Contacts of the helix formed by residues 49 - 61 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21O ARG* 3.9 20.4 - - - +
47O GLY 3.4 10.7 - - - +
48O VAL* 1.3 87.5 - - + +
50O PRO* 1.3 73.0 - - + +
51O GLU* 3.7 13.7 - - - +
52O GLU* 3.0 17.3 + - + +
53O CYS* 3.0 19.1 + - - +
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Residues in contact with PRO 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O MET* 3.4 15.8 - - + +
44O PRO* 4.4 3.4 - - + -
48O VAL 3.5 4.2 - - - +
49O PRO* 1.3 84.5 - - + +
51O GLU* 1.3 69.5 - - - +
53O CYS* 4.3 3.8 - - + -
54O GLY 2.9 24.3 + - - -
87O ILE* 3.5 14.0 - - + +
97O TYR* 3.8 51.8 - - + +
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Residues in contact with GLU 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O ARG* 3.7 31.7 + - - +
25O TYR* 3.7 43.5 + - + +
49O PRO* 3.7 9.4 - - - +
50O PRO* 1.3 91.4 - - - +
52O GLU* 1.3 57.7 + - - +
54O GLY* 3.9 0.5 - - - -
55O ALA* 2.9 30.6 + - - +
87O ILE* 3.6 12.1 - - + -
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Residues in contact with GLU 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O ASP* 3.4 13.5 - - - +
20O TYR* 2.8 25.2 + - - -
21O ARG* 2.9 41.2 + - - +
48O VAL* 4.5 3.4 - - + -
49O PRO* 3.0 27.6 + - + +
51O GLU* 1.3 77.5 - - - +
53O CYS* 1.3 59.5 + - - +
55O ALA* 3.4 1.1 + - - +
56O ALA* 2.9 29.0 + - - +
1481O EDO 2.7 42.3 + - - +
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Residues in contact with CYS 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O MET* 3.7 26.2 - - - -
44O PRO* 3.9 23.3 - - + -
48O VAL* 4.0 12.2 - - + +
49O PRO 3.0 15.1 + - - +
50O PRO 3.8 3.8 - - - +
52O GLU* 1.3 74.7 - - - +
54O GLY* 1.3 63.5 + - - +
56O ALA* 3.4 6.4 + - - +
57O VAL* 3.1 28.2 + - - +
129O ALA* 4.2 9.0 - - - -
130O LEU* 3.9 27.6 - - - -
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Residues in contact with GLY 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O MET* 3.5 15.3 - - - -
50O PRO 2.9 17.6 + - - -
51O GLU 3.9 0.9 - - - -
53O CYS* 1.3 75.0 - - - +
55O ALA* 1.3 57.4 + - - +
57O VAL* 3.3 5.9 + - - +
58O ALA* 3.0 28.1 + - - +
84O CYS* 3.7 23.3 - - - +
99O ALA* 4.3 4.9 - - - -
101O VAL* 4.7 1.4 - - - +
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Residues in contact with ALA 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O TYR* 3.7 6.7 - - - +
21O ARG* 3.5 35.0 - - + +
24O TYR* 3.5 14.7 - - + +
25O TYR* 4.0 11.2 - - + +
51O GLU 2.9 19.9 + - - +
52O GLU 3.6 3.4 - - - +
53O CYS 3.3 0.2 - - - -
54O GLY* 1.3 72.9 - - - +
56O ALA* 1.3 60.1 + - - +
58O ALA* 3.3 0.9 + - - -
59O ALA* 2.8 31.4 + - - +
84O CYS* 4.1 1.6 - - - +
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Residues in contact with ALA 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O TYR* 3.4 36.9 - - + +
52O GLU 2.9 15.3 + - - +
53O CYS* 3.7 8.7 - - - +
54O GLY 3.3 0.2 - - - -
55O ALA* 1.3 71.8 - - - +
57O VAL* 1.3 60.8 + - + +
60O GLU* 2.9 36.1 + - - +
124O VAL* 5.1 0.4 - - - -
127O PHE* 5.1 12.8 - - + -
129O ALA* 5.9 4.3 - - + -
130O LEU* 6.5 0.9 - - + -
1481O EDO 5.0 5.2 - - - -
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Residues in contact with VAL 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O PHE* 3.7 45.3 - - + -
42O MET* 4.7 5.2 - - - -
53O CYS 3.1 19.2 + - - +
54O GLY* 3.6 9.9 - - - +
56O ALA* 1.3 76.2 - - + +
58O ALA* 1.3 55.2 + - - +
61O SER* 2.7 34.7 + - - +
99O ALA* 6.1 0.9 - - + -
101O VAL* 4.5 3.6 - - + -
124O VAL* 3.4 16.8 - - + +
130O LEU* 3.9 27.4 - - + -
133O LEU* 4.3 14.8 - - + -
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Residues in contact with ALA 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O TYR* 4.1 4.9 - - + +
54O GLY 3.0 16.7 + - - +
55O ALA 3.6 4.3 - - - +
57O VAL* 1.3 76.2 - - - +
59O ALA* 1.3 55.3 + - - +
61O SER* 3.4 9.5 + - - -
62O SER* 2.6 32.1 + - - -
82O GLY* 4.0 10.9 - - - +
84O CYS* 3.6 28.5 - - + +
101O VAL* 3.8 20.2 - - + -
103O TYR* 4.6 0.2 - - - -
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Residues in contact with ALA 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O TYR* 3.4 31.4 - - + -
24O TYR* 3.5 32.4 - - + -
55O ALA 2.8 20.5 + - - +
56O ALA 3.3 0.9 + - - +
58O ALA* 1.3 74.0 - - - +
60O GLU* 1.3 57.9 + - - +
61O SER 3.2 0.4 - - - -
62O SER 3.2 13.5 + - - -
63O THR 3.2 1.2 + - - -
64O GLY* 2.8 26.0 + - - +
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Residues in contact with GLU 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O TYR* 2.7 29.8 + - + +
56O ALA 2.9 17.7 + - - +
59O ALA* 1.3 76.7 - - - +
61O SER* 1.3 57.1 + - - +
62O SER 3.5 0.4 - - - -
64O GLY 3.5 18.6 - - - +
65O THR* 3.3 10.6 - - - -
66O TRP 3.5 0.3 + - - -
119O SER 4.8 0.7 - - - +
123O ASN* 4.6 11.6 + - + +
124O VAL* 3.8 11.9 + - + +
127O PHE* 3.2 35.6 - - + -
177V LYS* 3.5 19.2 + - - -
204V GLU* 5.0 0.3 - - - +
334V LYS* 3.0 29.5 + - - -
1476V CAP 3.3 11.3 + - - -
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Residues in contact with SER 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57O VAL* 2.7 22.1 + - - +
58O ALA 3.4 3.5 + - - -
60O GLU* 1.3 79.0 - - - +
62O SER* 1.3 54.4 + - - +
103O TYR* 2.6 43.3 + - - -
107O LEU* 5.1 0.5 - - - +
119O SER* 3.1 42.4 + - - -
120O ILE 4.1 5.4 - - - -
124O VAL* 4.0 9.4 - - - -
177V LYS* 4.8 0.9 - - - +
205V ASN* 4.6 5.4 - - - -
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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