Contacts of the strand formed by residues 269 - 274 (chain D) in PDB entry 3THT
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 269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D LEU* 5.5 0.4 - - - +
130D PRO* 4.0 12.3 - - - +
261D ASP* 6.5 0.4 - - + -
262D PHE 3.6 5.2 - - - +
263D LYS* 4.2 23.3 - - - +
267D GLY 3.2 7.0 + - - +
268D ILE* 1.3 76.8 - - - +
270D VAL* 1.3 64.5 + - - +
271D PRO* 3.7 8.9 - - + +
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PRO* 3.8 25.6 - - + -
132D ALA 4.9 2.2 - - - +
134D PRO* 4.1 17.0 - - + -
261D ASP* 4.9 0.7 - - - -
262D PHE* 2.9 37.3 + - + +
268D ILE* 4.2 4.9 - - + -
269D ALA* 1.3 78.1 - - - +
271D PRO* 1.3 62.0 - - - +
272D VAL* 3.2 20.5 + - + +
290D TRP* 4.1 18.6 - - + -
312D ILE* 3.6 35.9 - - + -
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Residues in contact with PRO 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D PRO* 5.5 0.7 - - + -
259D VAL* 4.1 15.5 - - + -
260D MET 3.8 5.4 - - - +
261D ASP* 4.1 13.5 - - + +
269D ALA* 3.7 8.1 - - + +
270D VAL* 1.3 80.9 - - - +
272D VAL* 1.3 63.5 + - - +
273D MET 3.6 1.7 + - - -
297D ARG* 6.0 0.7 - - - +
311D GLY 3.7 1.9 - - - +
312D ILE* 3.8 9.9 - - + -
313D ILE* 3.3 52.4 + - + +
314D THR* 5.5 1.1 - - + -
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Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 4.7 9.2 - - + -
137D LEU* 3.8 17.3 - - + -
139D VAL* 4.5 13.7 - - + -
259D VAL* 3.4 3.1 - - - -
260D MET* 2.7 44.7 + - + +
262D PHE* 3.4 32.3 - - + -
270D VAL* 3.8 18.8 - - + +
271D PRO* 1.3 71.7 - - - +
273D MET* 1.3 64.7 + - - +
274D LEU* 3.5 24.0 + - + -
280D LEU* 4.7 1.1 - - + -
311D GLY 4.0 8.3 - - - +
312D ILE* 5.8 0.2 - - + -
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Residues in contact with MET 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D GLU* 4.3 20.0 - - + -
258D ILE 3.9 10.5 - - - +
259D VAL* 4.0 4.9 - - + -
271D PRO 3.6 1.2 + - - -
272D VAL* 1.3 71.8 - - - +
274D LEU* 1.3 64.6 + - - +
275D PRO* 2.9 25.7 - - + +
302D VAL* 3.5 34.5 - - + -
306D GLU 4.7 0.9 - - - +
307D SER 3.3 31.9 - - - +
308D LEU* 4.1 9.9 - - - -
309D LYS 4.2 16.4 - - - +
310D SER* 3.4 13.7 - - - -
311D GLY 3.4 16.2 + - - +
313D ILE* 4.0 14.8 - - + -
323D SER* 6.0 0.2 - - - +
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Residues in contact with LEU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D VAL* 4.1 13.7 - - + -
251D SER* 6.1 1.1 - - - -
253D SER* 4.1 23.0 - - - +
257D GLU* 3.6 1.0 - - - -
258D ILE* 2.8 41.0 + - + +
260D MET* 3.8 39.9 - - + -
272D VAL* 3.5 21.0 + - + +
273D MET* 1.3 72.1 - - - +
275D PRO* 1.3 68.1 - - - +
278D SER* 4.3 2.9 - - - +
280D LEU* 3.7 39.7 - - + -
328D ARG* 4.2 5.4 - - - +
403D AKG 5.1 0.2 - - - +
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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