Contacts of the helix formed by residues 267 - 283 (chain A) in PDB entry 1UWV
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 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASP* 4.7 3.5 - - - +
123A VAL 5.0 1.4 + - - -
127A TYR* 3.5 38.8 - - + +
265A GLN* 3.5 1.9 - - - +
266A VAL* 1.3 77.3 - - + +
268A ALA* 1.3 65.0 + - - +
269A GLY* 3.4 3.6 + - - -
270A VAL* 3.1 37.9 + - - +
271A ASN* 3.0 24.6 + - - +
416A MSE 2.8 45.7 + - + +
417A PHE* 5.2 0.6 - - - -
418A PRO* 4.2 4.0 - - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TYR 4.2 4.2 + - - +
129A ARG* 4.0 38.6 - - + +
251A SER* 5.0 1.9 + - - -
265A GLN 5.7 0.2 - - - -
266A VAL 3.6 4.4 + - - -
267A ASN* 1.3 73.2 + - - +
269A GLY* 1.3 58.2 + - - +
271A ASN* 3.4 6.6 + - - +
272A GLN* 2.9 29.7 + - - +
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Residues in contact with GLY 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 4.0 23.8 - - - -
267A ASN* 3.3 4.4 + - - -
268A ALA* 1.3 77.7 - - - +
270A VAL* 1.3 64.4 + - - +
272A GLN* 3.2 10.0 + - - +
273A LYS* 3.1 26.0 + - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 4.2 19.7 - - + +
121A ALA* 4.1 2.7 - - - -
122A ASP* 3.6 28.2 - - + +
267A ASN* 3.1 33.9 + - - +
269A GLY* 1.3 74.8 - - - +
271A ASN* 1.3 57.6 + - - +
273A LYS* 3.3 7.5 + - - +
274A MSE 2.8 28.3 + - + +
414A LEU* 4.8 2.7 - - + -
415A ASP 3.6 13.2 - - - +
416A MSE 3.7 34.3 - - + +
418A PRO* 6.2 0.2 - - + -
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Residues in contact with ASN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 5.3 4.7 + - - -
251A SER* 4.3 10.7 + - - -
252A ASN* 4.8 0.2 + - - -
265A GLN* 3.5 28.1 - - + +
267A ASN 3.0 19.7 + - - +
268A ALA* 3.5 6.2 - - - +
270A VAL* 1.3 75.9 - - - +
272A GLN* 1.3 65.2 + - - +
274A MSE 3.0 21.6 + - - +
275A VAL* 3.0 25.8 + - - +
299A ASN* 2.9 42.6 - - - +
416A MSE 4.3 6.1 - - - -
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASP 4.7 2.2 + - - -
251A SER* 3.7 14.2 - - - +
252A ASN* 2.9 65.7 - - - +
253A GLY 5.0 0.6 - - - +
268A ALA 2.9 18.1 + - - +
269A GLY* 3.7 7.7 - - - +
271A ASN* 1.3 76.7 + - - +
273A LYS* 1.3 59.1 + - + +
276A ALA* 3.1 18.2 + - + +
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Residues in contact with LYS 273 (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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120A ILE* 3.7 21.7 - - + +
121A ALA 2.6 31.3 + - - +
122A ASP* 3.4 24.6 + - + +
269A GLY 3.1 17.9 + - - +
270A VAL* 3.8 2.0 - - - +
272A GLN* 1.3 75.2 - - + +
274A MSE 1.4 60.8 + - - +
276A ALA* 3.3 5.8 + - - +
277A ARG* 2.9 31.5 + - - +
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Residues in contact with MSE 274 (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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120A ILE* 4.3 11.3 - - - +
265A GLN* 5.2 3.4 - - - +
270A VAL* 2.8 16.5 + - + +
271A ASN* 3.0 35.7 - - - +
273A LYS* 1.4 76.5 - - - +
275A VAL* 1.3 57.4 + - + +
277A ARG* 3.4 0.9 + - - -
278A ALA* 2.9 27.9 + - - +
299A ASN* 3.7 6.7 - - - +
300A PHE* 3.7 26.7 - - + -
363A ASP* 4.8 4.0 - - - +
387A VAL* 3.8 17.7 - - - -
414A LEU* 3.7 20.6 - - + -
416A MSE 3.6 25.6 - - + -
426A MSE 3.9 16.8 - - - +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 3.6 29.2 - - - +
271A ASN* 3.0 18.8 + - - +
273A LYS 3.3 0.2 - - - -
274A MSE 1.3 72.3 - - + +
276A ALA* 1.3 66.1 + - - +
278A ALA* 3.3 1.4 + - - +
279A LEU* 3.0 29.3 + - + +
299A ASN* 3.8 33.4 - - - +
300A PHE* 3.8 28.5 - - + -
303A PRO* 3.8 26.9 - - + -
