Contacts of the strand formed by residues 98 - 102 (chain B) in PDB entry 3BIL
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 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A THR* 4.3 14.0 - - - +
113A SER* 5.2 1.4 + - - -
67B THR* 4.4 0.8 - - - +
68B ILE* 3.7 15.3 - - + +
70B VAL* 3.7 26.9 - - + -
84B VAL 5.2 0.9 - - - +
88B GLN* 3.7 45.4 - - + +
91B ALA* 4.5 0.3 - - - +
96B LEU 4.0 4.2 + - - -
97B ALA* 1.3 81.7 + - - +
99B ILE* 1.3 71.5 + - - +
100B ILE* 3.8 22.4 + - + +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 2.6 42.4 - - + -
100A ILE 4.0 2.2 - - - -
101A THR* 4.4 13.9 - - + -
113A SER* 5.8 2.2 - - - +
116A PHE* 3.5 38.1 - - + -
117A LEU* 5.3 1.1 - - + -
67B THR* 3.7 21.3 - - + -
68B ILE 3.0 7.0 + - - +
69B GLY* 3.4 1.2 - - - -
70B VAL* 2.8 27.4 + - - +
97B ALA* 6.0 0.9 - - + -
98B THR* 1.3 83.8 - - - +
100B ILE* 1.3 61.4 + - - +
101B THR* 4.8 0.7 - - + -
116B PHE* 6.0 0.2 - - + -
117B LEU* 3.7 29.2 - - + +
122B VAL* 4.7 0.4 - - + -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.1 19.3 - - + -
99A ILE* 3.8 0.3 - - - -
100A ILE* 2.8 56.1 + - + +
101A THR* 4.3 4.7 - - - -
102A ASN* 4.2 6.3 - - + +
70B VAL* 3.2 13.7 - - + +
72B VAL* 4.9 1.3 - - + -
75B LEU* 4.2 23.3 - - + -
84B VAL* 4.4 22.9 - - + +
88B GLN* 4.1 13.2 - - - +
98B THR* 3.8 24.0 - - + +
99B ILE* 1.3 76.7 - - - +
101B THR* 1.3 78.9 + - - +
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR 4.2 8.1 - - - +
99A ILE* 4.2 20.9 - - + -
100A ILE* 3.9 4.7 - - - -
70B VAL 2.7 11.8 + - - +
71B ILE* 3.4 14.0 - - - +
72B VAL* 2.9 30.7 + - - +
99B ILE* 4.8 2.2 - - + -
100B ILE* 1.3 83.0 - - - +
102B ASN* 1.3 63.5 + - - +
113B SER* 2.8 34.4 + - - +
117B LEU* 3.7 27.8 - - + -
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Residues in contact with ASN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL 5.4 0.6 + - - -
85A THR* 4.3 19.4 + - - +
88A GLN* 2.9 43.8 + - - +
98A THR 5.2 0.2 + - - -
100A ILE* 4.0 5.8 - - + +
72B VAL 3.2 4.0 - - - +
73B PRO 3.3 10.2 - - - +
74B SER* 3.5 12.0 - - - +
75B LEU* 3.9 32.9 - - + +
101B THR* 1.3 78.5 - - - +
103B SER* 1.3 62.1 + - - +
104B ASN* 3.2 26.9 + - - +
109B THR* 4.2 5.4 - - - +
113B SER* 5.5 1.0 + - - -
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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
------------------------------------------------------------
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