Contacts of the strand formed by residues 51 - 59 (chain B) in PDB entry 3BN3
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 TRP 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASN* 3.7 10.3 - - - +
24B CYS 3.1 11.4 - - - +
25B SER* 4.0 7.9 - - - -
46B GLN* 3.5 33.0 - - + -
47B ARG* 3.4 17.0 + - - +
48B GLY* 2.9 51.6 + - - +
49B LEU 4.6 0.6 - - - +
50B ARG* 1.3 80.8 - - - +
52B LEU* 1.3 64.4 + - - +
53B ALA* 3.8 7.2 - - + -
70B PHE* 4.1 6.0 - - - -
1C NAG 3.4 64.1 + - + +
2C NAG 3.6 26.6 - - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU 4.0 0.3 - - - +
23B ASN* 4.0 1.8 - - - -
24B CYS* 2.7 48.2 + - + +
35B GLY* 3.7 37.2 - - - +
36B LEU* 4.0 9.0 - - + +
45B THR* 3.2 35.0 - - + -
46B GLN 3.4 4.0 - - - +
47B ARG* 3.4 34.5 - - + +
51B TRP* 1.3 74.4 - - - +
53B ALA* 1.3 57.0 + - - +
54B ARG* 4.1 21.9 + - + +
70B PHE* 4.7 7.6 - - + -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TRP* 3.8 14.5 - - + -
22B LEU 3.1 11.7 - - - +
23B ASN* 4.2 6.7 - - + +
45B THR* 3.2 6.6 - - - +
46B GLN* 2.8 33.9 + - + +
51B TRP* 3.8 8.4 - - + -
52B LEU* 1.3 74.3 - - - +
54B ARG* 1.3 59.8 + - - +
1C NAG 3.7 32.5 - - + -
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Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU 3.7 1.0 - - - +
21B TRP* 3.5 4.8 - - - -
22B LEU* 2.9 31.8 + - - +
35B GLY* 5.3 0.8 - - - -
36B LEU* 4.0 45.5 + - + +
42B ARG* 3.3 52.1 - - - +
44B GLY 3.3 5.2 - - - -
45B THR* 2.8 31.0 + - - +
47B ARG* 4.9 8.1 - - - +
52B LEU* 4.1 29.6 + - + +
53B ALA* 1.3 77.0 - - - +
55B GLN* 1.3 59.7 + - - +
56B LEU* 3.8 9.2 + - + +
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B SER* 3.6 14.1 + - - -
20B LEU 3.5 10.7 - - - +
21B TRP* 3.5 46.2 - - + +
42B ARG* 3.2 5.2 - - - +
43B ASN* 2.8 60.6 + - - +
44B GLY 2.9 12.2 + - - +
54B ARG* 1.3 69.4 - - - +
56B LEU* 1.3 67.2 + - - +
57B VAL* 4.1 6.3 - - + -
199B NAG 3.4 25.7 + - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B SER* 3.1 5.6 - - - -
20B LEU* 2.9 37.4 + - + +
22B LEU* 3.8 29.6 - - + -
36B LEU* 4.2 5.4 - - + -
38B THR* 3.9 27.8 - - + -
40B LEU* 3.8 31.9 - - + +
41B ARG 3.2 12.6 - - - +
42B ARG* 4.1 12.1 - - + -
54B ARG* 4.3 16.8 - - + +
55B GLN* 1.3 79.5 - - - +
57B VAL* 1.3 60.6 + - - +
59B ILE* 3.8 7.0 - - + +
66B PRO* 4.5 2.0 - - + -
83B ILE* 4.1 6.1 - - + -
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A THR* 6.2 0.4 - - + -
18B GLY 3.9 4.5 - - - -
19B SER* 3.8 13.5 - - - -
40B LEU* 4.7 1.9 - - - +
41B ARG* 2.8 52.1 + - + +
42B ARG 4.4 0.4 - - - +
43B ASN* 3.4 35.2 - - + +
55B GLN* 4.1 5.8 - - + -
56B LEU* 1.3 80.6 - - - +
58B ASP* 1.3 74.7 + - + +
59B ILE* 3.2 6.8 + - - +
199B NAG 3.8 23.8 - - + -
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Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A LYS* 4.8 14.0 + - - +
17B GLY* 3.7 12.9 + - - +
18B GLY 3.2 6.3 + - - -
19B SER* 5.0 0.2 - - - -
40B LEU* 4.7 2.9 - - - +
41B ARG* 4.7 16.8 + - + +
57B VAL* 1.3 83.0 - - + +
59B ILE* 1.3 63.3 + - - +
60B ARG* 2.7 49.8 + - - +
199B NAG 5.6 1.8 - - - +
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 4.3 7.2 - - + -
15B GLU 4.1 0.2 - - - +
16B ARG* 3.6 0.2 - - - -
17B GLY 2.7 26.2 + - - -
18B GLY 3.0 21.6 + - - +
19B SER* 4.0 1.8 - - - -
20B LEU* 4.0 23.6 - - + +
40B LEU* 4.0 35.0 - - + -
56B LEU* 3.8 17.0 - - + +
57B VAL 4.0 11.2 - - - +
58B ASP* 1.3 71.8 - - - +
60B ARG* 1.3 57.1 + - - +
61B GLU* 4.9 3.6 - - + +
64B THR* 5.2 2.7 - - + -
83B ILE* 3.9 23.8 - - + +
85B THR* 3.4 28.0 - - + +
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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