Contacts of the helix formed by residues 44 - 64 (chain C) in PDB entry 4UU9
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 GLY 44 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.5 21.7 + - - -
41C ILE* 4.6 3.8 + - - +
42C SER 3.4 4.2 - - - -
43C LEU* 1.3 77.7 - - - +
45C PRO* 1.3 76.3 - - - +
46C ARG 3.2 2.7 - - - -
47C CYS* 3.1 4.9 + - - +
48C ILE* 3.0 28.9 + - - +
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Residues in contact with PRO 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.5 32.3 - - + +
44C GLY* 1.3 82.2 - - - +
46C ARG* 1.3 59.5 + - + +
48C ILE* 3.7 12.3 - - + +
49C LYS* 2.9 31.8 + - - +
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASP* 2.9 41.2 + - - -
97A ASP* 5.7 0.2 - - - +
100A TYR* 2.9 91.0 + - + +
13C TYR* 4.7 1.9 - - - -
14C LYS* 5.7 0.2 - - - +
15C HIS* 3.7 9.3 - - - +
18C VAL* 3.5 17.5 - - + +
44C GLY 3.2 1.0 - - - -
45C PRO* 1.3 80.1 - - + +
47C CYS* 1.3 61.5 + - - +
49C LYS* 3.7 7.8 - - - +
50C ALA* 3.3 16.1 + - - +
1065C SO4 2.9 47.5 + - - +
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Residues in contact with CYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 4.0 5.2 - - + -
51B VAL* 3.9 7.0 - - - -
17C VAL* 5.4 0.7 - - + -
18C VAL* 4.4 5.8 - - + +
21C CYS* 2.0 52.6 - - - +
41C ILE* 3.7 24.7 - - + -
43C LEU* 3.8 22.7 - - + +
44C GLY 3.1 9.0 + - - +
46C ARG* 1.3 78.2 - - - +
48C ILE* 1.3 59.6 + - - +
50C ALA 3.3 1.0 + - - -
51C PHE* 2.8 31.7 + - - +
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ALA* 4.3 17.9 - - + +
41C ILE* 3.7 36.8 - - + +
44C GLY* 3.0 26.6 + - - +
45C PRO* 3.7 11.4 - - + +
47C CYS* 1.3 74.6 - - - +
49C LYS* 1.3 57.1 - - - +
51C PHE* 3.8 5.1 - - - +
52C THR* 2.7 46.1 + - - +
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TYR* 3.6 27.5 + - + +
45C PRO 2.9 17.7 + - - +
46C ARG* 3.7 8.7 - - - +
47C CYS 3.2 0.2 - - - -
48C ILE* 1.3 78.4 - - - +
50C ALA* 1.3 61.6 + - - +
52C THR* 3.8 3.6 - - - -
53C GLU* 3.1 28.0 + - - +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TYR* 3.7 27.1 - - + -
18C VAL* 3.5 44.2 - - + +
22C CYS* 4.0 5.6 - - + +
46C ARG 3.3 3.6 + - - +
47C CYS 3.3 3.4 + - - +
49C LYS* 1.3 76.7 - - - +
51C PHE* 1.3 66.9 + - - +
53C GLU* 3.5 0.7 + - - +
54C CYS* 3.1 30.1 + - - +
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Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.5 25.1 - - + -
52B ASN* 3.8 7.6 - - - -
21C CYS* 3.4 30.0 + - + +
22C CYS* 4.3 0.2 - - - +
25C GLY* 3.4 21.0 - - - -
34C CYS 4.2 5.6 - - - -
37C ARG* 3.6 47.3 - - + -
38C ALA* 4.0 13.9 - - + -
41C ILE* 3.3 29.4 - - + -
47C CYS 2.8 21.4 + - - +
48C ILE 3.8 1.8 - - - +
50C ALA* 1.3 74.0 - - - +
52C THR* 1.3 62.2 + - - +
55C CYS* 2.8 40.4 + - + +
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Residues in contact with THR 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C CYS* 5.4 7.0 - - + -
38C ALA* 3.9 20.5 - - + +
48C ILE* 2.7 27.1 + - - +
49C LYS* 3.8 4.3 - - - -
51C PHE* 1.3 78.0 - - - +
53C GLU* 1.3 66.9 + - - +
55C CYS* 3.3 3.4 + - - +
56C VAL* 2.9 43.2 + - + +
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 3.7 18.6 - - + +
12C LYS* 2.6 31.6 + - - -
13C TYR* 2.5 34.4 + - - +
49C LYS* 3.1 20.5 + - + +
50C ALA 4.0 3.1 - - - +
52C THR* 1.3 76.0 - - - +
54C CYS* 1.3 64.3 + - - +
56C VAL* 4.0 3.7 - - - +
