Contacts of the strand formed by residues 227 - 232 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B HIS* 4.5 1.8 - - - -
119B CYS* 3.6 19.5 - - - +
121B ILE* 4.2 21.1 - - + -
216B PHE* 4.3 16.8 - - + -
219B LEU* 6.2 0.2 - - + -
220B LEU* 4.3 19.3 - - + -
225B ARG 4.0 7.4 - - - +
226B PRO* 1.3 77.2 - - - +
228B HIS* 1.3 71.4 + - - +
229B LEU* 4.2 3.8 - - + +
264B ILE* 4.6 9.6 - - + -
267B THR* 3.8 22.0 - - + +
269B LEU* 3.0 23.0 + - + +
270B LEU* 3.9 10.2 - - + +
271B SER* 2.9 24.1 + - - -
272B GLY 3.2 6.8 + - - +
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Residues in contact with HIS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B SER* 5.4 2.0 - - - -
107B SER* 3.2 24.0 - - - -
108B ILE* 3.3 35.6 - - + +
111B HIS* 2.9 31.7 + - + +
118B LEU* 4.0 12.1 - - + -
119B CYS 2.8 15.4 + - - +
120B VAL* 3.3 6.5 - - + +
121B ILE 2.9 26.7 + - - +
227B ILE* 1.3 76.0 - - - +
229B LEU* 1.3 66.1 + - - +
230B SER* 3.7 3.1 + - - -
272B GLY* 3.3 16.7 + - - -
273B LEU 4.5 0.7 - - - -
274B ASP* 2.5 26.6 + - - -
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.5 20.4 - - + +
123B VAL* 3.6 26.2 - - + -
227B ILE* 4.0 3.8 - - + -
228B HIS* 1.3 73.1 - - - +
230B SER* 1.3 59.6 + - - +
231B PHE* 4.2 16.6 - - + -
260B ILE* 5.3 0.9 - - + -
261B THR* 4.4 3.8 - - + -
264B ILE* 3.6 33.7 - - + -
270B LEU* 4.2 10.3 - - + -
272B GLY 2.8 10.5 + - - +
273B LEU* 3.1 18.0 - - + +
274B ASP 2.8 24.9 + - - -
303B CYS* 3.8 28.9 - - - -
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B HIS* 2.8 29.3 + - - -
104B ALA* 3.9 3.1 - - - +
108B ILE* 4.8 0.7 - - - -
120B VAL* 4.8 1.3 - - - -
121B ILE 3.1 9.3 + - - -
122B TRP* 3.6 32.8 - - - -
123B VAL 3.3 22.2 + - - +
228B HIS* 3.7 9.2 + - - -
229B LEU* 1.3 70.5 - - - +
231B PHE* 1.3 59.7 + - - +
232B ASP 3.8 2.0 + - - -
274B ASP* 3.6 22.4 + - - +
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B HIS* 4.8 0.6 + - - -
123B VAL* 3.6 42.2 - - + -
229B LEU* 3.7 19.2 + - + -
230B SER* 1.3 70.3 - - - +
232B ASP* 1.3 77.4 + - - +
233B VAL* 3.4 9.9 + - + -
235B GLY* 5.2 0.9 - - - -
236B LEU* 4.5 17.9 - - + -
257B GLY* 4.6 9.9 - - - -
260B ILE* 5.0 4.0 - - + -
261B THR* 4.2 21.3 - - + -
273B LEU* 4.7 0.2 - - + -
274B ASP* 2.7 18.8 + - - +
275B ILE* 3.7 14.5 - - + +
276B MET* 2.9 28.9 + - - -
299B LEU* 3.7 33.7 - - + -
303B CYS* 5.9 0.2 - - - -
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B HIS* 3.6 7.8 - - + +
123B VAL 3.0 9.9 + - - +
124B ASP* 3.0 20.9 - - - +
230B SER 3.8 1.6 + - - -
231B PHE* 1.3 74.8 - - - +
233B VAL* 1.3 54.2 + - - +
234B ASP* 2.7 30.2 + - - +
235B GLY* 2.7 31.0 + - - -
276B MET 3.9 4.9 - - - -
277B GLU* 3.5 16.9 - - - +
500B MN 2.3 13.4 + - - -
501B MN 2.1 33.7 + - - +
1001B 2BH 2.6 3.1 + - - -
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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