Contacts of the strand formed by residues 23 - 33 (chain U) in PDB entry 3BT1
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 LEU 23 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1U LEU* 3.9 4.5 - - - +
3U CYS* 4.0 0.5 - - - -
22U ASP* 1.3 83.4 - - - +
24U CYS* 1.3 67.8 + - - +
45U CYS* 3.3 4.0 - - - -
46U THR* 2.7 38.8 + - + +
47U HIS 3.4 14.6 - - - +
48U SER* 3.1 31.9 - - - +
50U LYS* 3.6 14.4 - - + +
70U VAL* 4.1 20.2 - - + -
71U CYS* 3.1 30.1 - - - +
72U GLY* 4.0 6.5 - - - +
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Residues in contact with CYS 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1U LEU* 3.4 10.5 - - - +
2U ARG 3.4 11.2 - - - -
3U CYS* 2.1 44.6 - - - -
23U LEU* 1.3 77.7 - - - +
25U ARG* 1.3 63.1 + - - +
44U SER 3.4 4.5 - - - -
70U VAL* 3.8 2.1 - - - -
71U CYS* 3.0 33.0 + - - +
73U LEU 4.1 10.8 - - - -
75U LEU 4.8 0.4 - - - -
76U CYS* 4.6 8.5 - - - -
77U ASN* 3.5 23.6 - - + +
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Residues in contact with ARG 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER* 3.5 26.6 + - - +
24U CYS* 1.3 77.4 - - - +
26U THR* 1.3 62.9 + - - +
27U THR* 3.0 27.6 + - - -
42U GLU* 2.8 42.9 + - - +
43U LYS* 3.2 7.7 + - - -
44U SER* 2.8 70.4 + - - +
45U CYS 4.0 7.0 + - - +
46U THR* 4.0 16.3 + - + -
68U GLU* 4.6 7.6 - - + +
69U VAL 3.3 11.9 - - - +
70U VAL* 4.2 12.6 - - + -
71U CYS* 5.9 0.2 - - - -
77U ASN* 3.6 5.6 + - - -
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Residues in contact with THR 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U ARG* 1.3 71.2 + - - +
27U THR* 1.3 68.8 + - - +
28U ILE* 4.3 12.9 - - + +
41U VAL* 4.0 21.8 - - + -
42U GLU 3.2 9.4 - - - +
43U LYS* 3.7 10.4 - - + +
67U THR 4.0 0.2 - - - +
68U GLU* 3.0 4.0 - - - +
69U VAL* 2.7 53.6 + - + +
77U ASN* 3.2 32.1 + - - +
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Residues in contact with THR 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.8 28.9 - - + +
28A ILE* 4.4 14.9 - - + +
25U ARG* 3.0 24.7 + - - -
26U THR* 1.3 76.9 - - - +
28U ILE* 1.3 67.6 + - - +
29U VAL* 5.2 0.9 - - + -
40U LEU 3.7 0.3 - - - +
41U VAL* 3.3 4.2 - - - -
42U GLU* 2.8 34.6 + - - +
66U LEU* 5.8 0.4 - - + -
67U THR 3.3 9.9 - - - +
68U GLU* 2.4 32.1 + - + +
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Residues in contact with ILE 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U THR* 4.3 16.4 - - + +
27U THR* 1.3 81.7 - - - +
29U VAL* 1.3 70.6 + - - +
30U ARG* 4.6 4.3 - - + +
39U GLU* 3.9 25.4 - - + +
40U LEU 3.1 10.1 - - - +
41U VAL* 4.3 9.6 - - + -
65U SER 3.4 3.2 - - - +
66U LEU* 3.4 2.6 - - - +
67U THR* 2.6 56.7 + - + +
69U VAL* 6.2 2.7 - - + -
81U SER* 3.8 32.1 - - - +
82U GLY 5.5 0.4 - - - +
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Residues in contact with VAL 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.8 31.6 - - + -
30A TRP* 4.1 20.2 - - + -
27U THR* 5.2 0.9 - - + -
28U ILE* 1.3 79.0 - - - +
30U ARG* 1.3 60.0 + - - +
31U LEU* 3.0 30.4 + - + -
38U LEU 4.0 0.5 - - - +
39U GLU* 3.4 2.8 - - - -
40U LEU* 2.8 44.7 + - + +
64U THR* 4.4 4.0 - - + -
65U SER 3.6 3.4 - - - -
66U LEU* 3.1 29.4 - - + -
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Residues in contact with ARG 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B SER 3.1 24.2 + - - -
27B TYR* 3.0 27.3 + - - -
29B GLN* 4.0 14.1 - - - +
28U ILE* 4.1 4.0 - - + -
29U VAL* 1.3 72.3 - - - +
31U LEU* 1.3 67.6 + - - +
32U TRP* 3.7 14.9 + - + +
37U GLU* 2.8 38.7 + - - +
38U LEU 3.5 10.3 - - - +
39U GLU* 4.6 9.4 - - + +
63U ILE 3.8 0.7 - - - +
64U THR* 3.4 6.1 - - - -
65U SER* 3.1 45.8 + - - +
67U THR* 6.3 0.4 - - + -
116U ARG* 2.9 30.2 - - - +
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Residues in contact with LEU 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TRP* 4.0 20.9 - - + +
31A CYS 4.1 19.5 - - - +
33A CYS* 6.4 1.1 - - - -
39A GLY 5.3 3.1 - - - +
40A GLN* 5.8 2.2 - - - +
29U VAL* 3.0 38.4 - - + +
30U ARG* 1.3 73.9 - - - +
32U TRP* 1.3 58.0 + - - +
33U GLU* 4.3 15.2 - - - +
37U GLU* 3.2 4.6 - - - +
38U LEU* 3.0 58.5 + - + +
40U LEU* 5.2 7.2 - - + -
63U ILE 4.1 2.7 - - - -
64U THR* 4.5 8.1 - - + +
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Residues in contact with TRP 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 3.6 22.0 - - - -
24B LEU* 3.6 23.8 - - + -
26B SER* 3.4 23.2 + - - -
27B TYR* 3.3 38.7 - + + +
30U ARG* 3.7 17.5 - - + +
31U LEU* 1.3 74.3 - - - +
33U GLU* 1.3 64.0 + - - +
34U GLU* 3.0 36.3 + - - -
35U GLY 3.9 2.0 + - - -
36U GLU 3.7 3.8 - - - -
37U GLU* 3.7 29.6 + - + -
58U ARG* 6.0 0.2 - - - -
61U LEU 4.0 10.3 - - - -
62U LYS* 3.3 6.1 - - - +
63U ILE* 2.9 57.9 + - + +
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Residues in contact with GLU 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY* 5.4 6.4 - - - -
46A LYS* 3.7 13.3 + - - +
31U LEU* 4.3 20.0 - - - +
32U TRP* 1.3 79.3 - - - +
34U GLU* 1.3 69.0 + - - +
35U GLY 3.2 0.5 + - - -
36U GLU* 2.8 67.4 + - + +
37U GLU* 4.3 6.6 + - - -
38U LEU* 5.1 5.0 - - - +
61U LEU* 4.4 6.5 - - + +
62U LYS* 4.3 22.5 - - + +
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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