Contacts of the helix formed by residues 289 - 303 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275B ARG* 3.8 18.8 + - - +
288B MET* 1.3 71.7 - - - +
290B LYS* 1.3 56.3 + - - +
291B GLU* 3.1 3.4 - - + +
292B GLU* 2.6 52.8 + - + +
293B LYS* 2.9 5.8 + - - -
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Residues in contact with LYS 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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288B MET 3.3 5.8 + - - +
289B GLU* 1.3 68.6 - - - +
291B GLU* 1.3 65.1 + - - +
293B LYS* 3.1 17.5 + - - +
294B GLU* 2.8 38.3 + - + +
311B ARG* 4.6 18.4 - - + +
250D ILE* 4.5 21.3 - - + -
253D GLU* 2.9 54.1 + - - +
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Residues in contact with GLU 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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289B GLU* 2.7 6.1 + - + +
290B LYS* 1.3 84.4 - - + +
292B GLU* 1.3 76.2 + - + +
294B GLU* 3.6 5.9 + - - +
295B ARG* 3.2 28.3 + - - -
31D PHE* 3.9 32.2 - - + +
32D PRO* 4.4 7.4 - - - +
250D ILE* 3.9 6.2 - - - +
254D ARG* 2.8 51.3 + - - +
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Residues in contact with GLU 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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288B MET* 3.5 13.9 - - + +
289B GLU* 2.6 38.1 + - + +
291B GLU* 1.3 86.1 - - - +
293B LYS* 1.3 57.5 + - - +
295B ARG* 3.1 36.1 + - - +
296B LEU 3.0 21.7 + - - -
334B PHE* 3.5 13.7 - - + -
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Residues in contact with LYS 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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288B MET* 3.7 29.0 - - + +
289B GLU 2.9 6.5 + - - +
290B LYS* 3.2 18.7 - - - +
292B GLU* 1.3 76.1 - - - +
294B GLU* 1.3 77.2 + - - +
296B LEU* 3.1 4.5 + - - +
297B LEU* 2.9 45.0 + - + +
309B SER* 3.1 21.9 + - - +
310B PHE 2.8 22.6 + - - -
311B ARG* 4.5 5.4 + - - +
313B GLY* 3.6 28.3 - - - +
314B VAL* 3.8 13.0 - - + -
36D ASP* 3.8 8.1 + - - -
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Residues in contact with GLU 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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290B LYS* 2.8 29.2 + - + +
291B GLU* 3.9 9.4 - - - +
293B LYS* 1.3 81.8 + - - +
295B ARG* 1.3 65.8 + - - +
297B LEU* 3.2 7.8 + - - +
298B GLU* 3.0 21.4 + - - +
32D PRO* 5.7 6.7 - - + -
34D PRO* 3.5 14.9 - - + +
35D GLU* 3.2 25.2 + - + +
36D ASP* 2.7 50.9 + - - +
250D ILE* 5.0 7.4 - - + +
254D ARG* 4.7 9.2 - - - +
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Residues in contact with ARG 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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291B GLU* 3.2 16.0 + - - +
292B GLU* 3.1 36.6 + - - +
294B GLU* 1.3 80.5 - - - +
296B LEU* 1.3 60.6 + - - +
298B GLU* 3.5 8.5 + - - +
299B HIS* 3.2 22.0 + - - +
334B PHE* 3.6 33.8 + - + -
32D PRO* 5.8 9.6 - - + -
320D LYS* 5.7 7.0 - - - +
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Residues in contact with LEU 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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274B TYR* 4.9 4.5 - - + -
286B VAL* 6.3 0.2 - - + -
288B MET* 3.5 30.5 - - + -
292B GLU 3.0 14.9 + - - +
293B LYS 3.1 8.9 + - - +
295B ARG* 1.3 75.2 - - - +
297B LEU* 1.3 61.8 + - + +
299B HIS* 3.3 6.8 + - + +
300B LEU* 2.9 43.4 + - + +
314B VAL* 4.8 9.9 - - + -
331B LEU* 3.6 35.7 - - + -
