3.3 32.8 - - + +
111C HIS* 2.9 27.3 + - + +
118C LEU* 3.8 16.8 - - + +
119C CYS 2.8 16.2 + - - +
120C VAL* 3.4 6.6 - - + +
121C ILE 3.0 22.9 + - - +
226C PRO 4.2 0.2 + - - -
227C ILE* 1.3 74.3 - - - +
229C LEU* 1.3 68.0 + - - +
230C SER* 3.6 3.0 + - - -
272C GLY* 3.3 17.2 - - - +
273C LEU 4.4 0.7 - - - -
274C ASP* 2.5 26.3 + - - -
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Residues in contact with LEU 229 (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 ILE* 3.5 21.3 - - + +
123C VAL* 3.8 25.8 - - + -
227C ILE* 3.9 3.2 + - + -
228C HIS* 1.3 75.0 - - - +
230C SER* 1.3 57.8 + - - +
231C PHE* 4.4 16.2 - - + -
260C ILE* 5.3 0.4 - - + -
261C THR* 4.5 3.8 - - + -
264C ILE* 3.5 35.7 - - + -
270C LEU* 4.2 11.0 - - + -
272C GLY 2.8 12.1 + - - +
273C LEU* 3.1 16.0 - - + +
274C ASP* 2.8 25.1 + - - +
303C CYS* 3.9 28.0 - - - -
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Residues in contact with SER 230 (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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101C HIS* 2.7 31.3 + - - -
104C ALA* 3.9 2.3 - - - +
108C ILE* 4.7 0.4 - - - -
120C VAL* 4.8 1.3 - - - -
121C ILE 3.1 8.9 + - - -
122C TRP* 3.7 32.3 - - - -
123C VAL 3.3 21.5 + - - +
228C HIS* 3.6 9.3 + - - -
229C LEU* 1.3 71.9 - - - +
231C PHE* 1.3 61.4 + - - +
232C ASP 3.7 1.6 + - - -
274C ASP* 3.5 22.2 + - - +
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Residues in contact with PHE 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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101C HIS* 4.8 0.4 - - - -
123C VAL* 3.6 42.4 - - + -
229C LEU* 3.7 19.9 + - + -
230C SER* 1.3 70.9 - - - +
232C ASP* 1.3 78.2 + - - +
233C VAL* 3.5 8.2 + - + +
236C LEU* 4.6 20.0 - - + -
257C GLY* 4.5 8.3 - - - -
260C ILE* 5.0 4.0 - - + -
261C THR* 4.1 21.3 - - + -
273C LEU* 4.6 0.4 - - + -
274C ASP* 2.7 17.1 + - - +
275C ILE* 3.7 14.6 - - + +
276C MET* 2.9 28.3 + - - -
299C LEU* 3.8 34.1 - - + -
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Residues in contact with ASP 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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101C HIS* 3.4 7.7 + - + +
123C VAL 3.0 13.2 + - - +
124C ASP* 3.1 21.5 - - - +
230C SER 3.7 1.8 + - - -
231C PHE* 1.3 77.7 - - - +
233C VAL* 1.3 58.8 + - - +
234C ASP* 2.8 29.5 + - - +
235C GLY* 2.8 21.0 + - - -
276C MET* 4.0 4.0 - - - -
277C GLU* 3.4 18.4 - - - +
503C MN 2.1 33.7 + - - +
505C MN 2.5 12.3 + - - -
1002C 2BH 2.7 3.3 + - - -
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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