Contacts of the strand formed by residues 36 - 52 (chain A) in PDB entry 2BXJ
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 ARG 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU* 5.6 0.4 - - - -
34A GLY 4.0 0.6 + - - +
35A ALA* 1.3 73.6 - - - +
37A VAL* 1.3 67.2 + - - +
38A GLU* 3.4 11.8 + - + +
65A VAL* 3.4 3.7 - - - -
66A GLU* 2.9 45.6 + - + +
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Residues in contact with VAL 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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27A GLN* 3.6 36.6 - - + +
30A ALA* 4.8 8.3 - - + -
31A GLU* 4.2 17.5 + - + +
35A ALA 3.9 1.5 + - - +
36A ARG* 1.3 76.6 - - - +
38A GLU* 1.3 62.1 + - - +
39A LYS 3.9 9.0 - - - +
40A VAL* 3.5 32.5 - - + -
63A TYR* 4.2 9.2 - - + -
64A GLN 3.9 5.4 - - - +
65A VAL* 4.0 13.0 - - + -
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Residues in contact with GLU 38 (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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3A ARG* 2.7 49.7 + - - +
36A ARG* 3.9 18.7 - - + +
37A VAL* 1.3 76.9 - - - +
39A LYS* 1.3 63.9 + - - +
64A GLN* 2.8 36.4 + - - +
65A VAL* 4.5 0.6 - - - -
66A GLU* 4.3 13.0 - - + +
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Residues in contact with LYS 39 (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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37A VAL* 3.5 2.0 - - - +
38A GLU* 1.3 84.7 - - + +
40A VAL* 1.3 71.2 + - - +
41A GLU* 3.4 22.8 + - - -
62A TRP* 3.9 22.0 - - + -
63A TYR* 3.2 5.0 - - - +
64A GLN* 2.8 38.4 + - + +
97A PHE* 3.9 40.2 - - + -
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Residues in contact with VAL 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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23A LYS* 4.2 28.5 - - + -
27A GLN* 4.1 11.9 - - - +
37A VAL* 3.5 24.0 - - + -
39A LYS* 1.3 81.0 - - - +
41A GLU* 1.3 82.9 + - - +
61A LEU* 5.9 1.1 - - + -
62A TRP 3.3 7.2 - - - +
63A TYR* 3.6 34.5 - - + -
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Residues in contact with GLU 41 (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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23A LYS* 6.1 0.4 - - - +
39A LYS* 3.4 28.9 + - - -
40A VAL* 1.3 85.4 - - - +
42A GLU* 1.3 70.7 + - - +
43A LEU* 3.6 15.0 + - + +
61A LEU* 3.6 2.0 - - - +
62A TRP* 2.8 53.8 + - + -
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Residues in contact with GLU 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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16A GLN* 4.8 11.3 - - - +
19A LEU* 5.3 6.1 - - - +
20A ALA* 5.7 1.9 - - - -
23A LYS* 3.1 38.3 + - + +
41A GLU* 1.3 78.8 + - - +
43A LEU* 1.3 64.1 + - - +
44A GLY 3.4 0.4 + - - -
59A TYR* 2.7 33.0 + - + +
60A PHE 3.9 4.0 - - - -
61A LEU* 3.5 22.0 - - + -
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Residues in contact with LEU 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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7A ASN* 5.4 4.3 - - - +
41A GLU* 3.7 18.2 - - + +
42A GLU* 1.3 74.6 - - - +
44A GLY* 1.3 61.3 + - - +
45A LEU 5.2 1.0 - - - +
46A ARG* 4.3 24.0 - - - +
60A PHE* 2.8 31.3 + - + +
61A LEU 5.2 1.1 - - - +
62A TRP* 3.6 38.1 - - + +
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Residues in contact with GLY 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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42A GLU 3.4 3.2 + - - -
43A LEU* 1.3 81.0 - - - +
45A LEU* 1.3 63.4 + - - -
46A ARG* 3.7 2.0 + - - +
58A GLY 3.6 0.7 - - - +
59A TYR* 3.8 25.8 - - - -
60A PHE* 2.8 34.0 + - - +
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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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12A PRO* 4.4 18.8 - - + +
43A LEU 5.2 0.5 - - - +
44A GLY* 1.3 71.6 - - - -
46A ARG* 1.3 64.1 + - - +
57A GLN* 4.2 27.8 - - + +
58A GLY 3.4 6.1 - - - +
59A TYR* 3.5 39.9 - - + +
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Residues in contact with ARG 46 (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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43A LEU* 4.3 21.8 - - - +
44A GLY 3.8 4.9 - - - +
45A LEU* 1.3 80.1 - - - +
47A ARG* 1.3 64.8 + - - +
48A LEU 3.6 0.2 + - - -
57A GLN* 3.4 8.2 - - - +
58A GLY* 3.0 28.6 + - - -
60A PHE* 3.5 55.8 - - + -
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Residues in contact with ARG 47 (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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46A ARG* 1.3 75.9 - - - +
48A LEU* 1.3 84.5 + - - +
49A ALA 3.8 8.3 + - - -
51A PRO* 4.5 14.6 - - - +
56A PRO* 3.6 32.4 + - + +
57A GLN* 4.7 7.2 - - + +
60A PHE* 5.6 1.1 - - - -
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Residues in contact with LEU 48 (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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9A VAL* 3.9 17.5 - - + -
46A ARG 3.6 0.6 + - - -
47A ARG* 1.3 96.0 + - - +
49A ALA* 1.3 65.5 + - - +
50A TYR 3.3 21.8 - - - +
52A ILE* 4.0 20.0 - - + +
55A ASP 3.5 23.6 - - - +
56A PRO 2.8 15.8 + - - +
57A GLN 3.7 16.4 - - - +
58A GLY* 4.2 3.4 - - - +
60A PHE* 3.8 32.8 - - + -
86A ARG* 5.9 1.6 - - + +
87A ARG* 4.3 13.5 - - - +
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Residues in contact with ALA 49 (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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47A ARG* 3.8 4.5 + - - -
48A LEU* 1.3 74.3 - - - +
50A TYR* 1.3 77.9 + - + +
87A ARG* 4.7 10.7 - - - +
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Residues in contact with TYR 50 (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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47A ARG* 4.6 0.9 - - - +
48A LEU* 3.0 20.8 - - - +
49A ALA* 1.3 94.0 - - + +
51A PRO* 1.3 85.5 - - + +
52A ILE* 3.6 25.8 + - + +
87A ARG* 4.4 22.0 + - - +
89A MET* 6.0 0.9 - - - +
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Residues in contact with PRO 51 (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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47A ARG* 4.5 10.1 - - - +
50A TYR* 1.3 98.2 - - + +
52A ILE* 1.3 62.5 + - - +
53A ALA 4.2 0.4 - - - -
54A LYS* 4.6 7.6 - - - -
55A ASP 3.2 24.7 - - - +
56A PRO* 4.2 16.1 - - + -
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Residues in contact with ILE 52 (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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9A VAL* 5.7 0.4 - - + -
48A LEU* 4.0 16.9 - - + +
50A TYR* 3.6 28.0 + - + +
51A PRO* 1.3 78.1 - - - +
53A ALA* 1.3 75.8 + - + +
55A ASP* 3.0 22.2 + - - +
86A ARG* 3.5 50.7 + - + +
87A ARG* 4.1 25.6 - - + +
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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