334B PHE* 3.4 32.5 - - + -
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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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293B LYS* 2.9 46.8 + - + +
294B GLU* 3.2 18.1 + - - +
296B LEU* 1.3 75.6 - - + +
298B GLU* 1.3 60.6 + - - +
300B LEU* 3.2 8.5 + - + +
301B ARG* 2.8 30.3 + - - +
307B VAL* 3.6 32.8 - - + +
309B SER* 4.0 18.2 - - - +
314B VAL* 3.8 11.2 - - + -
35D GLU* 3.5 18.8 - - + -
36D ASP* 4.8 2.7 - - + -
39D ASP* 4.7 6.6 - - - +
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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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294B GLU 3.0 14.4 + - - +
295B ARG* 3.8 8.2 - - - +
297B LEU* 1.3 75.2 - - - +
299B HIS* 1.3 64.1 + - - +
301B ARG* 3.2 18.7 + - - +
302B THR* 3.1 24.7 + - - +
45C LEU 3.3 6.4 - - - +
46C ASN* 3.5 7.5 - - - +
47C SER* 2.8 46.0 + - - -
48C ASP* 4.5 3.7 + - - +
32D PRO* 5.5 2.3 - - - +
35D GLU* 3.2 22.1 - - + +
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Residues in contact with HIS 299 (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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295B ARG 3.2 11.7 + - - +
296B LEU* 3.5 14.6 - - + +
298B GLU* 1.3 80.0 - - - +
300B LEU* 1.3 68.9 + - + +
302B THR* 3.1 24.9 + - - +
303B LYS* 3.4 27.1 + - + +
330B GLU* 2.7 54.3 + - + +
333B VAL* 4.0 9.5 + - + -
334B PHE* 4.4 15.0 - + + -
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Residues in contact with LEU 300 (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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296B LEU* 2.9 42.8 + - + +
297B LEU* 3.6 7.9 - - + +
299B HIS* 1.3 79.8 - - + +
301B ARG* 1.3 57.1 + - - +
303B LYS* 3.0 17.6 + - - -
304B ASN 3.4 0.2 + - - -
305B VAL* 3.0 51.2 + - + +
307B VAL* 4.0 34.5 - - + -
314B VAL* 6.4 0.2 - - + -
316B ILE* 6.0 1.6 - - + -
327B ILE* 5.5 6.5 - - + +
330B GLU* 4.0 30.3 - - + -
331B LEU* 4.7 9.9 - - + -
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Residues in contact with ARG 301 (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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20B ASP* 5.0 3.1 - - - +
297B LEU 2.8 21.0 + - - +
298B GLU* 3.2 20.6 + - - +
299B HIS 3.2 0.2 - - - -
300B LEU* 1.3 69.4 - - - +
302B THR* 1.3 66.5 + - - +
303B LYS 3.3 0.5 + - - -
304B ASN* 3.4 3.7 + - - +
305B VAL 4.0 7.6 + - - +
42C PHE* 2.7 66.1 + - + -
43C ARG* 2.7 54.0 + - - +
45C LEU* 2.8 41.7 + - - +
35D GLU* 3.0 34.1 + - - +
38D VAL* 4.3 1.8 - - - +
39D ASP* 4.0 6.1 - - - +
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Residues in contact with THR 302 (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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298B GLU* 3.1 16.0 + - - +
299B HIS* 3.1 19.1 + - - +
301B ARG* 1.3 82.6 + - - +
303B LYS* 1.3 72.0 + - + +
304B ASN* 3.5 4.8 + - - -
43C ARG* 4.3 24.6 + - - +
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Residues in contact with LYS 303 (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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22B THR* 4.3 2.3 - - - +
299B HIS* 3.7 25.6 - - + +
300B LEU* 3.0 9.1 + - - +
302B THR* 1.3 92.4 + - + +
304B ASN* 1.3 72.7 + - - +
305B VAL* 3.2 18.5 - - + +
326B MET* 4.7 5.7 - - - +
330B GLU* 3.1 43.1 - - + +
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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