Contacts of the helix formed by residues 97 - 109 (chain B) in PDB entry 3LRB
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 CYS 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B TYR* 3.4 35.4 - - - -
94B TRP* 2.9 15.4 + - - -
96B ALA* 1.3 78.3 - - - +
98B TRP* 1.3 65.8 + - - +
100B GLY* 3.3 6.1 + - - -
101B ASN* 2.9 24.5 + - - +
293B TRP* 3.3 40.6 - - + +
294B THR* 6.1 0.2 - - - -
296B LEU* 4.7 1.8 - - - -
297B ALA* 3.7 24.5 - - + -
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Residues in contact with TRP 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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94B TRP* 2.9 58.7 + + + +
95B LEU* 3.8 29.2 - - + -
97B CYS* 1.3 80.3 - - - +
99B ILE* 1.3 83.9 + - + +
100B GLY 2.9 1.2 + - - -
101B ASN* 3.1 16.0 + - - +
102B ILE* 3.9 20.7 + - + +
294B THR* 6.4 0.4 - - - +
297B ALA* 4.2 6.5 - - + +
330B VAL* 3.8 26.9 - - + -
333B LEU* 3.3 38.4 - - + +
334B MET* 4.1 20.1 - - + +
337B PHE* 5.1 3.4 - - + +
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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
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95B LEU* 3.6 32.1 - - + +
96B ALA* 4.3 2.8 - - - +
97B CYS 3.5 0.2 - - - -
98B TRP* 1.3 104.5 - - + +
100B GLY* 1.3 62.9 + - - +
102B ILE* 3.5 22.5 + - + +
103B ALA* 3.9 5.0 + - - +
337B PHE* 4.9 12.4 - - + -
353B VAL* 3.6 29.4 - - + +
354B SER* 4.8 3.6 - - - -
357B SER* 3.1 31.6 - - - +
360B PHE* 5.0 5.4 - - + -
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Residues in contact with GLY 100 (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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96B ALA 4.0 7.0 + - - -
97B CYS 3.3 8.2 + - - -
98B TRP 2.9 2.0 + - - -
99B ILE* 1.3 76.8 - - - +
101B ASN* 1.3 67.2 + - - +
103B ALA* 3.2 7.9 + - - +
104B MET* 2.9 21.0 + - - +
293B TRP* 6.4 0.4 - - - -
354B SER* 5.6 1.8 - - - -
357B SER* 3.9 13.8 + - - -
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Residues in contact with ASN 101 (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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97B CYS 2.9 17.3 - - - +
98B TRP* 3.1 8.1 + - - +
100B GLY* 1.3 74.5 - - - +
102B ILE* 1.3 56.8 + - - +
104B MET* 2.3 36.0 + - - +
105B VAL* 2.9 14.1 + - - -
133B LEU* 4.6 1.5 - - + +
290B LEU* 3.1 32.3 + - + +
293B TRP* 3.8 13.7 - - - +
294B THR* 3.0 37.0 - - - +
334B MET* 3.7 17.3 - - + -
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Residues in contact with ILE 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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98B TRP* 3.9 23.1 - - + +
99B ILE* 3.6 13.7 - - - +
100B GLY 3.4 0.2 - - - -
101B ASN* 1.3 75.8 - - - +
103B ALA* 1.3 58.9 + - + +
105B VAL* 3.6 12.5 - - - +
106B VAL* 3.0 26.1 - - + +
133B LEU* 4.9 0.9 - - - +
334B MET* 3.3 29.4 - - + +
337B PHE* 3.0 58.8 - - + -
338B GLN* 3.6 25.6 + - + +
341B SER* 4.3 9.4 - - - +
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Residues in contact with ALA 103 (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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99B ILE 3.9 3.7 + - - +
100B GLY* 3.2 7.8 + - - +
101B ASN 2.7 3.4 + - - -
