Contacts of the helix formed by residues 36 - 47 (chain A) in PDB entry 1UVG
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ASP* 4.8 14.2 + - - +
19A PRO* 4.7 10.1 - - + -
21A ASP 4.3 2.0 - - - +
23A LYS* 3.0 35.4 - - + +
25A VAL* 3.6 26.9 - - + -
35A ASN* 1.3 91.4 - - - +
37A CYS* 1.3 64.4 + - - +
38A MET 3.0 1.3 - - - -
39A LEU* 2.8 28.1 + - - +
40A CYS 3.9 1.2 + - - -
52A ILE* 4.6 9.4 - - + +
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Residues in contact with CYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASP 5.7 2.9 - - - +
4A MET* 6.2 7.6 - - + -
16A TYR* 3.2 16.7 - - - -
17A LEU 2.7 18.2 - - - -
18A CYS* 2.0 50.8 - - + -
19A PRO* 3.4 13.7 - - + -
35A ASN* 2.4 16.6 + - - +
36A PRO* 1.3 74.9 - - - +
38A MET* 1.3 60.5 + - - +
39A LEU 2.9 1.3 + - - -
40A CYS* 3.2 16.1 + - - +
41A HIS 3.6 5.5 + - - -
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Residues in contact with MET 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A CYS* 4.3 11.0 - - + -
22A LEU* 5.7 0.7 - - - -
33A TYR* 4.2 10.3 - - + -
34A ASN* 4.4 14.4 - - + +
35A ASN* 2.8 46.8 + - + +
36A PRO 3.0 0.2 - - - -
37A CYS* 1.3 78.1 - - - +
39A LEU* 1.3 58.2 + - - +
41A HIS* 3.0 32.9 - - + +
42A GLU* 3.6 2.6 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASP* 5.8 0.7 - - - -
2A SER* 4.8 7.4 - - - +
25A VAL* 3.9 8.5 - - + -
26A CYS 4.1 2.9 - - - +
33A TYR* 2.9 50.0 - - + -
35A ASN 3.4 1.8 + - - -
36A PRO 2.8 17.6 + - - +
38A MET* 1.3 76.2 - - - +
40A CYS* 1.3 71.1 + - - +
41A HIS 2.9 1.6 - - - -
42A GLU* 2.7 18.0 + - - +
43A ASN* 2.7 12.3 + - - +
50A THR 3.1 26.9 - - - +
51A HIS* 3.5 25.1 - - - +
52A ILE* 3.6 23.1 - - + -
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Residues in contact with CYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASP 5.7 0.7 - - - +
4A MET* 6.0 1.3 - - + -
5A CYS* 2.0 50.7 - - - -
8A TYR* 4.5 2.0 - - - -
16A TYR* 2.7 30.5 - - + +
36A PRO 3.9 1.2 + - - -
37A CYS* 3.2 8.6 + - - +
39A LEU* 1.3 81.4 - - + +
41A HIS* 1.3 54.3 + - - +
43A ASN* 2.6 37.2 + - - +
44A LEU* 2.7 25.2 - - - +
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Residues in contact with HIS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 5.9 2.5 - - + -
15A GLY* 5.8 0.9 - - - -
16A TYR* 3.6 37.9 - + + +
18A CYS* 6.1 0.2 - - - -
37A CYS 3.6 3.7 + - - +
38A MET* 3.0 29.6 + - + +
39A LEU 2.8 1.0 + - - -
40A CYS* 1.3 79.5 - - - +
42A GLU* 1.3 62.8 + - - +
43A ASN 2.9 1.4 + - - -
44A LEU* 2.9 20.5 + - + +
45A ILE* 3.2 36.6 + - + +
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.9 2.0 - - - +
33A TYR* 2.9 52.1 - - + +
38A MET 3.6 1.9 + - - +
39A LEU 2.7 10.3 + - - +
41A HIS* 1.3 77.6 - - - +
43A ASN* 1.3 58.6 + - - +
44A LEU 3.4 0.2 - - - -
45A ILE* 4.0 11.8 - - - +
46A ARG* 2.5 74.6 + - - +
50A THR* 5.0 2.0 + - - +
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Residues in contact with ASN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 4.8 1.6 + - - -
5A CYS* 5.3 1.7 - - + -
39A LEU* 2.7 31.5 + - - +
40A CYS* 2.6 34.9 + - - +
42A GLU* 1.3 73.2 - - - +
44A LEU* 1.3 59.0 + - + -
47A GLN* 2.6 34.8 + - - +
48A THR 4.8 0.4 - - - +
49A ASN* 3.0 11.1 + - - +
50A THR* 2.3 57.1 + - - +
51A HIS* 4.8 0.2 + - - -
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 2.9 43.5 - - + +
10A VAL* 3.4 27.4 - - + -
16A TYR* 3.5 19.1 - - + -
40A CYS* 2.7 34.8 - - - +
41A HIS* 2.9 10.3 + - + +
43A ASN* 1.3 82.1 - - + +
45A ILE* 1.3 69.1 + - + +
47A GLN* 3.2 20.5 - - - +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A HIS* 3.2 41.7 + - + +
42A GLU* 4.2 17.0 - - - +
44A LEU* 1.3 87.9 - - + +
46A ARG* 1.3 66.9 + - + +
47A GLN* 3.9 4.2 - - - +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASP* 5.3 2.9 - - - -
31A GLN* 3.4 31.3 + - - +
42A GLU* 2.5 48.6 + - - +
45A ILE* 1.3 80.2 - - + +
47A GLN* 1.3 74.0 + - - +
48A THR* 3.2 30.7 + - + +
50A THR* 5.0 4.0 - - - -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASN 2.6 25.7 + - - +
44A LEU* 3.2 23.3 - - - +
45A ILE 3.9 5.2 - - - +
46A ARG* 1.3 76.9 - - - +
48A THR* 1.3 59.5 + - - +
49A ASN* 3.4 10.3 + - - +
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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