Contacts of the helix formed by residues 283 - 295 (chain A) in PDB entry 1UOU
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 HIS 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLY* 4.9 6.8 - - - -
153A GLY 4.5 6.4 + - - -
156A ASP* 3.5 20.0 + - + +
157A LYS* 3.7 39.3 - - + +
160A SER* 3.8 6.5 - - - -
282A GLY* 1.3 85.3 + - - -
284A ALA* 1.3 66.9 + - - +
285A LEU 3.3 2.4 - - - +
286A GLU* 3.3 5.0 + - - +
287A VAL* 3.2 23.2 + - - +
405A GLY* 6.5 0.7 - - - -
415A LEU* 3.9 26.8 - - + +
416A ARG 3.9 19.3 + - - -
417A LEU* 3.6 20.3 - - + +
419A VAL 4.2 6.8 + - - -
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Residues in contact with ALA 284 (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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160A SER* 3.5 18.0 + - - +
283A HIS* 1.3 78.0 - - - +
285A LEU* 1.3 62.7 + - + +
287A VAL* 3.4 4.6 + - - +
288A GLU* 3.1 36.6 + - - +
372A LEU* 4.3 7.6 - - + +
373A PRO* 3.3 26.2 - - + +
417A LEU 3.1 18.0 + - - +
418A GLY* 4.6 2.2 - - - -
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Residues in contact with LEU 285 (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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280A CYS* 3.7 25.7 - - + -
281A VAL 3.9 9.4 - - - +
282A GLY* 4.8 1.3 - - - -
283A HIS 3.3 2.4 - - - +
284A ALA* 1.3 78.2 - - + +
286A GLU* 1.3 56.7 + - - +
288A GLU* 3.4 22.0 - - + +
289A GLU 3.1 20.4 + - - -
369A ARG* 5.9 3.1 - - - -
418A GLY 5.0 6.9 - - - +
419A VAL 5.6 0.2 - - - +
420A GLY* 3.9 9.9 - - - -
421A ALA 3.6 40.2 - - - +
422A GLU* 4.1 15.3 - - + +
441A HIS* 3.9 37.0 - - + +
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Residues in contact with GLU 286 (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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122A GLY* 3.7 11.0 + - - -
124A LYS* 3.5 32.6 + - + +
127A LEU* 4.0 3.6 - - + +
157A LYS* 2.6 38.2 + - + -
280A CYS* 3.7 22.2 - - - +
281A VAL* 3.4 7.3 - - - +
282A GLY 3.0 36.8 + - - +
283A HIS 3.3 8.5 + - - +
285A LEU* 1.3 75.7 - - - +
287A VAL* 1.3 59.2 + - - +
290A ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 287 (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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127A LEU* 4.2 18.2 - - + -
157A LYS 3.4 30.1 - - - +
158A LEU* 4.6 1.1 - - - +
160A SER* 3.6 6.5 - - - +
161A ILE* 3.9 25.4 - - + -
283A HIS 3.2 10.1 + - - +
284A ALA 3.7 6.7 - - - +
286A GLU* 1.3 74.2 - - - +
288A GLU* 1.3 58.1 + - - +
290A ALA* 3.2 3.7 + - - +
291A LEU* 3.0 41.3 + - + +
343A PHE* 4.7 8.5 - - + -
360A LEU* 6.0 0.7 - - + -
372A LEU* 3.8 21.8 - - + -
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Residues in contact with GLU 288 (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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280A CYS* 6.0 0.4 - - - -
284A ALA* 3.1 24.2 + - - +
285A LEU* 3.4 29.4 - - + +
287A VAL* 1.3 77.4 - - - +
289A GLU* 1.3 56.7 + - - +
291A LEU* 3.5 10.0 + - - +
292A LEU* 3.1 25.5 + - - +
365A PRO* 5.2 1.1 - - + +
368A ARG* 3.9 26.8 + - + +
369A ARG* 3.4 31.9 - - + +
372A LEU* 3.4 29.1 - - + +
373A PRO 4.7 1.9 - - - +
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Residues in contact with GLU 289 (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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124A LYS* 2.4 40.0 + - + +
278A GLY* 3.6 5.7 - - - -
279A ARG* 2.9 37.5 + - - +
280A CYS* 3.5 12.7 + - + -