102B ILE* 1.3 77.6 - - + +
104B MET* 1.3 62.9 + - - +
106B VAL* 4.2 9.7 - - - +
107B ILE* 3.9 16.3 + - - +
337B PHE* 6.0 3.4 - - + -
341B SER* 5.8 3.8 - - - +
348B LYS 6.0 1.3 - - - -
349B GLU* 5.4 11.3 - - + +
354B SER* 3.9 31.2 - - - +
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Residues in contact with MET 104 (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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26B SER* 3.7 29.6 - - - +
100B GLY 2.9 12.6 + - - +
101B ASN* 2.3 34.0 + - - +
103B ALA* 1.3 65.8 - - - +
105B VAL* 1.3 64.1 + - - +
107B ILE* 3.1 10.6 + - + +
108B GLY* 3.0 12.8 + - - +
286B CYS* 3.0 44.2 - - + -
289B SER* 3.4 25.4 - - - +
290B LEU* 3.8 14.1 - - + -
293B TRP* 6.3 1.3 - - + -
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Residues in contact with VAL 105 (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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101B ASN 2.9 13.4 + - - +
102B ILE* 3.6 3.8 - - - +
104B MET* 1.3 70.3 - - - +
106B VAL* 1.3 53.8 + - - +
107B ILE 2.4 18.7 + - - -
108B GLY* 2.6 15.7 + - - +
109B VAL* 2.9 16.9 + - + +
129B CYS* 2.9 29.6 - - - -
132B VAL* 4.2 20.9 - - + -
133B LEU* 3.3 27.6 - - + -
286B CYS* 6.0 1.1 - - + +
290B LEU* 3.3 25.3 - - + +
338B GLN* 3.4 9.6 - - - +
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Residues in contact with VAL 106 (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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102B ILE* 3.0 23.1 + - + +
103B ALA* 4.3 9.6 - - - +
104B MET 3.4 0.6 - - - -
105B VAL* 1.3 76.4 - - - +
107B ILE* 1.3 58.2 + - + +
110B GLY* 3.8 12.8 + - - -
125B LEU* 4.4 17.8 - - + +
129B CYS* 3.9 7.4 - - + -
338B GLN* 3.9 18.8 - - - +
341B SER* 4.4 14.1 - - - +
342B ILE 5.1 8.7 - - - +
347B THR 5.8 2.0 - - - +
348B LYS* 5.5 17.2 - - + -
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Residues in contact with ILE 107 (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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26B SER* 4.8 9.2 - - - +
30B LEU* 3.5 36.8 - - + -
103B ALA 3.9 9.8 + - - +
104B MET* 3.1 18.9 + - + +
105B VAL 2.4 8.9 + - - -
106B VAL* 1.3 76.4 - - + +
108B GLY* 1.3 60.7 + - - +
109B VAL 3.3 1.1 - - - -
110B GLY* 2.9 16.5 + - - -
111B TYR* 2.8 44.0 + - + +
286B CYS* 5.0 0.9 - - - -
348B LYS* 4.3 31.4 - - + +
349B GLU* 3.6 16.6 - - + +
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Residues in contact with GLY 108 (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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104B MET* 3.0 16.0 + - - -
105B VAL* 2.6 12.3 + - - -
107B ILE* 1.3 75.7 - - - +
109B VAL* 1.3 61.0 + - - -
111B TYR* 3.5 12.6 + - - -
112B LEU* 3.9 2.8 + - - +
283B ALA* 3.1 26.9 - - - +
286B CYS* 4.3 12.8 - - - -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 2.9 11.5 + - + +
108B GLY* 1.3 74.7 - - - +
110B GLY* 1.3 54.6 + - - +
111B TYR 3.1 1.3 - - - -
112B LEU* 2.7 32.1 + - + +
113B SER* 3.0 8.1 + - - -
120B LYS* 3.5 27.1 - - + +
125B LEU* 3.5 26.0 - - + -
128B THR* 3.5 17.5 - - + -
129B CYS* 3.6 30.7 - - - -
132B VAL* 4.4 11.4 - - + -
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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