Contacts of the strand formed by residues 69 - 74 (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 LYS 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ARG* 1.3 76.4 - - - +
70A THR* 1.3 60.0 + - - +
71A ARG* 3.6 35.0 - - + +
97A GLU* 5.0 3.8 - - - +
98A LYS 4.5 5.6 + - - +
99A VAL* 3.3 13.4 - - + +
100A ASN* 3.0 23.7 + - - -
141A TYR* 3.5 3.4 - - - -
144A GLU 4.5 14.5 + - - -
145A ASN* 3.6 21.7 + - + +
146A VAL 6.2 0.4 - - - -
147A HIS* 5.8 3.5 - - - +
312A ASP* 5.1 9.9 + - - -
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Residues in contact with THR 70 (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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64A PHE* 3.3 12.9 - - + -
69A LYS* 1.3 72.7 - - - +
71A ARG* 1.3 66.6 - - - +
72A PHE* 3.7 27.8 - - + -
100A ASN* 3.2 28.7 + - + +
102A ILE* 3.7 17.3 - - + -
135A LEU* 5.5 1.3 - - + -
141A TYR* 2.7 25.7 + - - -
145A ASN 2.9 9.6 + - - +
146A VAL* 3.4 6.7 - - + +
147A HIS* 2.8 25.8 + - - +
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Residues in contact with ARG 71 (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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69A LYS* 3.6 32.2 - - + +
70A THR* 1.3 78.2 - - - +
72A PHE* 1.3 63.4 + - - +
73A ILE* 4.0 1.2 + - + -
93A MET* 3.7 37.2 - - + -
97A GLU* 2.9 38.0 + - - -
99A VAL* 4.0 11.4 - - + +
100A ASN 3.0 7.5 + - - -
101A CYS* 3.5 7.7 - - - -
102A ILE 3.0 22.6 + - - +
147A HIS* 2.9 48.5 + - + +
149A ILE* 4.7 1.6 - - + -
171A ARG* 4.3 7.9 - - - +
309A HIS* 3.4 17.3 + - - -
312A ASP* 5.2 4.9 + - - -
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Residues in contact with PHE 72 (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* 4.2 6.1 - + - -
70A THR* 3.7 24.7 - - + -
71A ARG* 1.3 73.0 - - - +
73A ILE* 1.3 61.0 + - - +
74A VAL* 4.7 4.9 - - + -
102A ILE* 3.2 30.3 - - + -
104A VAL* 3.9 22.7 - - + -
128A ILE* 4.0 17.9 - - + -
131A LEU* 3.9 27.4 - - + -
132A VAL* 4.2 16.6 - - + -
135A LEU* 5.1 4.9 - - + -
146A VAL* 3.8 18.8 - - + -
147A HIS 2.8 6.7 + - - +
148A LEU* 3.5 26.9 - - + -
149A ILE* 2.8 31.0 + - - +
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Residues in contact with ILE 73 (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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71A ARG 4.4 1.6 - - - +
72A PHE* 1.3 75.8 - - - +
74A VAL* 1.3 62.0 + - - +
85A TRP* 3.7 19.3 - - + -
86A LEU* 3.2 48.8 - - + +
89A MET* 3.9 25.6 - - + -
90A CYS* 3.8 1.6 - - - +
93A MET* 4.0 6.3 - - + -
101A CYS* 3.5 31.9 - - - -
102A ILE 2.9 10.0 + - - +
103A CYS* 3.5 2.9 - - - -
104A VAL 2.8 27.9 + - - -
149A ILE* 3.4 18.4 - - + +
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Residues in contact with VAL 74 (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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72A PHE* 4.7 2.9 - - + -
73A ILE* 1.3 79.6 - - - +
75A HIS* 1.3 71.2 + - - +
85A TRP* 4.3 2.8 - - - -
86A LEU* 4.2 3.1 - - - -
104A VAL* 3.7 26.2 - - + -
106A TRP* 3.7 19.5 - - + +
128A ILE* 3.8 9.9 - - + -
149A ILE 2.8 12.5 + - - +
150A GLY* 3.6 0.2 - - - -
151A HIS* 3.0 28.9 + - - +
154A GLY* 4.0 7.9 - - - +
157A VAL* 3.9 19.7 - - + -
158A VAL* 3.6 27.4 - - + -
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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