Contacts of the strand formed by residues 72 - 85 (chain C) in PDB entry 5JTM
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 THR 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C PRO* 5.9 7.3 - - + +
27C ASN* 3.9 22.3 - - - +
31C VAL* 4.2 0.7 - - - +
65C THR* 4.9 5.8 - - + -
66C ALA 3.7 12.1 - - - +
67C SER* 4.1 12.4 + - - +
70C GLU 3.3 7.8 + - - -
71C GLU* 1.3 84.8 + - - +
73C ALA* 1.3 64.7 - - - +
74C PHE* 3.8 19.5 - - - +
75C LEU* 4.8 3.4 - - + +
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Residues in contact with ALA 73 (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 ALA* 3.9 8.8 - - - +
26C PRO* 6.4 0.2 - - - -
27C ASN* 5.5 1.0 - - - +
31C VAL* 3.7 15.9 - - + +
36C TRP* 3.8 28.5 - - + -
66C ALA* 2.8 27.2 + - + +
68C LEU* 4.0 16.4 - - + -
71C GLU* 3.6 4.2 + - - +
72C THR* 1.3 75.1 - - - +
74C PHE* 1.3 61.6 + - + +
123C PHE* 3.2 21.2 - - + -
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Residues in contact with PHE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.7 24.9 - + + -
24C GLU 3.3 14.1 - - - +
25C ALA* 4.5 0.4 - - + +
26C PRO* 6.0 0.2 - - - -
36C TRP* 3.5 24.0 - + - -
64C VAL* 4.2 21.3 - - + -
65C THR* 3.8 1.9 - - - +
66C ALA* 3.0 39.9 + - + +
72C THR* 3.6 12.8 - - - +
73C ALA* 1.3 81.0 - - - +
75C LEU* 1.3 69.8 + - - +
76C CYS* 4.4 2.0 - - + -
118C VAL* 3.7 24.7 - - + -
123C PHE* 3.6 35.2 - + + -
126C LEU* 3.7 23.8 - - + -
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Residues in contact with LEU 75 (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 SER* 5.7 2.2 - - - +
23C PHE* 3.4 6.8 - - - -
24C GLU* 2.9 60.1 + - + +
63C THR* 4.0 19.7 - - + -
64C VAL 3.6 9.9 - - - +
65C THR* 3.3 33.4 - - + +
72C THR* 5.5 3.6 - - + -
74C PHE* 1.3 75.1 - - - +
76C CYS* 1.3 83.5 - - - +
77C GLU* 4.3 7.9 - - + +
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Residues in contact with CYS 76 (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 SER 3.3 17.9 - - - -
23C PHE* 3.8 11.0 - - + +
62C VAL 4.0 0.6 - - - +
63C THR* 3.3 4.7 - - - +
64C VAL* 2.8 38.7 + - + +
74C PHE* 4.5 5.2 - - + -
75C LEU* 1.3 79.3 - - - +
77C GLU* 1.3 59.7 + - - +
78C VAL* 4.4 3.4 - - - -
114C ILE* 3.6 49.1 - - + -
117C MET* 3.9 16.2 - - - -
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Residues in contact with GLU 77 (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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20C ASP* 3.7 10.8 - - - +
21C ILE* 3.4 2.9 - - - -
22C SER* 2.8 44.5 + - - -
61C ARG* 3.0 45.2 + - + -
62C VAL 3.5 3.8 - - - +
63C THR* 3.1 32.2 + - + +
75C LEU* 4.3 7.6 - - + +
76C CYS* 1.3 74.3 - - - +
78C VAL* 1.3 61.2 + - - +
79C GLN* 3.1 17.8 + - + -
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Residues in contact with VAL 78 (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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18C THR* 4.5 1.6 - - + -
20C ASP 3.4 11.2 - - - +
21C ILE* 4.3 10.3 - - + -
60C LEU 3.7 1.0 - - - +
62C VAL* 3.0 34.3 + - - +
76C CYS* 4.4 4.5 - - - -
77C GLU* 1.3 76.6 - - - +
79C GLN* 1.3 63.7 + - - +
80C GLN* 3.7 17.5 + - - +
110C ALA* 4.2 14.3 - - - +
113C CYS* 3.6 43.3 - - + +
