Contacts of the strand formed by residues 39 - 45 (chain A) in PDB entry 1BIK
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLY 3.4 9.5 + - - -
38A MET* 1.3 77.1 + - - +
40A SER* 1.3 77.2 + - - +
41A ARG* 4.2 21.0 + - - +
55A GLN* 3.2 9.9 - - - +
56A TYR* 2.7 42.3 + - - +
58A GLY* 5.5 1.2 + - - -
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Residues in contact with SER 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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39A THR* 1.3 82.8 - - - +
41A ARG* 1.3 67.5 + - - +
42A TYR* 5.8 1.2 - - - -
53A THR* 4.5 17.3 + - - +
54A PHE 3.4 4.7 + - - -
55A GLN* 2.8 22.3 + - - +
67A VAL 5.4 2.6 - - - +
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Residues in contact with ARG 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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39A THR* 4.2 15.0 + - - +
40A SER* 1.3 80.8 + - - +
42A TYR* 1.3 66.4 + - - +
53A THR* 2.9 7.6 - - - -
54A PHE* 2.7 54.8 + - + +
56A TYR* 3.6 40.7 - - + -
65A ASN* 2.9 27.8 + - - +
66A PHE 3.6 14.4 - - - +
67A VAL* 3.9 27.1 - - - +
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Residues in contact with TYR 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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40A SER 6.0 0.9 - - - -
41A ARG* 1.3 76.2 - - - +
43A PHE* 1.3 61.2 + - - +
51A CYS* 4.3 12.3 - - + -
52A GLU 3.0 15.7 - - - -
53A THR* 3.6 22.5 - - + +
54A PHE* 3.6 1.3 - - - -
65A ASN* 3.4 7.3 - - - -
66A PHE* 2.7 51.8 + - + +
67A VAL 3.6 26.0 - - - -
68A THR* 3.6 8.1 - - - -
69A GLU* 3.7 38.4 + - + +
72A CYS* 4.2 9.4 - - + -
114A GLY 4.9 8.3 + - - -
115A CYS* 5.8 2.8 - - - +
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Residues in contact with PHE 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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28A LEU 5.2 0.2 - - - -
29A GLY* 5.0 2.5 - - - -
30A TYR* 3.7 39.3 - + + -
42A TYR* 1.3 74.0 - - - +
44A TYR* 1.3 69.4 + - - +
45A ASN* 3.5 18.7 + - + -
51A CYS* 3.3 0.3 - - - -
52A GLU* 2.7 70.9 + - + -
53A THR 4.0 9.6 - - - -
54A PHE* 3.7 21.8 - + + -
64A ASN* 3.5 30.1 - - - +
66A PHE* 4.8 0.2 - - - -
72A CYS* 3.9 4.9 - - - -
148A NAG 3.9 20.4 - - + -
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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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26A CYS* 3.4 24.7 - - + +
28A LEU 4.6 0.5 - - - +
43A PHE* 1.3 74.0 - - - +
45A ASN* 1.3 59.0 + - - +
46A GLY* 3.5 24.5 + - - -
49A MET* 3.7 40.9 - - - +
50A ALA* 4.0 4.0 - - - -
51A CYS* 4.1 14.4 - - - -
64A ASN* 2.9 26.0 + - - +
72A CYS* 3.7 10.7 - - - -
73A LEU* 4.9 3.4 - - + -
76A CYS* 3.1 58.3 + - + -
77A ARG* 4.6 6.1 - - + -
78A THR* 4.3 15.5 + - + +
119A GLY* 6.3 0.2 - - - -
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Residues in contact with ASN 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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43A PHE* 3.5 11.2 + - + -
44A TYR* 1.3 71.7 - - - +
46A GLY* 1.3 52.7 + - - +
47A THR* 2.9 17.5 + - - -
48A SER* 3.0 13.3 + - - +
49A MET* 2.6 32.7 + - - -
50A ALA 2.8 17.6 + - - +
52A GLU* 3.2 19.0 + - - +
148A NAG 1.4 63.8 + - - +
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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