Contacts of the strand formed by residues 285 - 290 (chain C) in PDB entry 1TTT
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 ASN 285 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ASN* 4.1 10.9 - - - +
67C HIS* 3.6 15.2 + - - -
78C SER* 3.7 24.7 + - - +
80C VAL* 4.8 2.4 - - - +
98C GLN* 2.9 31.0 + - - +
240C GLY 3.4 11.2 + - - +
241C ARG* 4.1 3.0 - - + +
272C MET* 2.8 22.5 - - + +
273C HIS* 5.4 0.7 - - - -
283C GLY 3.3 1.8 + - - -
284C ASP* 1.3 70.7 - - - +
286C VAL* 1.3 54.7 + - - +
77F PHE* 2.6 57.1 + - + +
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Residues in contact with VAL 286 (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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223C MET* 4.0 20.0 - - - -
239C THR* 3.2 6.2 - - - -
240C GLY 3.1 25.6 + - - +
242C ILE* 4.1 17.3 - - + -
270C VAL* 4.6 3.4 - - + -
271C GLU 3.0 17.0 - - - +
272C MET* 5.0 0.4 - - + -
277C LEU* 4.4 11.4 - - + -
280C GLY* 4.5 2.2 - - - -
284C ASP* 2.9 38.8 + - + +
285C ASN* 1.3 79.3 + - - +
287C GLY* 1.3 59.6 + - - +
288C LEU* 3.3 25.1 - - + -
77F PHE* 3.7 5.7 - - - -
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Residues in contact with GLY 287 (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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237C VAL* 3.7 10.3 - - - -
238C ALA 3.4 7.6 - - - -
239C THR* 4.0 7.6 - - - -
270C VAL* 3.6 0.7 - - - -
271C GLU 3.2 14.6 + - - -
286C VAL* 1.3 75.7 - - - +
288C LEU* 1.3 66.7 + - - +
76F A 3.0 34.0 - - - +
77F PHE 4.2 0.6 + - - -
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Residues in contact with LEU 288 (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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221C PHE* 4.1 26.5 - - + -
223C MET* 4.4 5.6 - - + -
237C VAL* 2.9 8.8 - - - -
238C ALA 2.7 44.7 + - - +
247C VAL* 4.2 12.3 - - + -
253C VAL* 5.7 1.1 - - + -
267C VAL* 4.4 14.4 - - + -
269C GLY 3.3 11.0 - - - +
270C VAL* 4.2 11.9 - - + -
286C VAL* 3.3 25.8 - - + -
287C GLY* 1.3 82.3 - - - +
289C LEU* 1.3 61.8 + - - +
290C LEU* 3.5 18.8 - - + +
304C LEU* 4.6 13.0 - - + -
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Residues in contact with LEU 289 (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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234C ARG* 3.4 42.0 - - + +
235C GLY* 3.6 4.9 - - - +
236C THR 3.3 35.2 - - - +
237C VAL* 3.4 17.9 - - + -
267C VAL* 3.4 7.6 - - - -
268C THR* 3.0 44.2 + - - +
269C GLY* 3.2 20.9 + - - +
288C LEU* 1.3 71.6 - - - +
290C LEU* 1.3 65.1 + - - +
76F A 3.9 14.9 - - - +
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Residues in contact with LEU 290 (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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235C GLY* 5.9 0.2 - - - -
236C THR* 2.9 25.3 + - - +
238C ALA* 4.1 21.1 - - + +
253C VAL* 4.7 14.6 - - + -
255C ILE* 5.2 3.4 - - + -
265C THR* 3.7 15.7 - - + +
266C VAL 3.9 0.9 - - - -
267C VAL* 4.7 5.4 - - + -
268C THR* 4.6 1.8 - - - -
288C LEU* 3.5 22.4 - - + +
289C LEU* 1.3 89.0 - - - +
291C ARG* 1.3 60.9 + - - +
292C GLY 2.8 11.3 + - - -
293C VAL* 3.7 29.0 + - + +
298C VAL* 4.1 13.9 - - + -
304C LEU* 4.3 15.7 - - + -
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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