Contacts of the helix formed by residues 34 - 45 (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 PRO 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294B GLU* 3.5 22.9 - - + +
32D PRO* 3.4 1.4 - - + -
33D PHE* 1.3 101.6 - - + +
35D GLU* 1.3 60.4 + - - +
36D ASP* 3.4 7.4 - - - +
37D LEU* 3.2 23.7 + - + +
38D VAL* 3.0 26.2 + - - +
250D ILE* 3.8 12.8 - - + -
251D PHE* 3.7 21.3 - - + -
254D ARG* 3.8 21.3 - - - +
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Residues in contact with GLU 35 (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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294B GLU* 3.2 30.5 + - + +
297B LEU* 3.5 12.1 - - + -
298B GLU* 3.2 41.2 - - + +
301B ARG* 3.0 36.6 + - - +
47C SER* 3.9 6.0 - - - +
33D PHE 3.2 5.0 + - - +
34D PRO* 1.3 67.8 - - - +
36D ASP* 1.3 68.5 + - - +
37D LEU 3.0 2.0 - - - -
38D VAL* 2.9 20.6 + - - +
39D ASP* 2.6 45.9 + - - +
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Residues in contact with ASP 36 (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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293B LYS* 3.8 6.1 + - - -
294B GLU* 2.7 29.7 + - - +
297B LEU* 4.8 4.2 - - + +
309B SER* 3.2 33.6 + - - +
34D PRO* 3.5 8.1 - - - +
35D GLU* 1.3 76.9 - - - +
37D LEU* 1.3 73.1 + - - +
39D ASP* 3.6 13.6 - - - +
40D GLU* 3.2 22.5 + - - +
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Residues in contact with LEU 37 (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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33D PHE* 3.6 16.4 - - + -
34D PRO* 3.5 31.6 - - + +
35D GLU 3.0 0.8 - - - -
36D ASP* 1.3 95.5 + - - +
38D VAL* 1.3 60.3 + - - +
39D ASP 3.1 1.8 - - - -
40D GLU* 3.1 6.8 + - + +
41D VAL* 2.8 33.6 + - - +
243D VAL* 3.7 17.2 - - + +
247D HIS* 3.7 43.3 - - + +
250D ILE* 4.4 3.4 - - + -
251D PHE* 3.8 23.6 - - + -
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ARG* 4.3 2.9 - - - +
42C PHE* 4.1 11.6 - - + -
45C LEU* 4.0 30.3 - - + -
47C SER* 3.8 19.5 - - - +
50C LEU* 3.9 11.2 - - + -
33D PHE* 3.6 17.2 - - + -
34D PRO 3.0 18.8 + - - +
35D GLU* 2.9 21.7 + - - +
37D LEU* 1.3 75.4 - - - +
39D ASP* 1.3 61.8 + - - +
41D VAL* 3.4 1.7 + - - +
42D PHE* 3.2 26.2 + - + -
240D PHE* 4.1 9.9 - - + -
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Residues in contact with ASP 39 (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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297B LEU* 4.7 6.1 - - - +
301B ARG* 4.0 5.8 - - - +
42C PHE* 3.1 28.1 - - + -
35D GLU* 2.6 46.4 + - - +
36D ASP* 3.6 14.0 - - - +
38D VAL* 1.3 76.4 - - - +
40D GLU* 1.3 60.8 + - - +
42D PHE* 3.2 3.3 + - - +
43D ARG* 2.9 28.7 + - - +
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Residues in contact with GLU 40 (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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15B GLU* 3.0 25.6 - - - +
36D ASP 3.2 12.1 + - - +
37D LEU* 3.1 16.0 + - + +
39D ASP* 1.3 77.7 - - - +
41D VAL* 1.3 64.6 + - - +
43D ARG* 3.2 23.0 + - - +
44D ARG* 3.1 37.6 + - - +
243D VAL* 4.1 18.4 - - + -
247D HIS* 4.5 17.8 - - + +
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Residues in contact with VAL 41 (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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37D LEU 2.8 19.1 + - - +
38D VAL 3.6 6.7 - - - +
40D GLU* 1.3 75.5 - - - +
42D PHE* 1.3 64.7 + - + +
44D ARG* 3.2 3.3 + - - -
45D LEU* 2.9 27.9 + - + +
236D VAL* 4.3 9.2 - - + -
239D MET* 3.8 31.3 - - + +
240D PHE* 3.7 48.2 - - + -
243D VAL* 3.3 23.8 - - + -
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Residues in contact with PHE 42 (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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18B LYS* 3.1 22.3 + - - +
38C VAL* 3.7 23.9 - - + +
41C VAL* 4.0 13.7 - - + -
42C PHE* 3.6 50.9 - + + -
45C LEU* 3.6 31.6 - - + -
236C VAL* 4.9 4.3 - - + -
240C PHE* 4.5 5.8 - + - -
38D VAL* 3.2 24.2 + - + +
39D ASP 3.2 3.8 + - - +
41D VAL* 1.3 87.0 - - + +
43D ARG* 1.3 61.1 + - - +
45D LEU* 3.2 37.5 - - + +
236D VAL* 5.1 0.4 - - + -
240D PHE* 4.5 11.4 - + - -
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Residues in contact with ARG 43 (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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15B GLU* 3.4 53.8 + - + +
16B THR 3.0 23.6 + - - +
17B GLU* 3.1 40.5 + - - +
18B LYS* 3.2 36.4 + - + +
308B ARG* 5.6 3.4 - - - +
39D ASP 2.9 13.6 + - - +
40D GLU* 3.4 24.9 + - - +
41D VAL 3.2 0.2 - - - -
42D PHE* 1.3 77.7 - - - +
44D ARG* 1.3 59.7 + - - +
45D LEU 3.1 0.4 - - - +
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Residues in contact with ARG 44 (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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13B PRO* 5.6 6.7 - - - +
15B GLU* 3.4 35.0 + - + +
40D GLU* 3.1 28.2 + - - +
43D ARG* 1.3 73.7 - - - +
45D LEU* 1.3 63.9 + - - +
46D ASN* 3.2 6.6 + - - +
60D GLU* 3.0 36.5 + - - -
64D LYS* 3.7 5.3 - - - +
235D TYR* 3.6 7.3 + - - -
239D MET* 3.5 41.9 - - + +
242D LYS* 3.9 3.4 - - - +
243D VAL* 4.2 12.5 - - - +
246D ASP* 3.4 23.8 + - - -
247D HIS* 6.2 1.2 - - - -
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Residues in contact with LEU 45 (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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18B LYS* 2.9 25.7 + - - +
38C VAL* 4.4 12.3 - - + -
240C PHE* 4.5 3.6 - - + -
41D VAL* 2.9 13.3 + - + +
42D PHE* 3.2 53.6 - - + +
43D ARG 3.1 1.3 - - - +
44D ARG* 1.3 76.1 - - - +
46D ASN* 1.3 75.0 + - - +
47D SER* 3.8 5.1 + - - +
50D LEU* 4.0 19.5 - - + -
235D TYR* 3.9 19.1 - - + -
236D VAL* 4.0 22.0 - - + -
239D MET* 5.5 2.9 - - + -
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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