Contacts of the strand formed by residues 92 - 98 (chain A) in PDB entry 1BO1
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LYS* 3.5 22.7 - - - +
79A VAL 2.9 5.6 - - - -
80A ASP* 2.9 31.7 + - + +
81A ASN 5.6 0.2 - - - +
90A PRO* 3.5 11.8 - - - +
91A SER* 1.3 88.6 - - - +
93A PHE* 1.3 65.8 + - - +
191A VAL* 4.7 5.7 - - - +
192A ASP 5.4 1.7 + - - -
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Residues in contact with PHE 93 (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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45A VAL* 3.6 31.4 - - + -
48A TRP* 3.8 40.6 - + - -
78A LYS* 3.7 2.5 - - - +
79A VAL* 2.8 71.4 + - + +
80A ASP* 4.7 0.4 + - - -
81A ASN* 5.1 0.7 - - - -
89A LEU* 4.1 21.1 - - + -
90A PRO* 3.3 37.2 - - + -
92A ARG* 1.3 75.1 - - - +
94A LYS* 1.3 69.8 + - - +
190A THR* 3.5 16.2 - - - +
191A VAL* 4.8 2.0 - - + +
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Residues in contact with LYS 94 (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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45A VAL* 4.0 5.7 - - - +
76A LYS* 6.0 6.7 - - + -
77A ILE 3.2 8.3 - - - +
78A LYS* 3.2 50.0 - - + +
93A PHE* 1.3 82.3 - - - +
95A PHE* 1.3 62.0 - - - +
188A ARG* 4.6 11.9 - - - +
189A LEU* 3.6 2.8 - - - -
190A THR* 2.9 54.1 + - + +
195A GLU* 5.7 1.8 - - - +
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Residues in contact with PHE 95 (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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45A VAL* 3.7 22.0 - - + -
46A LEU* 4.2 6.7 - - + -
48A TRP* 4.1 15.5 - + + -
49A GLY* 3.3 40.8 - - - -
50A VAL 3.9 2.2 - - - -
53A THR* 3.6 17.3 - - + -
76A LYS* 3.5 1.8 - - - -
77A ILE* 2.8 55.7 + - + +
93A PHE* 5.2 0.7 - - + -
94A LYS* 1.3 75.9 - - - +
96A LYS* 1.3 63.9 + - - +
187A TYR* 3.3 43.5 - + + -
188A ARG 3.9 1.6 - - - -
189A LEU* 3.6 31.9 - - + -
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Residues in contact with LYS 96 (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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74A TYR* 3.2 42.4 - - + -
75A SER 3.2 11.2 - - - +
76A LYS* 3.9 13.5 - - + +
95A PHE* 1.3 80.1 - - - +
97A GLU* 1.3 63.8 + - - +
98A TYR* 3.1 38.3 + - + -
187A TYR* 3.3 7.4 - - - +
188A ARG* 2.9 76.8 + - + +
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Residues in contact with GLU 97 (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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53A THR* 3.3 39.9 + - + +
54A ILE* 5.6 1.0 - - - +
57A LEU* 4.3 4.7 - - - +
74A TYR* 3.3 5.9 - - - -
75A SER* 2.9 42.6 + - - +
95A PHE* 4.9 0.6 - - - -
96A LYS* 1.3 73.7 - - - +
98A TYR* 1.3 69.8 + - - +
100A PRO* 3.2 36.1 - - + +
103A PHE* 5.6 2.6 - - + +
107A ARG* 4.1 16.3 + - - -
186A MET 3.9 5.2 - - - +
187A TYR* 4.0 22.7 + - + -
84B PHE* 5.4 1.2 - - - -
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Residues in contact with TYR 98 (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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73A ALA 4.4 0.4 - - - -
74A TYR* 4.3 5.6 - + + -
96A LYS* 3.1 42.5 + - + -
97A GLU* 1.3 72.7 - - - +
99A CYS* 1.3 72.1 + - - +
100A PRO* 3.3 0.9 - - - +
103A PHE* 3.1 19.0 - - + -
157A VAL* 3.5 21.1 - - + +
161A HIS* 3.6 30.1 - + + +
186A MET* 3.1 49.7 + - + +
187A TYR* 4.1 6.3 - - - -
188A ARG* 3.6 23.7 + - + +
197A TYR* 3.0 29.5 - + - -
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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