Contacts of the helix formed by residues 24 - 37 (chain Y) in PDB entry 1UAC
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 SER 24 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18Y ASP* 3.6 4.3 - - - -
19Y ASN* 3.5 19.3 - - - +
22Y GLY 3.5 4.6 + - - -
23Y TYR* 1.3 75.6 - - - +
25Y LEU* 1.3 65.5 + - - +
26Y GLY 3.5 4.2 + - - -
27Y ASN* 2.9 32.8 + - - +
28Y TRP* 3.5 2.1 - - - -
120Y VAL* 3.3 17.5 - - - +
121Y HIS* 5.1 4.4 + - - -
124Y ILE* 6.5 0.2 - - - -
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Residues in contact with LEU 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y ALA* 3.8 13.9 - - + +
12Y MET* 3.5 33.9 - - + -
13Y LYS* 3.3 24.9 - - - +
17Y LEU* 4.7 6.7 - - + -
18Y ASP* 2.8 33.5 + - + +
24Y SER* 1.3 72.4 - - - +
26Y GLY* 1.3 64.0 + - - +
27Y ASN 3.0 1.2 + - - -
28Y TRP* 3.2 16.6 + - + -
29Y VAL* 3.3 19.5 + - + +
124Y ILE* 3.9 18.9 - - + +
129Y LEU* 3.8 24.9 - - + -
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Residues in contact with GLY 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Y SER* 3.0 5.0 + - - -
25Y LEU* 1.3 81.0 - - - +
27Y ASN* 1.3 56.4 + - - +
29Y VAL* 3.9 0.7 - - - -
30Y CYS* 2.9 32.6 + - - +
120Y VAL* 3.5 29.3 - - - +
121Y HIS* 5.0 0.4 - - - +
123Y TRP* 3.8 6.3 - - - +
124Y ILE* 4.2 20.3 - - - +
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Residues in contact with ASN 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Y TYR* 3.8 14.6 - - + +
24Y SER* 2.9 44.6 + - - +
26Y GLY* 1.3 77.5 - - - +
28Y TRP* 1.3 60.8 + - + +
30Y CYS* 3.4 4.9 - - - +
31Y ALA* 2.8 23.4 + - - +
105Y MET* 3.7 20.2 - - - -
111Y TRP* 2.8 36.7 + - - +
115Y CYS 5.0 0.2 - - - +
116Y LYS* 5.4 0.3 - - - -
120Y VAL* 3.5 24.1 - - - +
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Residues in contact with TRP 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Y MET* 3.8 23.7 - - + +
17Y LEU* 3.1 50.3 + - + -
20Y TYR* 4.0 26.5 - + + -
23Y TYR* 3.3 30.3 + + + +
24Y SER 3.5 13.2 - - - -
25Y LEU* 3.2 7.8 + - - +
27Y ASN* 1.3 76.0 - - - +
29Y VAL* 1.3 64.5 + - - +
31Y ALA* 3.8 2.7 - - - +
32Y ALA* 3.0 25.3 + - - +
56Y LEU* 4.2 7.8 - - + +
95Y ALA* 4.0 30.7 - - + -
99Y ALA* 3.5 26.5 - - + -
105Y MET* 3.6 29.2 - - + -
108Y TRP* 4.2 3.8 - + - -
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Residues in contact with VAL 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y ARG* 4.1 21.8 - - + +
8Y LEU* 4.7 2.9 - - + -
9Y ALA* 4.0 24.0 - - + +
12Y MET* 3.8 19.5 - - - -
25Y LEU* 3.3 20.5 + - + +
26Y GLY* 4.0 2.9 - - - +
28Y TRP* 1.3 75.5 - - - +
30Y CYS* 1.3 57.6 + - - +
32Y ALA 3.4 0.2 + - - -
33Y LYS* 3.0 26.4 + - - +
38Y PHE* 3.4 20.4 - - + -
123Y TRP* 3.8 29.8 - - + +
124Y ILE* 4.2 4.9 - - + -
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Residues in contact with CYS 30 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Y GLY 2.9 20.0 + - - +
27Y ASN* 3.4 4.5 - - - +
29Y VAL* 1.3 75.0 - - - +
31Y ALA* 1.3 65.3 + - - +
