Contacts of the strand formed by residues 36 - 46 (chain C) in PDB entry 3N6J
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 TYR 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ALA* 5.1 10.1 - - + -
21C GLY 3.3 15.7 - - - +
22C HIS* 3.9 27.1 - + - -
23C ASP* 5.0 0.7 - - - -
34C SER* 3.0 26.2 + - - +
35C PRO* 1.3 93.8 - - + +
37C PHE* 1.3 62.4 + - - +
38C THR* 4.3 6.6 + - + +
164C PRO* 3.2 42.6 + - + +
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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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20C ALA* 3.3 5.6 - - - +
21C GLY* 3.1 38.3 + - - -
22C HIS 3.4 27.4 - - - -
23C ASP* 4.3 8.0 - - + +
35C PRO 4.3 0.4 - - - -
36C TYR* 1.3 75.9 - - - +
38C THR* 1.3 61.8 + - - +
39C ARG* 3.7 21.1 - - + -
343C ASN* 3.6 38.1 - - + +
344C HIS* 4.1 2.7 - - - -
345C PHE* 3.4 41.3 - + - -
373C GLN* 3.5 30.7 - - + -
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Residues in contact with THR 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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19C VAL 3.4 7.6 - - - -
20C ALA* 4.4 8.5 - - + +
36C TYR* 4.9 7.0 - - + +
37C PHE* 1.3 78.9 - - - +
39C ARG* 1.3 71.9 + - - +
57C PRO* 4.1 0.9 - - - +
58C GLY* 3.0 31.1 + - - -
59C GLY* 3.6 3.7 + - - -
343C ASN 5.3 0.2 - - - +
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Residues in contact with ARG 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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18C PRO* 3.4 2.6 - - - +
19C VAL* 2.8 42.1 + - + +
37C PHE* 3.7 18.6 - - + -
38C THR* 1.3 80.0 + - - +
40C ASN* 1.3 71.1 + - - +
55C GLU* 2.7 33.6 + - + +
56C ALA 3.2 9.2 + - - +
57C PRO* 3.4 39.2 - - - +
58C GLY* 3.3 7.5 - - - +
316C HIS* 3.3 16.0 + - - -
342C ASN* 4.0 16.6 - - - +
343C ASN 3.0 24.3 + - - -
344C HIS* 3.5 12.3 - - - +
345C PHE* 4.5 2.0 - - + -
348C SER* 2.8 28.9 + - - -
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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
----------------------------------------------------------
16C VAL* 5.5 0.9 - - + -
17C ILE 3.7 2.6 - - - +
18C PRO* 3.3 23.0 - - - +
39C ARG* 1.3 79.9 - - - +
41C ILE* 1.3 64.4 + - - +
42C VAL* 4.0 2.1 + - - +
54C GLY 3.9 0.2 - - - +
55C GLU* 3.4 3.5 - - - -
56C ALA* 2.6 44.8 + - + +
57C PRO 3.3 18.3 + - - +
58C GLY* 3.8 3.4 - - - -
59C GLY 3.6 9.8 + - - +
62C ILE* 3.6 6.1 - - - +
63C GLU* 3.2 38.1 - - - +
66C LEU* 4.1 15.3 - - + -
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Residues in contact with ILE 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* 3.4 8.0 - - - +
17C ILE* 2.7 39.5 + - + +
19C VAL* 3.6 33.0 - - + -
40C ASN* 1.3 78.4 - - - +
42C VAL* 1.3 69.2 + - - +
43C ILE* 3.6 30.2 + - + +
53C VAL* 4.9 2.0 - - + -
54C GLY 3.5 5.6 - - - +
55C GLU* 3.9 18.6 - - + -
347C ILE* 3.8 21.3 - - + -
379C LEU* 3.5 26.7 - - + -
403C LEU* 5.4 0.4 - - + -
408C VAL* 4.9 9.0 - - + -
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Residues in contact with VAL 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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14C MSE 3.8 25.1 - - + -
15C LYS 3.9 3.1 - - - +
16C VAL* 5.5 0.2 - - + -
40C ASN 4.7 0.4 - - - +
41C ILE* 1.3 77.2 - - - +
43C ILE* 1.3 61.8 + - - +
44C LEU* 3.8 20.0 - - + -
52C GLY 3.9 0.3 - - - +
53C VAL* 3.1 10.9 - - - +
54C GLY 2.9 30.5 + - - +
66C LEU* 3.6 24.9 - - + -
116C ALA* 3.6 37.5 - - + +
117C LEU* 4.2 12.8 - - + -
120C ALA* 4.4 1.6 - - + -
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Residues in contact with ILE 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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13C ASP* 3.8 1.0 - - - +
14C MSE 3.5 1.2 - - - -
15C LYS* 3.0 59.7 + - + +
17C ILE* 3.7 34.5 - - + -
41C ILE* 3.6 24.7 - - + +
42C VAL* 1.3 77.0 - - - +
44C LEU* 1.3 69.0 + - - +
45C THR* 5.3 2.9 + - - +
51C THR* 3.8 26.0 - - + -
52C GLY 4.2 1.1 - - - -
53C VAL* 4.6 2.0 - - + -
403C LEU* 3.9 19.1 - - + -
405C MSE 4.7 8.5 - - - -
408C VAL* 4.7 7.2 - - + -
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Residues in contact with LEU 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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11C ILE* 4.8 8.1 - - + -
13C ASP 3.3 4.3 - - - +
14C MSE 3.6 33.4 - - + -
42C VAL* 3.8 11.0 - - + -
43C ILE* 1.3 85.9 - - - +
45C THR* 1.3 67.3 + - - +
50C HIS 3.7 0.2 - - - +
51C THR* 3.4 27.7 - - - +
52C GLY 3.3 8.9 + - - +
73C VAL* 4.7 9.0 - - + -
117C LEU* 4.1 12.8 - - + -
120C ALA* 3.6 28.3 - - + -
121C LEU* 4.0 16.2 - - + +
124C LEU* 3.6 25.9 - - + +
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Residues in contact with THR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.3 8.5 - - - +
12C THR* 2.7 34.0 + - - +
13C ASP* 3.1 33.9 + - - +
15C LYS* 5.4 2.6 - - - -
43C ILE* 5.3 3.8 - - - +
44C LEU* 1.3 78.3 + - - +
46C ASP* 1.3 66.9 + - - +
49C GLY* 4.7 8.5 - - - -
50C HIS 3.6 14.4 - - - +
51C THR* 5.1 4.7 - - - +
124C LEU* 5.1 2.2 - - - -
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Residues in contact with ASP 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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9C PRO* 3.2 23.2 - - + +
10C VAL 3.1 18.2 - - - +
11C ILE* 4.5 1.8 - - - -
12C THR* 3.7 9.0 + - - -
45C THR* 1.3 80.5 - - - +
47C ASN* 1.3 55.1 + - - +
48C SER* 2.7 34.7 + - - -
49C GLY 3.3 8.3 + - - -
50C HIS* 3.1 37.4 + - - +
78C ILE* 4.8 7.8 - - + +
124C LEU* 4.4 11.7 - - + +
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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