Contacts of the strand formed by residues 34 - 46 (chain A) in PDB entry 1JB3
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 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.3 7.7 - - - +
29A ASP* 2.5 61.9 + - + +
32A HIS* 4.2 12.3 - - + -
33A HIS* 1.3 77.4 - - - +
35A TYR* 1.3 61.7 + - - +
67A GLY* 2.8 31.7 + - - -
68A PHE 2.5 22.2 + - - -
70A ASP* 4.6 4.9 - - - -
99A HIS* 4.4 8.7 - - + -
104A MET* 5.5 1.8 - - + -
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 4.1 15.9 - - + -
26A MET 4.7 2.5 - - - +
27A ASN 3.5 12.8 - - - +
28A VAL* 4.1 15.7 - - + -
29A ASP* 4.5 0.7 - - - +
34A THR* 1.3 83.5 + - - +
36A SER* 1.3 67.2 + - - +
37A CYS* 3.7 24.5 - - - -
67A GLY 3.4 4.5 + - - -
68A PHE* 2.9 61.4 + + + +
69A GLY* 3.9 4.0 - - - -
77A GLN* 2.6 35.6 + - - -
78A VAL* 3.2 27.9 + - + -
99A HIS* 6.1 0.2 - - - -
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 2.6 42.0 + - - +
27A ASN 3.1 10.7 + - - -
35A TYR* 1.3 75.2 - - - +
37A CYS* 1.3 62.8 + - - +
64A VAL* 3.9 9.9 - - - -
65A ILE 3.1 11.0 - - - -
66A GLY* 3.4 5.9 - - - -
99A HIS* 4.2 7.8 + - - -
102A GLU* 3.1 33.6 + - - -
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Residues in contact with CYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.0 12.3 - - + -
24A GLU 3.2 9.4 - - - +
25A ILE* 3.9 16.4 - - - -
26A MET* 3.2 6.3 - - - -
35A TYR* 3.7 17.0 - - - -
36A SER* 1.3 82.2 - - - +
38A LYS* 1.3 63.0 + - - +
39A VAL* 3.7 4.5 + - + +
64A VAL* 3.3 2.3 - - - -
65A ILE* 2.9 31.8 + - - -
68A PHE* 3.8 14.8 - - + -
78A VAL* 3.5 28.3 - - - -
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.7 3.5 - - - +
23A GLU* 2.8 59.7 + - - +
24A GLU* 2.8 47.7 + - - +
26A MET* 3.5 21.5 - - + +
37A CYS* 1.3 71.1 - - - +
39A VAL* 1.3 60.5 + - - +
58A ASP* 4.0 20.2 - - + +
62A LYS* 4.1 17.7 - - + +
63A VAL 3.5 9.6 - - - +
64A VAL* 4.4 5.6 - - + +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.6 8.7 - - + -
20A GLY* 3.8 13.9 - - - -
21A THR 3.5 21.3 - - - +
22A VAL* 4.3 11.7 - - + -
37A CYS* 4.1 12.3 - - + +
38A LYS* 1.3 79.5 - - - +
40A ARG* 1.3 65.1 + - - +
41A VAL 3.5 2.5 + - - +
62A LYS* 3.2 6.6 - - - -
63A VAL* 2.7 45.9 + - + +
65A ILE* 4.0 19.1 - - + -
68A PHE* 5.0 0.2 - - + -
86A PHE* 4.0 24.5 - - + -
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLY* 2.9 3.6 - - - -
21A THR* 2.8 64.9 + - - +
23A GLU* 2.7 56.4 + - - +
39A VAL* 1.3 70.3 - - - +
41A VAL* 1.3 66.2 + - - +
42A TRP* 3.6 0.5 + - - +
61A ASN* 3.5 23.6 - - - +
62A LYS* 3.5 18.8 - - - +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.1 17.0 - - + -
19A THR 3.4 11.7 - - - +
20A GLY* 4.1 0.7 - - - -
39A VAL 4.3 0.4 - - - +
40A ARG* 1.3 75.9 - - - +
42A TRP* 1.3 73.4 + - - +
43A ARG 4.0 5.6 - - - +
44A TYR* 3.7 39.5 - - + +
61A ASN* 2.7 43.8 + - + +
63A VAL* 3.8 35.9 - - + -
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Residues in contact with TRP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 2.8 41.6 + - + +
20A GLY* 4.7 3.4 - - - -
21A THR* 6.1 3.4 - - + -
40A ARG 3.6 1.8 + - - +
41A VAL* 1.3 78.3 - - - +
43A ARG* 1.3 96.1 + - + +
44A TYR* 5.4 1.6 - - - -
45A LEU* 6.3 0.7 - - + -
112A ILE* 6.1 3.8 - - + -
117A LEU* 5.0 20.4 - - + -
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.7 0.3 - - - -
19A THR* 2.8 33.2 + - + +
41A VAL* 4.1 2.2 - - - -
42A TRP* 1.3 134.1 - - + +
44A TYR* 1.3 82.2 + - - +
45A LEU* 3.9 11.8 + - + +
121A GLU* 5.1 5.0 + - - -
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Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.9 0.4 - - + -
17A VAL 3.8 5.6 - - - +
18A LEU* 4.0 25.8 - - + +
41A VAL* 3.7 25.9 - - + +
42A TRP 5.4 1.6 - - - -
43A ARG* 1.3 90.8 + - - +
45A LEU* 1.3 62.9 + - - +
46A LYS 4.4 5.2 - - - +
48A LYS* 3.7 59.0 - - + +
51A VAL* 3.7 41.9 - - + +
57A LEU* 3.8 23.0 - - + +
61A ASN* 5.4 1.4 - - + -
63A VAL* 4.3 0.4 - - + +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 2.8 20.5 + - + +
18A LEU* 4.9 2.7 - - - -
19A THR* 5.1 2.9 - - + +
42A TRP* 6.3 0.7 - - + -
43A ARG* 4.5 18.4 - - + +
44A TYR* 1.3 80.0 - - - +
46A LYS* 1.3 62.8 + - + +
85A ILE* 4.2 17.5 - - + -
117A LEU* 4.0 32.3 - - + +
120A VAL* 3.7 32.1 - - + -
121A GLU* 3.8 31.6 - - + +
124A VAL* 3.6 16.8 - - + +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 2.7 49.6 + - - +
12A GLU 4.4 4.6 + - - -
14A ALA 2.8 21.1 + - - +
15A ASN* 3.7 17.3 + - - +
16A VAL* 3.3 4.5 - - - +
17A VAL* 2.8 46.7 + - + +
44A TYR* 3.4 2.6 - - - +
45A LEU* 1.3 83.7 + - - +
47A GLY* 1.3 69.3 + - - +
48A LYS 3.4 3.0 + - - -
124A VAL* 3.8 19.7 - - + -
127A HIS* 4.3 12.2 + - - -
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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