33Y LYS* 3.3 3.0 + - - +
34Y PHE* 3.2 27.9 + - - -
114Y ARG 4.0 4.9 - - - -
115Y CYS* 2.1 54.0 - - + -
118Y THR* 5.4 0.9 - - - -
120Y VAL* 4.8 2.7 - - + -
123Y TRP* 3.6 36.5 - - + +
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Residues in contact with ALA 31 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Y ASN 2.8 20.4 + - - +
28Y TRP* 3.3 5.1 + - - +
30Y CYS* 1.3 73.1 - - - +
32Y ALA* 1.3 58.0 + - - +
34Y PHE* 3.1 3.3 + - - +
35Y GLU* 2.7 40.8 + - + +
56Y LEU* 4.0 12.3 - - + -
105Y MET* 4.2 11.2 - - + -
108Y TRP* 4.8 5.6 - - + -
110Y ALA* 4.7 0.2 - - - +
111Y TRP* 4.1 22.0 - - + +
115Y CYS* 3.6 7.1 - - - -
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Residues in contact with ALA 32 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y LEU* 3.8 27.1 - - + -
12Y MET* 4.4 2.5 - - + -
28Y TRP 3.0 16.1 + - - +
29Y VAL 3.8 0.9 - - - +
31Y ALA* 1.3 74.9 - - - +
33Y LYS* 1.3 61.1 + - - +
36Y SER* 2.8 30.7 + - - -
37Y ASN 3.1 5.2 + - - -
38Y PHE* 3.4 5.0 + - + -
55Y ILE* 3.5 26.5 - - + +
56Y LEU* 3.6 9.8 - - + +
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Residues in contact with LYS 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Y VAL 3.0 17.8 + - - +
30Y CYS 3.6 4.7 - - - +
31Y ALA 3.3 0.2 - - - -
32Y ALA* 1.3 74.9 - - - +
34Y PHE* 1.4 97.4 + - + +
37Y ASN* 2.8 42.7 + - - +
38Y PHE* 3.6 20.5 - - + -
123Y TRP* 3.3 45.6 - - + -
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Residues in contact with PHE 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y CYS* 3.2 29.1 + - - +
31Y ALA 3.1 2.8 + - - -
33Y LYS* 1.4 117.5 - - + +
35Y GLU* 1.3 64.9 + - - +
37Y ASN 4.7 0.2 - - - -
110Y ALA* 3.9 24.6 - - + +
114Y ARG* 3.3 69.5 - - + -
115Y CYS* 4.1 1.8 - - - -
123Y TRP* 4.0 15.5 - + - -
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Residues in contact with GLU 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Y ALA* 2.7 25.6 + - + +
32Y ALA* 4.3 0.2 - - - -
34Y PHE* 1.3 81.4 - - - +
36Y SER* 1.3 58.5 + - - +
37Y ASN 3.9 0.2 - - - -
44Y ASN* 5.5 2.6 + - - -
55Y ILE 4.0 11.4 - - - +
56Y LEU* 4.1 5.6 - - - +
57Y GLN* 3.2 41.2 - - + +
108Y TRP* 3.7 33.7 - - + +
109Y VAL* 4.0 4.3 + - - +
110Y ALA* 3.0 31.7 + - + +
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Residues in contact with SER 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Y ALA 2.8 10.8 + - - -
35Y GLU* 1.3 77.7 - - - +
37Y ASN* 1.3 68.6 + - - +
38Y PHE 3.1 11.6 + - - -
39Y ASN* 3.2 19.1 + - - +
42Y ALA* 3.7 16.9 - - - +
54Y GLY 3.4 18.2 - - - -
55Y ILE* 2.8 31.2 + - - +
57Y GLN* 4.3 0.4 - - - -
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Residues in contact with ASN 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y VAL* 4.4 8.8 - - - +
33Y LYS* 2.8 40.8 + - - +
34Y PHE 4.7 0.2 - - - -
36Y SER* 1.3 79.6 - - - +
38Y PHE* 1.3 77.7 + - - +
39Y ASN* 3.4 2.6 + - + +
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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