Contacts of the helix formed by residues 289 - 303 (chain D) in PDB entry 1UU1
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 GLU 289 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275D ARG* 5.6 7.5 + - - +
288D MET* 1.3 73.1 - - - +
290D LYS* 1.3 84.5 + - + +
291D GLU 3.2 3.4 + - - +
292D GLU* 3.3 24.4 + - + +
293D LYS* 2.8 22.2 + - - +
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Residues in contact with LYS 290 (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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288D MET 3.7 2.8 + - - -
289D GLU* 1.3 87.9 - - + +
291D GLU* 1.3 64.6 + - + +
293D LYS* 3.3 9.7 + - - +
294D GLU* 2.9 36.8 + - - +
311D ARG* 4.3 26.3 + - - +
312D GLU* 5.6 1.8 - - - +
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Residues in contact with GLU 291 (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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289D GLU* 3.4 2.0 - - + +
290D LYS* 1.3 77.6 - - + +
292D GLU* 1.3 64.6 + - - +
293D LYS 2.9 5.6 + - - -
294D GLU* 3.4 12.8 + - - +
295D ARG* 3.1 26.8 + - - +
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Residues in contact with GLU 292 (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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274D TYR* 5.2 3.3 - - - -
287D PHE 5.2 0.7 - - - +
288D MET* 3.5 32.4 - - + +
289D GLU* 3.3 40.6 + - + +
291D GLU* 1.3 78.7 - - - +
293D LYS* 1.3 62.4 + - - +
295D ARG* 3.9 26.7 + - - +
296D LEU 3.5 12.6 + - - -
334D PHE* 3.5 19.8 - - - -
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Residues in contact with LYS 293 (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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288D MET* 3.7 28.5 - - + +
289D GLU 2.8 20.1 + - - +
290D LYS* 3.3 8.4 - - - +
292D GLU* 1.3 75.1 - - - +
294D GLU* 1.3 87.9 + - - +
295D ARG 3.1 1.3 - - - -
296D LEU* 3.1 12.1 + - - +
297D LEU* 3.0 24.1 + - - +
309D SER* 3.0 23.7 + - - -
310D PHE 3.0 22.0 + - - +
311D ARG* 4.7 5.7 + - - +
312D GLU 4.9 0.2 - - - -
313D GLY* 3.4 24.7 - - - +
314D VAL* 4.0 14.8 - - + -
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Residues in contact with GLU 294 (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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290D LYS* 2.9 29.9 + - - +
291D GLU* 4.1 15.8 - - - +
293D LYS* 1.3 96.4 + - - +
295D ARG* 1.3 66.4 + - - +
296D LEU 3.0 1.8 - - - -
297D LEU* 3.5 17.8 - - + +
298D GLU* 3.0 25.8 + - - +
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Residues in contact with ARG 295 (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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291D GLU* 3.1 21.4 + - - +
292D GLU* 3.6 30.9 + - - +
294D GLU* 1.3 78.4 - - - +
296D LEU* 1.3 60.8 + - - +
298D GLU* 3.6 6.6 + - - +
299D HIS* 3.2 20.4 + - - +
334D PHE* 3.2 50.8 + - - -
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Residues in contact with LEU 296 (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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288D MET* 4.2 12.3 - - + -
292D GLU 3.5 2.9 + - - +
293D LYS 3.1 8.0 + - - +
294D GLU 3.0 0.6 - - - -
295D ARG* 1.3 77.5 - - - +
297D LEU* 1.3 67.0 + - + +
299D HIS* 3.1 4.3 + - + +
300D LEU* 2.7 74.5 + - + +
314D VAL* 4.5 14.8 - - + -
316D ILE* 6.0 0.7 - - + -
330D GLU 5.3 0.7 - - - +
331D LEU* 3.7 28.0 - - + -
334D PHE* 3.3 36.2 - - + -
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Residues in contact with LEU 297 (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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293D LYS* 3.0 27.8 - - + +
294D GLU* 3.1 22.8 + - + +
296D LEU* 1.3 83.5 - - + +
298D GLU* 1.3 53.3 + - - +
300D LEU* 3.1 5.4 + - - +
301D ARG* 2.6 57.3 + - - +
307D VAL* 4.7 11.7 - - + +
309D SER* 3.8 28.9 - - - +
314D VAL* 3.8 26.9 - - + -
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Residues in contact with GLU 298 (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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294D GLU 3.0 15.7 + - - +
295D ARG* 3.8 6.3 - - - +
297D LEU* 1.3 77.0 - - - +
299D HIS* 1.3 61.2 + - - +
301D ARG* 3.4 38.4 + - - +
302D THR* 3.2 24.3 + - - -
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Residues in contact with HIS 299 (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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295D ARG 3.2 12.7 + - - +
296D LEU* 3.1 13.9 + - + +
297D LEU 3.1 0.6 - - - -
298D GLU* 1.3 75.8 - - - +
300D LEU* 1.3 66.7 + - - +
301D ARG 3.1 0.2 - - - -
302D THR* 3.1 23.0 + - + +
303D LYS* 3.3 34.1 + - - +
330D GLU* 3.1 29.2 + - + -
333D VAL* 3.6 18.3 - - + +
334D PHE* 3.9 24.2 - + + -
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Residues in contact with LEU 300 (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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296D LEU* 2.7 59.3 + - + +
297D LEU* 3.7 4.5 - - - +
299D HIS* 1.3 73.6 - - + +
301D ARG* 1.3 62.7 + - - +
303D LYS* 3.1 12.2 + - - +
304D ASN 3.4 0.2 + - - -
305D VAL* 3.1 36.9 + - + +
307D VAL* 3.7 36.3 - - + -
316D ILE* 5.4 3.4 - - + -
326D MET* 4.6 8.1 - - + -
327D ILE* 5.0 6.5 - - + -
330D GLU* 3.7 31.6 - - + -
331D LEU* 5.4 3.1 - - + -
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Residues in contact with ARG 301 (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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20D ASP* 4.4 5.3 - - - +
297D LEU* 2.6 40.3 + - - +
298D GLU* 3.4 43.8 + - - +
300D LEU* 1.3 73.4 - - - +
302D THR* 1.3 62.3 + - - +
304D ASN* 3.0 16.8 + - - +
305D VAL 4.1 9.6 - - - -
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Residues in contact with THR 302 (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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298D GLU* 3.2 15.3 + - - -
299D HIS* 3.1 17.0 + - - +
301D ARG* 1.3 78.7 - - - +
303D LYS* 1.3 71.0 + - + +
304D ASN* 3.0 16.7 + - - +
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Residues in contact with LYS 303 (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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22D THR* 4.2 2.6 - - - +
299D HIS* 3.3 25.7 + - - +
300D LEU* 3.1 9.4 + - - +
302D THR* 1.3 85.2 - - + +
304D ASN* 1.3 70.1 + - - +
305D VAL* 2.9 19.8 - - + +
326D MET* 5.2 3.4 - - + -
330D GLU* 2.9 41.6 + - + +
333D VAL* 5.8 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