Contacts of the strand formed by residues 36 - 48 (chain C) in PDB entry 5J0Z
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 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C SER 4.2 1.9 + - - -
30C LEU* 3.4 6.9 - - - +
31C ASP* 2.9 34.3 + - - +
34C ALA* 3.3 23.8 - - + +
35C GLU* 1.3 82.6 - - - +
37C PHE* 1.3 71.0 + - - +
38C LYS* 6.1 0.7 - - - +
82C GLU* 3.5 24.7 - - - +
109C ARG* 3.4 27.2 + - - +
110C VAL 3.2 15.3 - - - +
111C LEU* 4.1 3.6 - - + +
112C SER 4.7 2.0 - - - +
114C LEU* 5.1 1.5 - - - +
126C LEU* 6.0 0.4 - - - +
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Residues in contact with PHE 37 (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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27C CYS* 5.0 6.3 - - + -
28C TYR 4.1 2.7 - - - +
29C SER 3.3 9.2 - - - -
30C LEU* 3.9 19.3 - - + -
36C THR* 1.3 82.2 - - - +
38C LYS* 1.3 71.1 + - - +
39C VAL* 4.0 22.7 - - + -
109C ARG* 4.6 1.1 - - - -
110C VAL* 2.9 64.2 + - + +
112C SER* 4.4 7.0 - - - -
126C LEU* 3.7 50.9 - - + -
127C HIS 4.7 0.4 - - - -
128C ILE* 4.1 14.1 - - + -
157C LEU* 5.2 3.1 - - + -
188C LEU* 4.4 12.6 - - + -
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Residues in contact with LYS 38 (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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27C CYS* 3.5 2.9 - - - -
28C TYR* 2.8 74.7 + - + +
29C SER* 3.8 12.5 + - - +
36C THR* 6.1 0.2 - - - -
37C PHE* 1.3 78.1 - - - +
39C VAL* 1.3 60.2 + - - +
83C ASN* 5.1 3.2 + - - -
108C ALA 3.5 6.5 - - - +
109C ARG* 3.7 44.8 - - + +
401C SO4 3.7 34.7 + - - +
82D GLU* 4.9 1.6 - - - +
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Residues in contact with VAL 39 (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 LEU* 3.4 33.4 - - + -
26C GLU 3.4 10.8 - - - +
27C CYS* 4.8 4.0 - - - -
28C TYR* 4.3 4.3 + - - -
37C PHE* 4.0 15.2 + - + -
38C LYS* 1.3 75.0 - - - +
40C ASN* 1.3 64.1 + - - +
41C ALA* 4.4 4.3 - - + -
106C PHE* 3.9 25.4 - - + -
107C SER* 3.2 5.7 - - - -
108C ALA 3.0 39.2 + - - +
110C VAL* 4.0 15.9 - - + -
128C ILE* 4.3 9.9 - - + -
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Residues in contact with ASN 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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25C ILE* 2.8 31.0 + - - +
26C GLU* 2.8 35.3 + - + +
28C TYR* 4.2 5.8 - - + -
39C VAL* 1.3 74.9 - - - +
41C ALA* 1.3 56.8 + - - +
105C ARG* 3.1 39.3 + - - +
106C PHE 3.3 12.8 - - - +
107C SER* 3.9 14.1 - - - -
81D VAL* 3.0 26.5 + - - +
82D GLU 4.2 5.1 + - - -
84D ALA* 5.6 4.6 - - - +
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Residues in contact with ALA 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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22C ILE* 3.9 10.1 - - + -
23C TYR 3.3 16.6 - - - +
24C LEU* 3.7 15.9 - - + -
25C ILE* 3.8 9.4 - - - -
39C VAL* 4.4 1.1 - - + -
40C ASN* 1.3 76.5 + - - +
42C PHE* 1.3 57.8 + - - +
105C ARG* 3.5 1.3 - - - -
106C PHE* 2.8 62.7 + - + +
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Residues in contact with PHE 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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21C GLY 3.5 0.5 - - - +
22C ILE* 3.2 8.8 - - - +
23C TYR* 2.9 53.9 + + + +
25C ILE* 3.6 10.9 - - + +
41C ALA* 1.3 71.8 - - - +
43C LEU* 1.3 58.5 + - - +
44C SER 4.0 0.2 - - - -
90C VAL* 4.5 2.0 - - + -
