Contacts of the helix formed by residues 49 - 61 (chain R) in PDB entry 1UW9
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 49 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21R ARG* 3.9 21.3 - - - +
47R GLY 3.5 10.3 - - - +
48R VAL* 1.3 85.4 - - + +
50R PRO* 1.3 72.9 - - + +
51R GLU* 3.7 13.2 - - - +
52R GLU* 3.0 17.6 + - + +
53R CYS* 3.0 18.9 + - - +
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Residues in contact with PRO 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R MET* 3.4 14.5 - - + +
44R PRO* 4.5 2.9 - - + -
48R VAL 3.5 4.6 - - - +
49R PRO* 1.3 83.8 - - + +
51R GLU* 1.3 68.8 + - - +
53R CYS* 4.3 4.3 - - + -
54R GLY 2.8 26.2 + - - -
87R ILE* 3.5 14.2 - - + +
97R TYR* 3.9 52.7 - - + +
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Residues in contact with GLU 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R ARG* 3.6 32.9 + - - +
25R TYR* 3.7 43.5 + - + +
49R PRO* 3.7 8.7 - - - +
50R PRO* 1.3 92.7 - - - +
52R GLU* 1.3 57.5 + - - +
54R GLY* 3.9 0.5 - - - -
55R ALA* 2.9 29.1 + - - +
87R ILE* 3.6 11.9 - - + -
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Residues in contact with GLU 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19R ASP* 3.4 13.2 - - - +
20R TYR* 2.8 25.7 + - - -
21R ARG* 2.8 42.5 + - - +
48R VAL* 4.5 2.2 - - + -
49R PRO* 3.0 26.8 + - + +
51R GLU* 1.3 76.4 - - - +
53R CYS* 1.3 61.4 + - - +
55R ALA* 3.4 1.1 + - - -
56R ALA* 2.9 28.6 + - - +
1481R EDO 2.8 42.9 + - - +
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Residues in contact with CYS 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R MET* 3.7 25.4 - - - -
44R PRO* 3.8 23.6 - - + -
48R VAL* 3.9 12.7 - - + +
49R PRO 3.0 14.4 + - - +
50R PRO 3.8 4.0 - - - +
52R GLU* 1.3 75.3 - - - +
54R GLY* 1.3 64.0 + - - +
56R ALA* 3.3 7.8 + - - +
57R VAL* 3.1 27.4 + - - +
129R ALA* 4.2 9.2 - - - -
130R LEU* 3.9 27.1 - - - -
1481R EDO 6.3 0.2 - - - -
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Residues in contact with GLY 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R MET* 3.4 15.5 - - - -
50R PRO 2.8 20.4 + - - -
51R GLU 4.0 0.2 - - - -
53R CYS* 1.3 71.2 - - - +
55R ALA* 1.3 57.3 + - - +
57R VAL* 3.3 6.0 + - - +
58R ALA* 3.0 28.4 + - - +
84R CYS* 3.7 24.0 - - - +
99R ALA* 4.3 4.3 - - - -
101R VAL* 4.7 1.4 - - - +
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Residues in contact with ALA 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R TYR* 3.6 6.5 - - - +
21R ARG* 3.4 35.4 - - - +
24R TYR* 3.5 13.8 - - - +
25R TYR* 4.0 10.3 - - + +
51R GLU 2.9 20.3 + - - +
52R GLU 3.6 3.6 - - - +
54R GLY* 1.3 76.4 - - - +
56R ALA* 1.3 56.6 + - - +
58R ALA 3.3 0.3 + - - -
59R ALA* 2.8 32.1 + - - +
84R CYS* 4.2 2.3 - - - +
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Residues in contact with ALA 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R TYR* 3.5 33.1 - - + +
52R GLU 2.9 17.8 + - - +
53R CYS* 3.3 9.4 + - - +
55R ALA* 1.3 72.3 - - - +
57R VAL* 1.3 60.3 + - + +
60R GLU* 2.9 36.9 + - - +
124R VAL* 4.4 0.8 - - - +
127R PHE* 5.1 13.7 - - + -
129R ALA* 5.9 4.0 - - + -
130R LEU* 6.4 0.9 - - + -
1481R EDO 5.1 5.4 - - - -
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Residues in contact with VAL 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R PHE* 3.7 44.6 - - + -
42R MET* 4.7 6.3 - - - -
53R CYS 3.1 15.4 + - - +
54R GLY* 3.6 9.0 - - - +
55R ALA 3.3 0.2 - - - -
56R ALA* 1.3 76.3 - - + +
58R ALA* 1.3 54.3 + - - +
61R SER* 2.7 35.4 + - - +
99R ALA* 6.2 0.7 - - + -
101R VAL* 4.6 3.1 - - + -
124R VAL* 3.4 20.4 - - + +
130R LEU* 3.9 26.9 - - + -
133R LEU* 4.3 13.7 - - + -
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Residues in contact with ALA 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R TYR* 4.1 5.6 - - + +
54R GLY 3.0 16.5 + - - +
55R ALA 3.7 4.3 - - - +
57R VAL* 1.3 75.1 - - - +
59R ALA* 1.3 56.0 + - - +
61R SER* 3.4 9.9 + - - -
62R SER* 2.6 31.9 + - - -
82R GLY* 4.0 10.7 - - - +
84R CYS* 3.6 27.1 - - + +
101R VAL* 3.8 20.6 - - + +
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Residues in contact with ALA 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H LYS* 3.9 0.2 - - - +
20R TYR* 3.4 31.6 - - + -
24R TYR* 3.5 31.1 - - + -
55R ALA 2.8 21.2 + - - +
56R ALA 3.7 0.7 - - - +
58R ALA* 1.3 74.8 - - - +
60R GLU* 1.3 57.6 + - - +
61R SER 3.2 0.2 - - - -
62R SER 3.2 2.3 + - - -
63R THR 3.2 10.7 + - - -
64R GLY* 2.8 26.3 + - - +
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Residues in contact with GLU 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H LYS* 3.5 20.0 + - - -
204H GLU* 5.1 0.2 - - - +
334H LYS* 3.0 28.6 + - - -
1478O CAP 3.3 10.6 + - - -
20R TYR* 2.7 30.3 + - + +
56R ALA 2.9 18.6 + - - +
59R ALA* 1.3 76.3 - - - +
61R SER* 1.3 57.3 + - - +
62R SER 3.5 0.4 - - - -
64R GLY 3.5 17.3 - - - +
65R THR* 3.2 12.0 - - - -
66R TRP 3.4 0.2 + - - -
119R SER 4.8 0.5 - - - +
123R ASN* 4.6 11.0 + - + +
124R VAL* 3.8 11.7 - - + +
127R PHE* 3.3 36.2 - - + -
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Residues in contact with SER 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H LYS* 4.8 0.7 - - - +
205H ASN* 4.6 4.0 - - - -
57R VAL* 2.7 23.2 + - - +
58R ALA* 3.4 3.1 + - - -
60R GLU* 1.3 77.6 - - - +
62R SER* 1.3 56.9 + - - +
103R TYR* 2.7 41.2 + - - -
107R LEU* 5.1 0.5 - - - +
119R SER* 3.1 44.5 - - - -
120R ILE* 4.2 5.8 - - - -
124R VAL* 4.1 9.9 - - - -
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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