Contacts of the strand formed by residues 41 - 49 (chain A) in PDB entry 1BKL
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TYR* 3.7 36.3 - + - -
31A VAL* 4.3 7.2 - - + -
32A ARG 3.3 17.0 - - - +
33A GLU* 4.1 12.7 - - + +
34A SER* 4.0 4.9 + - - +
39A GLY 3.9 15.2 + - - -
40A ALA* 1.3 78.0 - - - +
42A CYS* 1.3 71.7 + - - +
60A LYS* 3.6 7.4 - - - +
61A ILE* 2.8 42.2 + - + -
63A LYS* 5.1 0.2 - - + -
69A PHE* 3.4 38.3 - + - -
80A LEU* 4.0 20.5 - - + +
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Residues in contact with CYS 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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12A ARG* 6.4 0.4 - - - -
30A LEU 3.6 2.6 - - - +
31A VAL* 3.6 1.0 - - - -
32A ARG* 2.8 73.5 + - - +
34A SER* 4.1 15.5 - - - -
41A TYR* 1.3 83.7 - - - +
43A LEU* 1.3 63.4 - - - +
44A SER* 3.6 0.9 + - - +
58A HIS* 5.1 6.7 - - + -
59A TYR 3.1 16.8 - - - +
60A LYS* 4.7 8.3 - - - -
61A ILE* 4.3 3.8 - - - -
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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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29A PHE* 4.0 22.9 - - + -
30A LEU 3.5 14.6 - - - +
31A VAL* 3.8 16.8 - - + +
42A CYS* 1.3 71.8 - - - +
44A SER* 1.3 65.5 + - - +
45A VAL* 3.9 12.3 - - + -
57A LYS 3.6 1.7 - - - +
58A HIS* 3.5 2.8 - - - -
59A TYR* 2.7 51.0 + - + -
61A ILE* 3.7 21.2 - - + +
71A ILE* 4.4 9.9 - - + -
83A LEU* 4.5 9.0 - - + -
84A VAL* 5.4 0.2 - - + -
87A TYR* 5.4 0.9 - - + -
94A LEU* 3.8 28.9 - - + -
98A LEU* 4.1 14.6 - - + -
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A SER* 4.3 0.4 - - - -
19A LEU* 3.5 25.7 - - - +
28A THR 3.7 0.5 - - - +
29A PHE* 3.3 5.2 - - - +
30A LEU* 2.8 49.6 + - - +
32A ARG* 2.8 32.7 + - - -
42A CYS* 3.6 1.6 + - - +
43A LEU* 1.3 75.9 + - - +
45A VAL* 1.3 60.9 + - - +
57A LYS 3.6 3.4 - - - -
58A HIS* 2.9 13.4 + - - -
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Residues in contact with VAL 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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27A GLY* 3.7 20.2 - - - +
28A THR 3.4 9.4 - - - +
29A PHE* 4.5 1.3 - - + -
43A LEU* 3.9 16.8 - - + -
44A SER* 1.3 77.7 - - - +
46A SER* 1.3 78.4 + - - +
47A ASP* 3.4 1.9 + - - +
56A VAL* 3.6 4.2 - - - +
57A LYS* 2.9 37.8 + - - +
59A TYR* 3.9 15.5 - - + -
94A LEU* 4.6 3.1 - - + -
95A CYS* 4.1 17.9 - - - -
96A HIS 4.9 3.4 - - - +
98A LEU* 3.8 26.0 - - + -
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Residues in contact with SER 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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19A LEU* 3.8 31.4 - - - +
20A LEU* 5.9 0.2 - - - -
24A ASN* 4.3 4.9 + - - +
25A PRO 3.2 22.5 + - - -
26A ARG* 3.8 1.7 - - - +
27A GLY 2.9 30.0 + - - -
28A THR* 2.9 23.8 + - - -
45A VAL* 1.3 75.9 - - - +
47A ASP* 1.3 62.6 + - - +
54A LEU* 5.3 7.4 - - - -
55A ASN 3.6 8.3 - - - -
56A VAL* 4.2 2.5 - - - -
95A CYS* 5.1 0.5 - - - -
96A HIS* 5.2 0.2 - - - +
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Residues in contact with ASP 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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26A ARG* 2.7 43.0 + - - +
45A VAL 3.4 0.2 + - - -
46A SER* 1.3 75.4 - - - +
48A PHE* 1.3 70.4 + - - +
54A LEU* 3.6 10.1 - - - +
55A ASN* 2.8 48.6 + - - +
57A LYS* 2.7 34.5 + - + -
95A CYS* 3.5 21.0 - - - +
96A HIS* 4.5 0.9 - - - +
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Residues in contact with PHE 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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26A ARG* 3.4 37.1 + - + +
47A ASP* 1.3 85.4 + - - +
49A ASP* 1.3 76.6 + - - +
50A ASN* 3.0 34.8 - - - -
53A GLY* 3.4 20.4 - - - -
54A LEU* 3.3 38.1 - - + -
55A ASN* 4.3 0.9 - - - +
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASP* 6.1 0.2 - - - +
48A PHE* 1.3 83.2 - - - +
50A ASN* 1.3 59.3 + - - +
51A ALA* 3.6 11.8 - - - +
52A LYS* 2.7 59.2 + - - +
53A GLY* 2.7 37.9 + - - -
55A ASN* 3.7 4.1 + - - +
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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