Contacts of the helix formed by residues 49 - 61 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21V ARG* 3.9 25.8 - - - +
47V GLY 3.4 10.7 - - - +
48V VAL* 1.3 88.3 - - + +
50V PRO* 1.3 75.0 - - + +
51V GLU* 3.9 6.5 - - - +
52V GLU* 3.0 17.4 + - + +
53V CYS* 3.0 19.1 + - - +
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Residues in contact with PRO 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V MET* 3.5 14.7 - - + +
44V PRO* 4.5 4.5 - - + -
48V VAL 3.5 4.5 - - - +
49V PRO* 1.3 84.0 - - + +
51V GLU* 1.3 70.6 + - - +
53V CYS* 4.3 3.8 - - + -
54V GLY 2.9 24.9 + - - -
87V ILE* 3.5 13.9 - - + +
97V TYR* 3.8 51.6 - - + +
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Residues in contact with GLU 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V ARG* 3.6 32.6 + - - +
25V TYR* 3.6 45.1 + - + +
49V PRO* 3.9 7.6 - - - +
50V PRO* 1.3 93.1 - - - +
52V GLU* 1.3 59.1 + - - +
54V GLY* 4.0 0.5 - - - -
55V ALA* 3.0 27.7 + - - +
87V ILE* 3.6 12.4 - - + +
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Residues in contact with GLU 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V ASP* 3.5 14.5 - - - +
20V TYR* 2.8 27.4 + - - -
21V ARG* 2.9 41.0 + - - +
48V VAL* 4.4 2.2 - - + -
49V PRO* 3.0 29.1 + - + +
51V GLU* 1.3 75.0 - - - +
53V CYS* 1.3 61.1 + - - +
55V ALA* 3.3 1.4 + - - +
56V ALA* 2.9 28.6 + - - +
1480V EDO 2.8 39.4 + - - +
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Residues in contact with CYS 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V MET* 3.6 28.9 - - - -
44V PRO* 3.8 22.9 - - + -
48V VAL* 4.0 12.2 - - + +
49V PRO 3.0 13.6 + - - +
50V PRO 3.8 2.5 - - - +
52V GLU* 1.3 74.8 - - - +
54V GLY* 1.3 63.6 + - - +
56V ALA* 3.4 7.0 + - - +
57V VAL* 3.1 27.9 + - - +
129V ALA* 4.2 9.4 - - - -
130V LEU* 3.9 26.9 - - - -
1480V EDO 6.1 0.4 - - - -
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Residues in contact with GLY 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V MET* 3.5 14.5 - - - -
50V PRO 2.9 17.8 + - - -
51V GLU 4.1 0.2 - - - -
53V CYS* 1.3 76.2 - - - +
55V ALA* 1.3 56.0 + - - +
57V VAL* 3.3 5.6 + - - +
58V ALA* 3.0 27.5 + - - +
84V CYS* 3.6 25.5 - - - +
99V ALA* 4.3 4.3 - - - -
101V VAL* 4.7 1.9 - - - +
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Residues in contact with ALA 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V TYR* 3.7 6.7 - - - +
21V ARG* 3.4 34.8 - - - +
24V TYR* 3.4 14.3 - - + +
25V TYR* 4.0 11.0 - - + +
51V GLU 3.0 20.5 + - - +
52V GLU 3.6 3.6 - - - +
53V CYS 3.3 0.2 - - - -
54V GLY* 1.3 74.8 - - - +
56V ALA* 1.3 54.8 + - - +
58V ALA* 3.3 1.0 + - - -
59V ALA* 2.8 36.0 + - - +
84V CYS* 4.1 1.2 - - - +
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Residues in contact with ALA 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V TYR* 3.5 34.7 - - + +
52V GLU 2.9 17.0 + - - +
53V CYS* 3.7 8.7 - - - +
54V GLY 3.4 0.2 - - - -
55V ALA* 1.3 71.9 - - - +
57V VAL* 1.3 61.9 + - + +
60V GLU* 2.9 35.5 + - - +
124V VAL* 5.1 0.2 - - - -
127V PHE* 5.1 12.5 - - + -
129V ALA* 5.8 3.8 - - + -
130V LEU* 6.5 0.9 - - + -
1480V EDO 4.8 6.7 - - - -
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Residues in contact with VAL 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40V PHE* 3.7 45.8 - - + -
42V MET* 4.7 5.4 - - - -
53V CYS 3.1 16.0 + - - +
54V GLY* 3.6 9.4 - - - +
56V ALA* 1.3 75.0 - - + +
58V ALA* 1.3 55.6 + - - +
61V SER* 2.7 35.0 + - - -
99V ALA* 6.2 0.7 - - + -
101V VAL* 4.6 2.9 - - + -
124V VAL* 3.4 19.1 - - + +
130V LEU* 3.9 27.8 - - + -
133V LEU* 4.3 13.2 - - + -
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Residues in contact with ALA 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24V TYR* 4.1 6.7 - - + +
54V GLY 3.0 17.2 + - - +
55V ALA 3.3 4.5 + - - +
57V VAL* 1.3 77.8 - - - +
59V ALA* 1.3 54.2 + - - +
61V SER* 3.3 13.6 + - - -
62V SER* 2.6 27.9 + - - -
82V GLY* 4.1 11.8 - - - +
84V CYS* 3.6 26.7 - - + +
101V VAL* 3.8 19.7 - - + +
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Residues in contact with ALA 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V TYR* 3.3 31.0 - - + -
24V TYR* 3.4 32.5 - - + -
55V ALA 2.8 21.4 + - - +
56V ALA 3.8 0.7 - - - +
58V ALA* 1.3 74.2 - - - +
60V GLU* 1.3 58.5 + - - +
61V SER 3.2 0.2 - - - -
62V SER 3.2 2.9 + - - -
63V THR 3.1 11.4 + - - -
64V GLY* 2.9 25.6 + - - +
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Residues in contact with GLU 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O LYS* 3.5 20.6 + - - -
204O GLU* 5.0 0.3 - - - +
334O LYS* 3.0 28.3 + - - -
1476O CAP 3.4 10.4 + - - -
20V TYR* 2.7 29.4 + - + +
56V ALA 2.9 18.8 + - - +
59V ALA* 1.3 75.7 - - - +
61V SER* 1.3 56.1 + - - +
62V SER 3.4 0.7 - - - -
64V GLY 3.5 16.9 - - - +
65V THR* 3.2 11.3 + - - -
66V TRP 3.4 0.3 + - - -
119V SER 4.8 0.9 - - - +
123V ASN* 4.6 10.8 + - + +
124V VAL* 3.9 11.9 - - + +
127V PHE* 3.3 38.6 - - + -
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Residues in contact with SER 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O LYS* 4.8 0.7 - - - +
205O ASN* 4.6 4.0 - - - -
57V VAL* 2.7 21.8 + - - -
58V ALA 3.3 3.5 + - - -
59V ALA 3.2 0.2 - - - -
60V GLU* 1.3 76.3 - - - +
62V SER* 1.3 56.8 + - - +
103V TYR* 2.6 43.5 + - - -
107V LEU* 5.1 0.5 - - - +
119V SER* 3.1 43.6 - - - +
120V ILE* 4.2 5.2 - - - -
124V VAL* 4.0 9.4 - - - -
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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