Contacts of the strand formed by residues 39 - 48 (chain C) in PDB entry 4M75
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 ILE 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B PHE* 4.0 1.3 - - - -
8C LEU* 5.4 0.2 - - + -
18C ILE* 3.6 17.3 - - + -
30C LEU* 3.2 30.7 - - + -
32C ALA 3.5 3.6 - - - +
33C PHE* 4.1 13.0 - - + -
37C SER* 3.0 20.6 - - - +
38C ASN* 1.3 76.3 - - - +
40C VAL* 1.3 71.9 + - - +
41C LEU* 4.0 11.4 - - + -
67C PHE* 3.4 1.9 - - - -
68C ILE* 2.5 52.0 + - + +
73C VAL* 4.6 4.5 - - + -
76C ILE* 3.2 36.1 - - + -
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Residues in contact with VAL 40 (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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3B PHE* 3.2 33.0 - - + -
6B PHE* 4.8 12.8 - - + -
72B LEU* 5.3 1.3 - - + -
82B LEU* 4.0 22.0 - - + -
31C GLN* 2.9 25.7 + - + -
32C ALA* 3.1 22.5 + - + +
39C ILE* 1.3 79.1 - - - +
41C LEU* 1.3 71.9 + - - +
65C MSE 4.1 25.6 - - + -
66C VAL 3.4 11.2 - - - +
67C PHE* 4.5 5.6 - - + +
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Residues in contact with LEU 41 (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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16C VAL* 4.0 11.0 - - + -
18C ILE* 4.6 7.4 - - + -
26C LEU* 3.6 33.7 - - + -
27C VAL 4.3 0.9 - - - -
28C GLY* 3.8 20.4 - - - +
29C THR 3.1 18.6 - - - +
30C LEU* 3.9 8.1 - - - -
31C GLN* 4.4 0.2 - - - -
39C ILE* 4.0 12.3 - - + -
40C VAL* 1.3 82.6 - - - +
42C SER* 1.3 60.8 + - - +
43C ASP 3.8 0.3 + - - -
44C ALA* 3.8 21.5 - - + +
64C GLU 3.8 0.3 - - - +
65C MSE 3.3 6.6 - - - -
66C VAL* 3.1 33.8 + - + -
68C ILE* 3.8 17.3 - - + -
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Residues in contact with SER 42 (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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74B LYS* 5.7 0.4 - - - -
79B THR* 4.5 4.2 - - - +
29C THR* 3.0 27.9 + - - +
31C GLN* 2.4 37.7 + - - +
41C LEU* 1.3 68.9 - - - +
43C ASP* 1.3 82.2 + - - +
65C MSE 2.4 31.8 - - - +
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Residues in contact with ASP 43 (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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15C ARG* 2.1 43.7 + - - +
28C GLY* 3.3 0.9 - - - -
29C THR* 4.3 3.8 + - - +
42C SER* 1.3 83.9 + - - +
44C ALA* 1.3 55.7 + - - +
63C SER 4.3 0.7 - - - -
64C GLU* 2.5 26.0 + - - +
65C MSE 5.3 0.3 - - - +
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Residues in contact with ALA 44 (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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15C ARG* 4.3 0.2 - - - +
26C LEU* 4.5 7.6 - - + -
27C VAL 2.8 15.7 - - - +
28C GLY* 3.6 8.5 - - - -
41C LEU* 3.8 28.7 - - + +
43C ASP* 1.3 77.1 - - - +
45C VAL* 1.3 60.0 - - - +
62C ARG* 3.2 21.1 - - - +
63C SER 3.3 20.2 + - - +
66C VAL* 4.7 5.4 - - + -
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Residues in contact with VAL 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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15C ARG* 4.5 9.9 - - - +
26C LEU* 3.5 1.1 - - - -
27C VAL* 2.5 63.2 + - + +
44C ALA* 1.3 76.1 - - - +
46C GLU* 1.3 60.5 + - - +
47C THR* 5.5 0.4 - - - +
60C GLU* 3.2 42.2 - - + +
61C ARG 3.8 7.9 - - - +
62C ARG* 4.0 13.2 - - + -
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Residues in contact with GLU 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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69B TYR* 3.6 22.5 + - - -
71B TYR* 4.2 13.2 + - - -
24C ARG* 4.0 4.3 + - + +
25C THR 3.3 10.8 - - - +
26C LEU* 3.6 19.2 - - + +
45C VAL* 1.3 75.3 - - - +
47C THR* 1.3 64.7 + - - +
48C ILE* 4.0 3.4 - - + +
60C GLU* 2.8 31.1 - - - +
61C ARG* 2.8 77.2 + - + +
62C ARG* 5.7 0.5 - - - -
66C VAL* 6.0 0.5 - - - +
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Residues in contact with THR 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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24C ARG* 3.8 2.3 - - - -
25C THR* 2.5 43.0 + - - +
45C VAL* 5.5 0.5 - - - +
46C GLU* 1.3 78.1 + - - +
48C ILE* 1.3 59.8 + - - +
49C TYR* 3.1 36.5 + - + +
58C GLU* 4.1 19.3 - - + +
59C SER 3.3 9.6 - - - +
60C GLU* 4.1 13.3 + - - +
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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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22C GLY 5.0 0.9 - - - +
23C ALA* 3.8 9.9 - - + +
24C ARG* 3.7 33.0 - - + +
46C GLU* 4.4 4.3 - - - +
47C THR* 1.3 73.4 - - - +
49C TYR* 1.3 73.5 + - - +
50C GLN* 5.2 9.2 - - + +
58C GLU* 3.7 0.2 - - - -
59C SER* 3.0 52.4 + - - +
60C GLU 4.7 0.2 - - - +
61C ARG* 3.4 50.0 - - + +
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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