285A LEU 3.1 15.6 + - - +
286A GLU 3.4 0.2 + - - -
287A VAL 3.3 0.2 - - - -
288A GLU* 1.3 73.9 - - - +
290A ALA* 1.3 66.6 + - - +
292A LEU* 3.2 14.9 + - + +
293A CYS* 2.9 21.7 + - - +
299A PRO* 3.8 25.3 - - + +
302A LEU* 4.0 9.0 - - + +
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Residues in contact with ALA 290 (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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124A LYS* 4.3 9.1 - - + +
127A LEU* 3.9 23.1 - - + -
128A VAL* 3.6 25.0 - - + +
286A GLU 2.9 19.5 + - - +
287A VAL 3.6 4.0 - - - +
289A GLU* 1.3 76.4 - - - +
291A LEU* 1.3 56.0 + - - +
293A CYS* 3.3 6.9 + - - +
294A MET* 3.0 36.8 + - + +
302A LEU* 4.7 0.2 - - - -
343A PHE* 6.0 1.1 - - + -
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Residues in contact with LEU 291 (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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287A VAL* 3.0 33.9 + - + +
288A GLU* 3.6 8.7 - - - +
290A ALA* 1.3 72.7 - - - +
292A LEU* 1.3 65.2 + - - +
294A MET* 2.9 7.3 + - + +
295A ASP* 2.9 25.8 + - - +
340A LEU* 3.8 20.6 - - + +
343A PHE* 3.6 34.8 - - + -
360A LEU* 4.3 14.1 - - + +
361A CYS* 4.3 10.8 - - - -
368A ARG* 3.4 41.1 - - + +
372A LEU* 5.2 1.1 - - + -
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Residues in contact with LEU 292 (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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288A GLU 3.1 12.2 + - - +
289A GLU* 3.3 22.4 - - + +
291A LEU* 1.3 74.4 - - - +
293A CYS* 1.3 63.2 + - - +
295A ASP* 3.1 24.9 + - - +
297A ALA* 3.1 28.0 + - + -
298A GLY* 4.0 23.1 - - - +
299A PRO* 5.2 1.1 - - + -
365A PRO* 3.9 29.6 - - + -
368A ARG* 3.9 3.2 - - - +
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Residues in contact with CYS 293 (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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128A VAL* 3.8 27.6 - - + -
289A GLU 2.9 12.6 + - - +
290A ALA 3.4 9.4 - - - +
291A LEU 3.2 0.2 - - - -
292A LEU* 1.3 75.8 - - - +
294A MET* 1.3 56.1 + - - +
296A GLY* 2.9 20.3 + - - -
297A ALA 3.4 13.2 + - - +
298A GLY* 4.4 1.3 - - - -
302A LEU* 3.8 22.2 - - + -
303A ARG* 4.3 12.9 + - - -
306A VAL* 4.2 11.0 - - - -
334A LEU* 4.0 24.6 - - - +
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Residues in contact with MET 294 (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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127A LEU 4.2 7.0 - - - +
128A VAL* 4.2 20.6 - - + +
131A PRO* 4.1 13.2 - - - -
290A ALA* 3.0 30.9 + - + +
291A LEU* 2.9 14.3 + - + +
293A CYS* 1.3 71.4 - - - +
295A ASP* 1.3 56.2 + - - +
296A GLY 3.1 5.6 - - - -
334A LEU* 3.2 18.9 - - + +
337A GLY* 4.6 6.1 - - - -
339A ALA* 4.2 20.6 - - + +
340A LEU* 3.8 31.1 + - + +
343A PHE* 3.6 54.3 - - + -
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Residues in contact with ASP 295 (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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291A LEU 2.9 13.0 + - - +
292A LEU* 3.1 20.0 + - - +
294A MET* 1.3 75.1 - - - +
296A GLY* 1.3 58.3 + - - +
297A ALA* 3.5 6.9 + - + +
334A LEU 3.8 2.2 - - - -
335A ASP* 5.3 3.1 - - - +
340A LEU* 4.0 13.4 - - - +
361A CYS 4.3 0.2 - - - +
363A GLY 5.2 0.5 - - - +
365A PRO* 4.7 5.9 - - - +
368A ARG* 2.8 41.1 + - - -
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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