Contacts of the helix formed by residues 11 - 23 (chain B) in PDB entry 1UXI
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 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B GLY 3.2 8.7 + - - -
10B ALA* 1.3 77.2 - - - +
12B PHE* 1.3 55.6 + - - -
13B VAL 3.5 2.0 - - - -
14B GLY 4.1 0.6 - - - +
15B SER* 2.6 36.3 + - - -
42B LYS* 4.1 8.5 - - - -
77B THR 4.7 0.2 + - - -
1310B NAD 3.1 32.8 + - - -
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Residues in contact with PHE 12 (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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12A PHE* 3.9 35.0 - + - -
42A LYS* 6.2 0.7 - - - -
11B GLY* 1.3 69.9 - - - -
13B VAL* 1.3 60.6 + - - +
15B SER* 3.2 3.9 + - - -
16B THR* 2.6 33.8 + - - -
222B THR 5.8 4.5 - - - -
223B GLY* 5.9 7.4 - - - -
224B SER 5.7 0.9 - - - -
226B TYR* 3.4 54.2 - + + +
1310B NAD 2.9 39.6 + - - +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 1.3 70.3 - - - +
14B GLY* 1.3 55.9 + - - +
16B THR* 3.3 1.9 + - - -
17B THR* 2.7 44.3 + - - +
77B THR* 3.8 22.9 - - + -
118B VAL* 4.2 10.8 - - + -
225B ALA 3.8 10.8 - - - +
226B TYR* 4.0 7.0 - - + -
229B PRO* 4.4 5.4 - - + +
230B ALA* 3.8 19.4 - - - +
233B THR* 4.8 1.6 - - - +
1310B NAD 2.7 61.7 + - + +
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Residues in contact with GLY 14 (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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7B ILE* 3.6 18.5 - - - +
9B GLY 3.4 12.2 + - - -
11B GLY 3.6 3.0 + - - +
12B PHE 3.4 0.2 - - - -
13B VAL* 1.3 78.8 - - - +
15B SER* 1.3 60.5 + - - +
17B THR* 3.2 6.7 + - - -
18B ALA* 3.1 18.7 + - - +
31B LEU* 4.1 3.6 - - - -
77B THR* 3.2 26.3 + - - -
1310B NAD 4.2 0.6 + - - -
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 4.7 2.3 + - - -
227A TYR* 3.2 28.5 + - - -
10B ALA 4.3 2.6 - - - -
11B GLY 2.6 25.6 + - - -
12B PHE* 3.2 7.8 + - - -
14B GLY* 1.3 74.6 - - - +
16B THR* 1.3 66.7 + - - +
18B ALA* 3.1 8.2 + - - +
19B HIS* 3.0 17.3 + - - +
31B LEU* 4.3 12.0 - - - +
42B LYS* 3.9 26.3 + - - +
46B LEU* 5.0 0.9 - - - +
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 4.0 9.9 - - + +
227A TYR* 4.6 5.0 + - - -
12B PHE* 2.6 22.1 + - - -
15B SER* 1.3 80.9 + - - +
17B THR* 1.3 62.0 + - - +
19B HIS* 3.2 7.5 + - + +
20B TRP* 3.0 36.4 + - + +
226B TYR* 3.4 22.6 - - - +
227B TYR* 4.0 20.7 - - + -
230B ALA* 3.5 20.9 - - + -
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Residues in contact with THR 17 (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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7B ILE* 4.1 11.0 - - + -
13B VAL* 2.7 27.4 + - - +
14B GLY* 3.4 10.2 - - - -
15B SER 3.1 0.2 - - - -
16B THR* 1.3 75.8 - - - +
18B ALA* 1.3 60.3 - - - +
19B HIS 3.2 0.2 + - - -
20B TRP* 3.2 2.7 + - - +
21B LEU* 2.8 51.0 + - + +
75B VAL* 4.8 4.7 - - + -
77B THR* 5.0 1.7 - - - +
230B ALA* 3.5 26.2 - - - +
