Contacts of the helix formed by residues 337 - 350 (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 GLY 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A MET 4.6 6.5 - - - -
333A ALA 3.9 3.5 + - - -
334A LEU 4.3 1.4 + - - -
335A ASP 3.3 5.1 + - - -
336A ASP* 1.3 76.6 + - - +
338A SER* 1.3 57.4 + - - +
339A ALA 3.5 2.5 - - - -
340A LEU* 3.5 18.8 - - - +
341A GLY* 3.1 23.2 + - - -
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Residues in contact with SER 338 (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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135A ALA* 3.5 26.1 + - - +
333A ALA* 3.6 8.3 + - - +
336A ASP* 2.6 33.2 + - - -
337A GLY* 1.3 77.2 - - - +
339A ALA* 1.3 67.1 + - - +
341A GLY* 3.3 3.1 + - - +
342A ARG* 3.1 20.3 + - - +
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Residues in contact with ALA 339 (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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131A PRO* 3.3 21.1 - - - +
132A ALA* 3.5 31.9 - - + +
135A ALA* 4.0 2.9 - - - +
294A MET* 4.2 11.0 - - + -
333A ALA 3.1 22.1 + - - +
334A LEU* 4.1 11.0 - - + -
338A SER* 1.3 76.0 + - - +
340A LEU* 1.3 65.1 + - - +
342A ARG 3.1 3.3 + - - -
343A PHE* 3.0 18.5 + - - +
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Residues in contact with LEU 340 (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* 3.8 25.1 - - + +
294A MET* 3.8 32.9 + - + +
295A ASP* 4.0 16.8 - - - +
337A GLY* 3.5 14.5 - - - +
339A ALA* 1.3 78.8 - - - +
341A GLY* 1.3 62.3 + - - +
343A PHE* 3.1 6.6 + - - +
344A GLU* 3.1 21.7 + - - +
361A CYS* 3.3 46.2 - - + +
362A SER* 5.5 0.4 - - - -
368A ARG* 4.6 0.2 - - - +
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Residues in contact with GLY 341 (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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337A GLY 3.1 14.9 + - - -
338A SER* 3.3 4.2 + - - -
339A ALA 3.2 0.4 - - - -
340A LEU* 1.3 76.9 - - - +
342A ARG* 1.3 68.3 + - - +
344A GLU* 3.5 11.9 + - - +
345A ARG* 3.2 29.5 + - - +
358A ARG* 6.3 0.4 - - - -
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Residues in contact with ARG 342 (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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131A PRO* 3.6 17.0 - - + +
134A ALA* 4.0 5.8 - - + -
135A ALA* 3.8 26.5 - - + +
179A GLN 3.3 24.5 + - - -
180A ALA* 3.2 26.0 - - - +
181A GLY* 5.4 0.2 - - - -
182A CYS* 4.4 0.7 - - - -
338A SER 3.1 15.8 + - - +
339A ALA 3.1 10.2 + - - +
341A GLY* 1.3 82.1 + - - +
343A PHE* 1.3 57.2 + - - +
345A ARG* 3.3 31.8 + - - +
346A MET* 2.9 27.2 + - - +
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Residues in contact with PHE 343 (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* 3.9 29.4 - - + -
131A PRO* 3.6 25.6 - - + -
158A LEU* 4.6 0.7 - - + -
161A ILE* 4.5 11.2 - - + -
287A VAL* 4.7 6.7 - - + -
290A ALA* 6.0 0.9 - - + -
291A LEU* 3.6 30.7 - - + -
294A MET* 3.6 22.4 - - + -
339A ALA 3.0 12.2 + - - +
340A LEU 3.1 8.9 + - - +
342A ARG* 1.3 74.3 - - - +
344A GLU* 1.3 58.8 + - - +
346A MET* 3.2 27.3 + - + +
347A LEU* 2.9 58.0 + - + +
360A LEU* 6.5 0.2 - - + -
361A CYS* 4.0 8.7 - - - -
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Residues in contact with GLU 344 (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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340A LEU 3.1 8.1 + - - +
341A GLY* 3.7 13.0 - - - +