114C ILE* 3.6 30.7 - - + +
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Residues in contact with GLN 79 (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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19C LYS* 3.2 28.0 + - + +
20C ASP* 2.9 50.2 + - + +
47C ALA* 5.3 5.4 - - - +
59C VAL* 4.0 17.8 - - + +
60C LEU 3.7 5.6 - - - -
61C ARG* 3.1 54.1 + - + +
77C GLU* 3.1 14.5 + - - +
78C VAL* 1.3 70.2 - - - +
80C GLN* 1.3 62.1 + - - +
81C GLY 3.4 0.7 + - - -
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Residues in contact with GLN 80 (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 ILE* 3.2 19.1 - - - +
17C TYR* 3.0 25.5 + - - +
18C THR* 3.3 28.3 - - - +
59C VAL* 3.4 3.2 - - - -
60C LEU* 3.1 33.1 + - + +
78C VAL* 3.7 3.8 + - + +
79C GLN* 1.3 68.9 - - - +
81C GLY* 1.3 57.8 + - - +
106C LEU* 3.5 42.6 - - + +
109C TYR* 3.4 22.8 + - + +
110C ALA* 3.7 26.7 - - + +
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Residues in contact with GLY 81 (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 ILE* 3.8 0.9 - - - -
17C TYR* 2.8 47.4 + - - +
19C LYS* 3.7 20.5 - - - +
57C GLU* 5.0 0.2 - - - -
58C VAL 3.6 4.3 - - - -
59C VAL* 4.1 8.1 - - - -
79C GLN 3.4 5.3 + - - -
80C GLN* 1.3 78.4 - - - +
82C GLY* 1.3 57.5 + - - -
106C LEU* 4.0 3.5 - - - +
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Residues in contact with GLY 82 (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 3.5 8.7 - - - -
16C ILE* 4.3 1.1 - - - -
17C TYR* 4.6 0.2 - - - -
57C GLU* 4.6 2.6 - - - +
58C VAL 2.9 35.7 + - - +
81C GLY* 1.3 74.8 - - - -
83C ILE* 1.3 65.5 + - - -
84C PHE* 3.2 16.1 - - - -
106C LEU* 3.7 17.2 - - - +
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Residues in contact with ILE 83 (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 ILE* 3.9 0.5 - - - +
14C GLN* 3.0 42.4 + - + -
15C ARG* 2.9 22.9 + - + +
17C TYR* 3.4 32.1 - - + +
51C LEU* 3.6 36.1 - - + -
55C VAL* 3.7 20.0 - - + -
56C TYR 3.9 5.4 - - - +
57C GLU* 3.7 17.3 - - + -
82C GLY* 1.3 71.2 - - - -
84C PHE* 1.3 66.9 + - - +
29D PRO* 3.7 8.1 - - + -
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Residues in contact with PHE 84 (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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11C PHE* 3.5 32.5 - + + -
12C GLN 3.8 3.8 - - - -
13C ILE* 3.6 30.5 - - + -
14C GLN* 4.2 4.6 - - - +
16C ILE* 4.6 0.7 - - + -
55C VAL* 3.9 2.6 - - - +
56C TYR 3.1 27.8 + - - +
58C VAL* 3.7 26.2 - - + -
82C GLY* 3.2 27.4 - - - -
83C ILE* 1.3 77.2 - - - +
85C SER* 1.3 60.5 + - - +
86C ILE* 3.3 20.2 - - + +
102C CYS* 3.4 32.3 - - + -
105C ILE* 4.0 12.3 - - + -
106C LEU* 3.6 24.0 - - + -
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Residues in contact with SER 85 (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 MET* 3.6 1.7 - - - +
10C THR* 3.1 20.9 - - - +
11C PHE* 3.2 20.0 - - - -
12C GLN* 3.0 25.1 + - - +
14C GLN* 2.8 34.1 + - - -
54C ASP* 3.4 9.2 - - - -
55C VAL* 5.0 4.0 - - - +
84C PHE* 1.3 71.0 - - - +
86C ILE* 1.3 60.0 + - - +
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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