Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 1LBI
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 ALA 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B LEU 4.0 14.8 - - - +
64B ILE* 4.7 13.5 - - + -
84B LYS* 6.0 0.3 - - - +
87B ALA* 2.8 42.6 + - + +
88B ASP* 4.2 5.9 + - - +
90B LEU* 4.5 14.1 - - + +
91B GLY* 1.3 75.5 - - - +
93B SER* 1.3 62.8 + - - +
94B VAL 4.1 0.3 + - - -
301B VAL* 5.7 0.9 - - + -
305B LEU* 5.6 6.1 - - + -
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Residues in contact with SER 93 (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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113A ASN* 3.5 23.4 + - - -
62B LEU 3.3 11.7 + - - -
63B LEU* 3.3 25.2 - - - +
64B ILE* 2.8 27.7 + - - +
91B GLY 5.5 0.2 + - - -
92B ALA* 1.3 74.1 - - - +
94B VAL* 1.3 64.3 + - - +
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Residues in contact with VAL 94 (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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96A VAL 4.4 2.1 - - - +
97A SER* 4.2 15.6 + - - -
98A MET* 5.0 2.9 + - + -
113A ASN* 5.7 0.5 - - - +
63B LEU* 4.6 0.4 - - - +
64B ILE* 3.3 36.8 - - + +
66B VAL* 3.7 25.8 - - + -
80B VAL* 6.0 0.7 - - + -
83B ILE* 4.0 6.7 - - + -
84B LYS* 3.9 34.3 - - + +
87B ALA* 3.4 17.9 - - + -
92B ALA 4.1 0.4 + - - -
93B SER* 1.3 75.0 - - - +
95B VAL* 1.3 65.4 + - - +
96B VAL* 3.8 17.2 - - + +
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Residues in contact with VAL 95 (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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95A VAL* 3.8 26.9 - - + -
96A VAL 3.6 7.6 - - - +
97A SER* 5.2 6.3 - - - +
113A ASN* 5.1 5.8 - - + +
114A LEU* 5.4 2.0 - - + -
117A GLN* 4.0 18.6 - - + +
63B LEU* 3.9 20.6 - - + -
64B ILE 3.0 5.7 + - - -
65B GLY* 3.1 21.0 - - - -
66B VAL 3.2 1.8 + - - -
93B SER 3.9 0.2 + - - -
94B VAL* 1.3 73.9 - - - +
96B VAL* 1.3 59.4 + - - +
114B LEU* 3.3 22.2 - - + +
117B GLN* 4.5 7.4 - - + -
119B VAL* 4.0 15.9 - - + -
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Residues in contact with VAL 96 (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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94A VAL 4.3 0.2 - - - +
95A VAL* 3.8 7.8 - - - +
96A VAL* 3.1 54.7 + - + +
98A MET* 4.6 13.9 - - + -
66B VAL* 3.7 15.3 - - + +
68B THR* 3.8 27.6 - - + -
80B VAL* 4.0 25.4 - - + -
94B VAL* 3.8 20.6 - - + -
95B VAL* 1.3 74.7 - - - +
97B SER* 1.3 66.3 + - - +
98B MET* 5.0 1.8 - - + -
114B LEU* 4.6 0.9 - - - -
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Residues in contact with SER 97 (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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94A VAL 4.5 9.6 + - - -
95A VAL* 6.2 0.4 - - - -
66B VAL 2.6 19.2 + - - +
67B ALA* 3.2 2.1 - - - -
68B THR* 2.9 25.8 + - - +
96B VAL* 1.3 76.2 - - - +
98B MET* 1.3 67.1 + - - +
110B ALA* 3.5 25.0 + - - +
113B ASN* 4.3 10.2 + - - +
114B LEU* 3.9 24.0 - - - -
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Residues in contact with MET 98 (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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77A SER 5.1 2.0 - - - +
80A VAL* 3.6 34.3 - - + -
81A ALA* 4.2 15.9 - - + +
84A LYS* 3.2 47.2 - - + +
94A VAL* 4.8 8.5 + - + +
96A VAL* 4.6 10.7 - - + +
68B THR* 4.0 11.7 - - + -
69B SER* 3.2 21.3 - - - +
70B SER* 3.7 24.5 - - - +
71B LEU 5.5 1.1 - - - +
96B VAL* 4.4 4.7 + - + -
97B SER* 1.3 79.9 + - - +
99B VAL* 1.3 61.3 + - - +
100B GLU* 3.6 6.8 + - - +
110B ALA* 4.7 1.2 - - - +
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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