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 3.7 7.8 + - - +
272A GLN* 3.1 18.3 + - + +
273A LYS* 3.6 7.2 - - - +
275A VAL* 1.3 76.7 - - - +
277A ARG* 1.3 63.8 + - - +
279A LEU* 3.3 11.0 + - - +
280A GLU* 3.1 31.7 + - - +
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Residues in contact with ARG 277 (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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118A GLU* 2.7 40.7 + - - +
120A ILE* 3.8 19.5 - - + -
273A LYS 2.9 18.0 + - - +
274A MSE 3.9 1.8 - - - +
276A ALA* 1.3 75.3 - - - +
278A ALA* 1.3 65.5 + - - +
280A GLU* 2.4 48.2 + - - +
281A TRP* 2.9 55.8 + - + +
410A ARG* 4.3 14.3 - - - +
426A MSE 3.9 3.1 - - + -
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MSE 2.9 21.2 + - - +
275A VAL 3.3 2.2 + - - +
277A ARG* 1.3 71.2 - - - +
279A LEU* 1.3 63.7 + - + +
281A TRP* 3.3 6.3 + - - +
282A LEU* 3.0 28.7 + - - +
300A PHE* 3.6 25.4 - - + -
361A LEU* 3.8 16.4 - - + -
385A VAL* 4.3 4.6 - - + +
426A MSE 3.9 17.8 - - - +
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Residues in contact with LEU 279 (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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275A VAL* 3.0 29.4 + - + +
276A ALA* 3.5 11.2 - - - +
278A ALA* 1.3 82.5 - - + +
280A GLU* 1.3 62.3 + - - +
282A LEU* 3.4 5.3 + - - +
283A ASP* 3.2 18.4 + - - -
284A VAL* 4.1 5.2 + - + +
300A PHE* 4.6 5.6 - - + +
303A PRO* 3.7 30.5 - - + +
304A LEU* 3.8 36.1 - - + +
306A THR* 5.1 0.9 - - - +
307A GLN* 3.9 29.4 - - + +
361A LEU* 5.7 0.2 - - + -
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Residues in contact with GLU 280 (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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276A ALA* 3.1 19.7 + - - +
277A ARG* 2.4 57.5 + - - +
279A LEU* 1.3 74.8 - - + +
281A TRP* 1.3 63.4 + - - +
283A ASP* 3.3 17.1 + - - +
383A ARG* 5.0 0.9 + - - -
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Residues in contact with TRP 281 (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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117A SER* 5.6 0.2 - - - -
118A GLU* 3.8 18.1 + - + -
277A ARG* 2.9 55.4 + - + +
278A ALA* 3.6 4.9 - - - +
279A LEU 3.2 0.2 - - - -
280A GLU* 1.3 77.6 - - - +
282A LEU* 1.3 58.5 + - - +
383A ARG* 2.9 32.7 + - - +
385A VAL* 4.1 11.7 - - + -
410A ARG* 3.7 28.3 - - + +
411A LEU 4.1 1.6 - - - -
412A ALA* 3.6 24.0 - - + -
426A MSE 3.5 55.2 - - + -
427A VAL 4.2 0.4 - - - -
428A LEU* 3.5 42.9 - - + +
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Residues in contact with LEU 282 (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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278A ALA 3.0 13.7 + - - +
279A LEU* 4.1 0.9 - - - +
281A TRP* 1.3 76.1 - - - +
283A ASP* 1.3 68.8 + - - +
284A VAL* 3.2 14.1 - - + -
290A VAL* 4.4 5.4 - - + -
304A LEU* 3.9 24.5 - - + -
359A LYS* 2.9 40.5 + - + +
360A VAL 3.7 15.9 - - - +
361A LEU* 4.1 25.8 - - + -
383A ARG* 3.8 28.3 - - + +
385A VAL* 3.6 26.0 - - + +
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Residues in contact with ASP 283 (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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279A LEU 3.2 8.4 + - - -
280A GLU* 3.3 13.8 + - - +
281A TRP 3.1 1.6 - - - -
282A LEU* 1.3 76.3 - - - +
284A VAL* 1.3 65.6 + - - +
285A GLN* 3.2 21.0 + - - +
359A LYS* 2.9 16.2 + - - +
383A ARG* 3.7 30.9 + - - +
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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