Contacts of the strand formed by residues 245 - 251 (chain A) in PDB entry 1TW2
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 ALA 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A HIS* 3.6 18.2 - - - +
182A VAL 4.3 0.7 - - - -
183A LEU* 3.8 34.5 - - + +
243A ARG* 5.5 0.2 - - - +
244A LYS* 1.3 77.0 - - - +
246A ASP* 1.3 62.8 + - - +
247A ALA 3.8 5.6 - - - +
248A ILE* 4.0 7.0 - - + -
272A ALA 3.0 6.9 + - - -
273A LEU* 3.6 11.3 - - - +
274A GLU* 3.2 27.0 + - - -
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Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TYR* 5.0 0.9 + - - -
178A ASN 4.2 10.3 - - - +
179A VAL* 4.0 20.2 - - + +
180A ARG* 3.2 30.1 + - - +
181A HIS* 3.1 16.4 + - - +
245A ALA* 1.3 72.9 - - - +
247A ALA* 1.3 59.7 + - - +
273A LEU* 4.7 0.2 - - - -
274A GLU* 3.9 21.3 - - - +
275A PRO 4.7 6.4 - - - +
277A GLY* 3.0 31.5 - - - -
278A ARG 3.1 5.2 + - - -
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TYR* 4.7 9.6 - - + +
176A TRP* 3.8 32.1 - - + -
179A VAL* 4.3 11.2 - - + -
181A HIS 3.5 2.4 + - - -
182A VAL* 3.3 9.3 - - + +
183A LEU 3.0 22.9 + - - -
245A ALA* 3.4 0.9 - - - +
246A ASP* 1.3 79.9 - - - +
248A ILE* 1.3 64.9 + - - +
249A ILE* 5.2 0.7 - - + -
278A ARG 3.2 8.3 - - - +
280A LEU* 4.9 6.1 - - + -
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 3.3 13.9 - - + +
185A VAL* 3.7 28.5 - - + -
245A ALA* 4.0 11.0 - - + -
247A ALA* 1.3 79.4 - - - +
249A ILE* 1.3 64.9 + - - +
250A LEU* 5.4 0.4 - - + -
269A CYS* 3.3 44.6 - - - +
272A ALA* 3.7 25.4 - - + +
273A LEU* 3.6 17.7 - - + -
278A ARG 3.0 5.7 + - - -
279A ILE* 3.2 16.6 - - + +
280A LEU 2.9 24.5 + - - -
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TRP* 4.3 4.9 - - + -
182A VAL* 3.8 16.6 - - + -
183A LEU 2.8 14.4 + - - +
184A ASP* 3.4 21.3 - - - +
185A VAL* 3.0 32.9 + - - +
192A PHE* 3.5 36.3 - - + -
196A ILE* 3.9 22.0 - - + -
247A ALA 5.2 0.9 - - - -
248A ILE* 1.3 75.2 - - - +
250A LEU* 1.3 65.0 + - - +
251A SER* 3.8 6.5 - - - +
280A LEU* 3.5 39.3 - - + +
282A HIS* 5.3 0.2 - - + -
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.8 33.9 - - + +
249A ILE* 1.3 74.0 - - - +
251A SER* 1.3 60.9 + - - +
252A PHE 3.8 2.2 + - - -
253A VAL* 4.3 15.3 + - + -
254A LEU* 4.0 23.1 - - + -
265A ILE* 3.7 23.8 - - + -
266A LEU* 3.8 28.7 - - + -
269A CYS* 4.0 18.4 - - - -
279A ILE* 4.1 11.9 - - + -
280A LEU 2.9 10.9 + - - +
281A ILE* 3.4 10.2 - - + +
282A HIS 3.0 20.5 + - - +
283A GLU* 5.0 0.9 - - - +
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PHE* 3.7 3.6 - - - -
184A ASP* 4.7 2.2 + - - -
185A VAL 4.8 0.2 + - - -
192A PHE* 3.5 29.6 - - - -
249A ILE* 3.8 3.5 + - - +
250A LEU* 1.3 71.4 - - - +
252A PHE* 1.3 62.8 + - - +
253A VAL* 3.3 5.0 + - - +
282A HIS* 2.9 29.5 - - - -
635A SAH 2.7 60.1 + - - +
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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