103C LEU* 3.9 33.0 - - + -
104C GLU 3.3 8.1 - - - +
105C ARG* 3.6 31.0 - - + -
106C PHE* 4.1 1.6 - - - -
77D ARG* 3.7 20.2 - - - -
133D ARG* 4.5 7.0 - - - -
176D LEU* 3.6 29.4 - - + -
177D GLU* 4.5 11.0 - - - +
181D GLU* 3.6 23.8 - - - -
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Residues in contact with LEU 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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21C GLY 3.5 8.5 - - - +
22C ILE* 4.0 9.2 - - + -
41C ALA 3.7 2.0 + - - -
42C PHE* 1.3 73.2 - - - +
44C SER* 1.3 64.6 + - - +
45C LEU* 4.2 23.7 + - + -
76C ILE* 4.1 17.0 - - + -
78C PHE* 4.7 4.7 - - + -
85C ARG* 4.1 16.6 - - - +
102C TYR* 4.3 1.4 - - - +
103C LEU* 3.6 2.1 - - - +
104C GLU* 2.8 65.0 + - + +
106C PHE* 3.9 11.8 - - + -
130C LEU* 4.0 30.1 - - + -
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Residues in contact with SER 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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19C ASN 3.3 1.5 - - - +
20C THR* 3.2 5.5 - - - -
21C GLY* 2.8 47.3 + - - -
43C LEU* 1.3 74.2 - - - +
45C LEU* 1.3 63.4 + - - +
102C TYR 3.4 6.7 - - - -
103C LEU* 3.5 18.8 - - - -
148C LYS* 3.2 34.7 + - - +
177D GLU* 3.9 6.7 - - - -
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Residues in contact with LEU 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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18C VAL* 4.5 4.7 - - + -
19C ASN 3.4 3.6 - - - -
20C THR* 3.8 26.7 - - + -
43C LEU* 4.3 15.5 - - + -
44C SER* 1.3 77.2 - - - +
46C SER* 1.3 63.0 + - - +
47C TRP* 4.0 9.2 - - + -
73C ILE* 5.1 2.5 - - + -
74C PRO* 4.9 9.6 - - + +
76C ILE* 3.4 45.8 - - + -
85C ARG* 5.6 1.6 - - - +
101C GLN* 3.7 3.3 + - - -
102C TYR* 2.8 70.9 + - + +
148C LYS* 5.1 1.1 - - - -
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Residues in contact with SER 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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17C THR 4.2 1.2 - - - +
18C VAL* 3.7 1.5 - - - +
19C ASN* 2.7 52.7 + - - +
45C LEU* 1.3 78.9 - - - +
47C TRP* 1.3 62.2 + - - +
99C THR* 4.4 9.2 - - - +
100C VAL 3.0 17.6 + - - -
101C GLN* 3.0 21.9 + - - +
145C ASP* 5.0 5.1 + - - -
148C LYS* 5.2 1.8 - - - -
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Residues in contact with TRP 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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8C PRO* 4.6 0.4 - - + -
16C LEU* 4.1 10.3 - - + -
17C THR 4.0 16.6 - - - +
18C VAL* 4.3 9.0 - - + -
45C LEU* 4.0 7.9 - - + -
46C SER* 1.3 82.5 - - - +
48C LYS* 1.3 61.5 + - - +
49C ASP* 4.0 16.2 - - + +
71C ILE* 3.7 6.3 - - + -
72C TRP* 3.2 49.6 + + - -
73C ILE* 3.8 15.0 - - + -
74C PRO* 3.6 32.3 - - + -
99C THR* 3.3 6.6 - - - +
100C VAL* 2.6 72.4 + - + +
102C TYR* 3.6 27.4 - + + -
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Residues in contact with LYS 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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8C PRO* 3.7 17.0 - - - +
14C GLU* 5.9 0.9 - - - -
16C LEU* 4.1 15.4 - - + +
17C THR 4.7 0.4 + - - -
47C TRP* 1.3 75.0 - - - +
49C ASP* 1.3 61.6 + - - +
50C ARG* 3.5 46.6 + - + +
97C ASP* 4.5 13.5 - - - +
98C GLY 3.6 4.9 - - - +
99C THR* 4.1 20.4 - - + +
138C ARG* 5.0 1.4 + - - -
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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