Contacts of the strand formed by residues 37 - 42 (chain A) in PDB entry 1BU8
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASP* 3.2 31.9 - - - +
36A THR* 1.3 75.6 - - - +
38A PHE* 1.3 62.0 + - - +
39A LEU* 3.7 27.6 + - + +
49A TYR* 3.1 32.5 + - - -
51A LYS* 4.4 24.7 - - - +
103A CYS 3.4 3.5 - - - +
104A VAL* 3.5 3.6 - - - +
105A ASP* 2.8 67.6 + - + +
107A ARG* 4.2 8.3 - - - +
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Residues in contact with PHE 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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36A THR* 3.9 15.0 - - + -
37A ARG* 1.3 72.9 - - - +
39A LEU* 1.3 61.4 + - - +
40A LEU 3.7 1.1 + - - -
51A LYS* 3.5 8.3 - - - +
52A ILE* 3.1 53.9 + - + +
53A SER* 5.3 2.9 - - - -
54A ALA* 5.6 3.8 - - + -
72A PHE* 4.2 6.5 - + - -
102A ILE* 3.8 13.0 - - + -
103A CYS 3.8 1.6 - - - -
104A VAL* 3.8 22.2 - - + -
127A GLU* 3.6 51.4 - - + -
128A ILE* 3.7 23.1 - - + -
131A LEU* 3.7 21.3 - - + -
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Residues in contact with LEU 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 ARG* 3.8 41.7 - - + +
38A PHE* 1.3 76.7 - - - +
40A LEU* 1.3 63.6 + - - +
41A TYR* 3.4 16.8 - - + +
49A TYR* 3.5 55.4 - - + -
50A GLN 4.3 0.9 - - - -
51A LYS* 4.6 4.5 - - + -
102A ILE* 3.5 2.1 - - - +
103A CYS* 2.9 43.3 + - + +
105A ASP* 4.1 15.0 - - + +
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Residues in contact with LEU 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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38A PHE 3.7 1.8 + - - -
39A LEU* 1.3 71.3 - - - +
41A TYR* 1.3 77.3 + - - +
42A THR* 4.0 8.5 - - + -
45A ASN* 3.1 8.9 + - - +
49A TYR* 3.2 3.8 - - - -
50A GLN* 2.9 57.3 + - - +
52A ILE* 4.2 16.6 - - + -
62A SER* 3.7 25.6 - - - +
64A PHE* 3.9 25.4 - - + +
100A ASN* 4.0 13.7 - - + -
101A CYS 3.7 8.7 - - - +
102A ILE* 3.7 22.9 - - + +
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Residues in contact with TYR 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 LEU* 3.4 32.4 - - + +
40A LEU* 1.3 74.3 - - - +
42A THR* 1.3 64.7 + - - +
45A ASN* 3.5 13.5 - - - +
46A PRO 3.7 10.1 - - - -
47A ASN 3.8 11.8 + - - -
48A ASN 3.7 7.2 - - - -
49A TYR* 3.5 42.9 + - + -
87A LEU* 3.6 41.7 - - + +
90A CYS* 4.6 1.3 - - - -
94A PHE* 3.6 17.7 - - + -
101A CYS* 2.8 37.6 + - + +
103A CYS* 3.9 21.8 - - + -
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Residues in contact with THR 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 LEU* 4.0 14.6 - - + -
41A TYR* 1.3 78.4 - - - +
43A ASN* 1.3 66.2 + - - +
44A GLU* 3.4 8.8 + - - -
45A ASN* 2.5 52.2 + - - +
46A PRO* 3.1 4.5 - - - +
63A ASN* 3.2 34.4 + - - +
68A ARG* 4.4 2.7 - - - +
94A PHE* 3.4 9.4 - - - -
99A VAL 3.8 7.9 - - - +
100A ASN* 3.9 16.6 - - - +
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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