342A ARG 3.4 0.2 - - - -
343A PHE* 1.3 74.5 - - - +
345A ARG* 1.3 90.6 + - - +
347A LEU* 3.3 5.8 + - - +
348A ALA* 3.1 24.8 + - - +
354A PRO 5.1 0.5 - - - +
357A ALA* 3.6 28.1 - - + +
358A ARG* 3.3 54.6 + - - +
361A CYS* 3.6 23.9 - - - +
362A SER* 5.1 0.3 + - - -
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Residues in contact with ARG 345 (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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179A GLN* 3.6 15.9 - - + +
180A ALA* 3.6 16.8 - - + -
341A GLY* 3.2 20.9 + - - +
342A ARG* 3.4 36.0 - - - +
344A GLU* 1.3 108.0 + - - +
346A MET* 1.3 64.1 + - - +
348A ALA* 3.4 11.3 + - - +
349A ALA* 2.9 27.0 + - - +
354A PRO* 6.3 0.4 - - - +
357A ALA* 6.2 0.2 - - - +
358A ARG* 5.7 2.4 - - - +
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Residues in contact with MET 346 (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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130A ALA* 5.0 3.4 - - - -
131A PRO* 5.1 2.2 - - + -
158A LEU* 4.2 3.8 - - + -
164A PHE* 4.2 21.8 - - + -
176A LEU* 5.6 0.4 - - + -
180A ALA* 3.6 7.6 - - - +
182A CYS* 3.6 37.5 - - - +
183A CYS* 3.9 13.2 - - - -
184A ILE* 3.8 29.8 - - + -
342A ARG 2.9 16.3 + - - +
343A PHE* 3.2 36.1 + - + +
345A ARG* 1.3 77.2 - - - +
347A LEU* 1.3 64.6 + - + +
349A ALA* 3.4 3.1 + - - +
350A GLN* 3.0 34.2 + - + +
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Residues in contact with LEU 347 (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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158A LEU* 4.9 0.2 - - + -
161A ILE* 3.5 33.4 - - + -
164A PHE* 3.7 23.3 - - + -
343A PHE* 2.9 49.4 + - + +
344A GLU 3.7 3.8 - - - +
345A ARG 3.3 0.2 - - - -
346A MET* 1.3 78.1 - - + +
348A ALA* 1.3 62.8 + - - +
350A GLN* 3.2 10.2 + - - +
351A GLY 3.3 0.9 + - - -
352A VAL* 3.1 32.4 + - + +
357A ALA* 4.2 17.5 - - + -
360A LEU* 4.3 17.5 - - + -
361A CYS* 4.6 8.1 - - - -
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Residues in contact with ALA 348 (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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344A GLU 3.1 13.1 + - - +
345A ARG* 4.1 13.7 - - - +
347A LEU* 1.3 79.8 - - - +
349A ALA* 1.3 61.3 + - - +
351A GLY* 3.2 13.3 + - - -
352A VAL* 3.4 19.3 - - - +
354A PRO* 4.5 19.7 - - + -
357A ALA* 4.4 4.2 - - + +
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Residues in contact with ALA 349 (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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168A GLN* 3.9 5.5 - - - +
176A LEU* 3.1 32.2 - - + +
179A GLN* 3.4 33.5 + - + +
180A ALA* 5.0 1.3 - - + -
345A ARG 2.9 20.1 + - - +
346A MET* 3.8 3.4 - - - +
348A ALA* 1.3 78.4 - - - +
350A GLN* 1.3 55.7 + - - +
351A GLY 3.4 1.2 + - - -
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Residues in contact with GLN 350 (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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163A GLY 3.6 0.5 - - - +
164A PHE* 3.4 24.6 - - + -
165A ASN* 3.2 46.9 + - - +
166A VAL* 4.4 0.2 - - - +
168A GLN* 3.9 11.8 - - - +
176A LEU* 3.5 27.6 - - + -
183A CYS* 3.2 11.1 - - - +
184A ILE 2.8 46.9 + - - -
185A VAL* 3.8 8.1 - - - +
346A MET* 3.0 23.4 + - - +
347A LEU 3.2 3.8 + - - -
349A ALA* 1.3 73.5 - - - +
351A GLY* 1.3 56.7 + - - +
352A VAL 3.6 0.4 + - - -
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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