233B THR* 4.0 25.8 - - + +
234B ALA* 4.4 5.2 - - + +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.8 15.6 - - + +
14B GLY 3.1 9.6 + - - +
15B SER 3.1 9.2 + - - +
17B THR* 1.3 77.1 - - - +
19B HIS* 1.3 52.5 + - - +
21B LEU* 3.6 4.4 - - - +
22B ALA* 2.7 37.6 + - - +
29B ILE* 3.7 12.6 - - + +
31B LEU* 3.8 27.4 - - + -
46B LEU* 3.6 12.1 - - + +
59B VAL* 5.1 0.2 - - + -
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Residues in contact with HIS 19 (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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16A THR* 4.1 8.2 - - + +
19A HIS* 3.4 42.5 + + + -
20A TRP* 3.1 60.4 - + - -
227A TYR* 3.7 25.6 - + + -
15B SER 3.0 11.7 + - - +
16B THR* 3.3 13.2 - - - +
17B THR 3.1 0.4 - - - -
18B ALA* 1.3 76.6 - - - +
20B TRP* 1.3 69.7 + + - +
21B LEU 3.3 0.3 + - - -
22B ALA* 3.8 1.2 - - - +
23B ALA* 3.3 17.6 + - + +
46B LEU* 3.8 11.6 - - + +
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Residues in contact with TRP 20 (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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19A HIS* 3.4 36.8 - + - -
23A ALA* 4.9 8.5 - - + -
46A LEU* 4.4 8.7 - - + -
49A ALA* 4.1 8.3 - - + -
53A GLU* 3.2 43.3 - - + +
55A PHE* 3.9 23.3 - + - -
16B THR* 3.0 32.9 + - + +
17B THR 3.8 3.8 - - - +
19B HIS* 1.3 78.8 - + - +
21B LEU* 1.3 62.7 + - - +
23B ALA* 3.5 12.1 + - + +
24B LYS* 3.4 21.2 - - - +
227B TYR* 3.0 27.2 + - + -
230B ALA* 3.5 7.6 - - + -
231B ALA* 3.3 28.4 - - + +
234B ALA* 3.8 15.3 - - + -
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Residues in contact with LEU 21 (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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5B ILE* 4.1 38.6 - - + -
7B ILE* 4.2 9.6 - - + -
17B THR* 2.8 34.3 + - + +
18B ALA 3.6 3.6 - - - +
20B TRP* 1.3 75.1 - - - +
22B ALA* 1.3 58.5 + - - +
24B LYS* 2.6 34.5 + - + +
25B GLU 3.4 3.5 + - - -
26B LEU* 3.9 26.9 + - + +
29B ILE* 3.7 11.4 - - + -
234B ALA* 3.5 32.5 - - + +
237B VAL* 4.2 10.5 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA 2.7 21.0 + - - +
19B HIS 3.8 4.7 - - - +
21B LEU* 1.3 72.3 - - - +
23B ALA* 1.3 62.0 + - - +
24B LYS 3.1 1.0 + - - -
25B GLU* 3.1 10.2 + - - -
26B LEU 5.9 0.2 - - - +
29B ILE* 3.5 11.3 - - + +
46B LEU* 4.0 17.3 - - + -
55B PHE* 3.7 31.0 - - + +
57B VAL* 3.2 26.6 - - + +
59B VAL* 4.7 0.4 - - + -
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Residues in contact with ALA 23 (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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20A TRP* 4.8 16.4 - - + -
19B HIS* 3.3 10.7 + - + +
20B TRP* 3.6 14.6 - - + +
21B LEU 3.0 0.4 + - - -
22B ALA* 1.3 78.7 - - - +
24B LYS* 1.3 62.4 + - + +
25B GLU* 3.5 4.0 - - - +
55B PHE* 4.2 16.0 - - + +
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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