Contacts of the helix formed by residues 288 - 298 (chain B) in PDB entry 4UTX
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 PRO 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B GLU* 3.0 24.2 - - + +
272B MET* 3.7 28.4 - - + -
287B GLY* 1.3 81.0 - - - +
289B CYS* 1.3 56.2 + - - +
290B GLY* 5.1 0.2 - - - -
291B SER* 2.8 43.4 + - - +
292B THR* 3.0 13.6 + - + +
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Residues in contact with CYS 289 (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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56B GLY 5.0 3.4 - - - -
57B VAL* 4.6 7.2 - - + -
60B GLU* 2.5 16.8 + - - +
113B ALA* 3.8 19.4 - - + +
244B VAL* 3.7 20.2 - - + -
245B GLY* 3.8 13.9 - - - -
270B PHE* 3.5 27.8 - - + -
271B ASN* 4.7 3.6 - - - -
272B MET* 6.5 0.4 - - - -
287B GLY 3.3 0.8 + - - -
288B PRO* 1.3 70.5 - - - +
290B GLY* 1.3 63.7 + - - +
292B THR* 3.5 10.5 - - - -
293B LEU* 2.9 31.8 + - + +
294B PRO* 3.3 1.0 - - - +
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Residues in contact with GLY 290 (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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60B GLU* 2.9 20.5 + - - -
111B ASN* 4.6 0.9 - - - -
112B PRO* 3.5 21.2 - - - +
113B ALA* 3.9 17.5 - - - +
288B PRO* 5.1 0.4 - - - -
289B CYS* 1.3 76.7 - - - +
291B SER* 1.3 56.2 + - - +
294B PRO* 3.2 22.5 - - - +
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Residues in contact with SER 291 (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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288B PRO* 2.8 33.7 + - - +
290B GLY* 1.3 71.6 - - - -
292B THR* 1.3 67.3 + - - -
293B LEU 3.4 1.3 - - - -
294B PRO* 3.9 0.7 - - - -
295B PRO* 3.2 22.7 - - - +
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Residues in contact with THR 292 (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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36B LEU* 6.1 0.5 - - - +
270B PHE* 3.3 27.3 - - - +
285B PHE* 4.1 10.3 - - + +
286B GLU 3.7 9.2 - - - +
287B GLY* 3.5 27.7 + - - +
288B PRO* 3.0 12.5 + - + +
289B CYS* 3.5 12.8 - - - -
291B SER* 1.3 78.4 - - - +
293B LEU* 1.3 67.2 + - - +
295B PRO* 3.4 11.4 - - - +
296B ALA* 3.6 11.6 + - - +
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Residues in contact with LEU 293 (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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51B ILE* 6.0 0.2 - - + -
113B ALA* 3.9 23.3 - - + +
116B ALA* 4.9 0.9 - - + -
117B ILE* 3.9 28.3 - - + -
242B LEU* 4.6 4.9 - - + -
244B VAL* 4.2 19.7 - - + -
270B PHE* 3.7 37.5 - - + -
289B CYS* 2.9 17.8 + - + +
292B THR* 1.3 83.1 + - - +
294B PRO* 1.3 70.2 - - + +
296B ALA* 2.8 14.2 + - - +
297B LEU* 3.1 32.7 + - + +
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Residues in contact with PRO 294 (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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106A ARG 4.5 1.4 - - - +
107A SER* 3.7 23.3 - - - +
109A MET* 4.2 8.1 - - + -
112B PRO* 4.0 23.6 - - + +
113B ALA* 5.0 0.2 - - - -
116B ALA* 3.8 18.4 - - + -
289B CYS 3.3 4.5 - - - +
290B GLY* 3.2 27.4 - - - +
291B SER 3.8 0.4 - - - +
292B THR 3.7 0.4 - - - -
293B LEU* 1.3 91.7 - - + +
295B PRO* 1.3 72.0 - - + +
297B LEU* 3.2 2.1 + - - +
298B GLU* 3.0 24.8 + - - +
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Residues in contact with PRO 295 (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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107A SER* 4.2 15.0 - - - +
36B LEU* 5.1 13.2 - - + -
40B ARG* 3.7 6.6 + - - -
291B SER 3.2 24.5 - - - +
292B THR* 3.4 7.9 - - - +
294B PRO* 1.3 95.9 - - + +
296B ALA* 1.3 63.8 + - - +
298B GLU* 3.0 28.7 - - + +
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Residues in contact with ALA 296 (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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36B LEU* 4.3 15.2 - - + +
39B PHE* 3.6 30.5 - - + -
40B ARG* 3.1 21.1 + - - -
43B PHE* 3.8 2.9 - - - -
270B PHE* 3.8 28.3 - - + -
285B PHE* 6.0 0.2 - - + -
292B THR 3.6 5.6 + - - +
293B LEU* 2.8 15.2 + - + +
295B PRO* 1.3 81.6 - - - +
297B LEU* 1.3 56.9 + - + +
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Residues in contact with LEU 297 (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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39B PHE* 4.8 4.5 - - + -
40B ARG* 3.6 0.9 - - - -
43B PHE* 3.3 32.5 - - + -
49B ILE* 6.2 0.4 - - + -
51B ILE* 5.2 3.6 - - + -
116B ALA* 4.0 29.8 - - + +
117B ILE* 4.1 13.2 - - + +
120B CYS* 4.3 15.0 - - + -
123B ARG* 2.6 29.9 + - - +
242B LEU* 4.1 25.4 - - + -
293B LEU* 3.1 36.7 + - + +
294B PRO 4.1 2.9 - - - +
296B ALA* 1.3 78.8 - - - +
298B GLU* 1.3 60.4 + - - +
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Residues in contact with GLU 298 (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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103A GLU 5.0 2.7 - - - +
106A ARG* 2.8 89.6 + - + +
107A SER* 3.5 19.3 + - - +
40B ARG* 2.2 38.9 + - - +
43B PHE* 3.8 3.8 - - - -
123B ARG* 3.9 14.8 + - - +
294B PRO 3.0 13.0 + - - +
295B PRO* 3.0 28.3 + - + +
297B LEU* 1.3 80.3 - - - +
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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