57C VAL* 3.1 38.7 + - + +
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Residues in contact with CYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.8 13.3 - - + +
9C ILE* 3.3 29.4 - - - -
22C CYS* 2.0 64.8 - - - +
26C ALA* 3.9 3.7 - - - +
50C ALA 3.1 13.2 + - - +
51C PHE 4.1 0.4 - - - +
53C GLU* 1.3 75.2 - - - +
55C CYS* 1.3 65.7 + - - +
57C VAL* 4.6 1.6 - - - -
58C ALA* 3.0 27.0 + - - +
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Residues in contact with CYS 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLY* 3.3 26.6 - - - +
26C ALA* 4.5 0.2 - - - +
33C THR 5.1 0.2 - - - -
34C CYS* 2.0 51.4 - - + -
37C ARG* 3.7 18.6 - - - -
51C PHE* 2.8 25.9 + - + +
52C THR 3.7 3.4 - - - +
54C CYS* 1.3 77.1 - - - +
56C VAL* 1.3 58.7 + - - +
58C ALA* 3.8 1.9 - - - +
59C SER* 2.9 31.3 + - - -
62C ARG* 5.2 0.3 + - - -
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C CYS* 4.1 17.0 - - + -
52C THR* 2.9 33.9 + - + +
53C GLU* 4.0 4.7 - - - +
55C CYS* 1.3 73.2 - - - +
57C VAL* 1.3 63.3 + - + +
59C SER* 3.3 4.4 + - - -
60C GLN* 2.9 53.4 + - + +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LYS* 4.2 20.9 - - + +
6C ILE* 4.3 5.8 - - + -
9C ILE* 3.6 29.8 - - + -
53C GLU* 3.1 25.7 + - + +
54C CYS 4.1 2.0 - - - +
56C VAL* 1.3 78.2 - - + +
58C ALA* 1.3 57.4 + - - +
60C GLN* 3.3 13.4 + - - +
61C LEU* 2.9 49.8 + - + +
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 4.0 19.0 - - + +
6C ILE* 4.2 1.3 - - + -
26C ALA* 3.7 21.5 - - + +
54C CYS 3.0 19.8 + - - +
55C CYS 3.8 2.5 - - - +
57C VAL* 1.3 77.1 - - - +
59C SER* 1.3 57.2 + - - +
61C LEU* 3.6 1.6 + - - +
62C ARG* 3.1 58.7 + - - +
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C CYS* 3.9 11.9 - - - -
55C CYS* 2.9 19.8 + - - -
56C VAL* 3.6 7.2 - - - -
57C VAL 3.2 0.2 - - - -
58C ALA* 1.3 75.2 - - - +
60C GLN* 1.3 65.9 + - - +
62C ARG* 3.4 11.4 + - - +
63C ALA* 3.0 24.9 + - - +
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Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C VAL* 2.9 41.5 + - + +
57C VAL* 3.3 15.9 + - - +
59C SER* 1.3 79.6 - - - +
61C LEU* 1.3 66.7 + - + +
63C ALA* 3.4 12.2 + - - +
64C ASN* 2.9 21.0 + - - +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C THR* 4.5 4.3 - - - +
2C LEU* 3.7 37.2 - - + +
5C LYS* 3.9 32.3 - - + +
57C VAL* 2.9 33.3 + - + +
58C ALA 3.9 3.8 - - - +
60C GLN* 1.3 82.8 - - + +
62C ARG* 1.3 58.8 + - + +
64C ASN* 3.0 33.0 + - - +
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C LEU* 3.6 34.0 - - + +
25C GLY 5.2 0.6 + - - -
26C ALA 2.9 30.1 + - - -
27C CYS 4.1 1.2 + - - -
28C VAL* 3.8 36.8 - - - +
55C CYS 5.2 0.2 + - - -
58C ALA* 3.1 36.2 + - - +
59C SER* 4.1 9.7 + - - +
60C GLN 3.4 0.2 - - - -
61C LEU* 1.3 73.8 - - - +
63C ALA* 1.3 65.8 + - - +
64C ASN 3.2 7.8 + - - -
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C SER 3.0 19.0 + - - +
60C GLN* 3.5 9.6 - - - +
61C LEU 3.3 0.2 - - - -
62C ARG* 1.3 75.6 - - - +
64C ASN* 1.3 61.5 + - - +
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Residues in contact with ASN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLN* 2.9 20.1 - - - +
61C LEU* 3.0 20.5 + - - +
62C ARG* 3.6 6.7 - - - -
63C ALA* 1.3 82.6 - - - +
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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