Contacts of the helix formed by residues 97 - 109 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.3 36.6 - - - -
94A TRP* 2.8 15.8 + - - -
96A ALA* 1.3 78.7 - - - +
98A TRP* 1.3 65.4 + - - +
100A GLY* 3.3 6.4 + - - -
101A ASN* 2.9 24.3 + - - +
293A TRP* 3.3 40.2 - - + +
294A THR* 6.1 0.2 - - - -
296A LEU* 4.8 1.8 - - - -
297A ALA* 3.6 25.1 - - + -
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Residues in contact with TRP 98 (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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94A TRP* 3.0 58.8 + + + +
95A LEU* 3.8 27.8 - - + -
97A CYS* 1.3 81.0 - - - +
99A ILE* 1.3 84.4 + - + +
100A GLY 2.9 1.7 + - - -
101A ASN* 3.1 16.0 + - - +
102A ILE* 3.9 20.4 + - + +
294A THR* 6.5 0.4 - - - +
297A ALA* 4.2 6.2 - - + +
330A VAL* 3.9 26.9 - - + -
333A LEU* 3.3 37.1 - - + +
334A MET* 4.1 20.1 - - + +
337A PHE* 5.1 3.4 - - + +
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Residues in contact with ILE 99 (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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95A LEU* 3.7 32.1 - - + +
96A ALA* 4.3 2.2 - - - +
97A CYS 3.5 0.6 - - - -
98A TRP* 1.3 106.6 - - + +
100A GLY* 1.3 61.5 + - - +
101A ASN 3.5 0.3 + - - -
102A ILE* 3.5 21.4 + - + +
103A ALA* 3.9 4.7 + - - +
337A PHE* 4.9 13.6 - - + -
353A VAL* 3.6 30.3 - - + +
354A SER* 4.8 3.5 - - - -
357A SER* 3.2 30.7 - - - +
360A PHE* 5.0 5.4 - - + -
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Residues in contact with GLY 100 (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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96A ALA 4.0 7.0 + - - -
97A CYS 3.3 8.2 + - - -
98A TRP 2.9 2.0 + - - -
99A ILE* 1.3 77.2 - - - +
101A ASN* 1.3 67.2 + - - +
103A ALA* 3.2 7.6 + - - +
104A MET* 3.0 20.7 + - - +
293A TRP* 6.4 0.4 - - - -
354A SER* 5.6 1.8 - - - -
357A SER* 4.0 13.7 + - - -
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Residues in contact with ASN 101 (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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97A CYS 2.9 16.9 - - - +
98A TRP* 3.1 7.3 + - - +
100A GLY* 1.3 75.9 - - - +
102A ILE* 1.3 57.3 + - - +
104A MET* 2.3 36.1 + - - +
105A VAL* 2.8 14.1 + - - +
133A LEU* 4.6 1.7 - - + +
290A LEU* 3.1 32.4 + - + +
293A TRP* 3.8 14.0 - - - +
294A THR* 3.0 37.0 - - - +
334A MET* 3.8 18.1 - - + +
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Residues in contact with ILE 102 (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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98A TRP* 3.9 23.3 - - + +
99A ILE* 3.6 11.2 - - - +
100A GLY 3.4 0.4 - - - -
101A ASN* 1.3 75.2 - - - +
103A ALA* 1.3 58.3 + - - +
105A VAL* 3.6 13.3 - - - +
106A VAL* 3.0 25.6 - - + +
133A LEU* 4.9 0.4 - - - -
334A MET* 3.3 31.2 - - + +
337A PHE* 3.0 59.5 - - + -
338A GLN* 3.6 26.3 + - + +
341A SER* 4.3 10.3 - - - +
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Residues in contact with ALA 103 (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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99A ILE 3.9 4.2 + - - +
100A GLY 3.2 7.4 + - - +
101A ASN 2.7 3.4 + - - -
102A ILE* 1.3 77.9 - - + +
104A MET* 1.3 61.6 + - - +
106A VAL* 4.2 9.5 - - - +
107A ILE* 4.0 16.8 + - - +
337A PHE* 6.0 3.1 - - + -
341A SER* 5.8 3.8 - - - +
348A LYS 6.0 1.6 - - - -
349A GLU* 5.4 11.4 - - + +
354A SER* 3.9 32.3 - - - +
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Residues in contact with MET 104 (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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26A SER* 3.8 30.1 - - - +
100A GLY 3.0 12.8 + - - +
101A ASN* 2.3 35.2 + - - +
103A ALA* 1.3 65.4 - - - +
105A VAL* 1.3 64.3 + - - +
107A ILE* 3.1 9.5 + - + +
108A GLY* 3.0 12.6 + - - +
286A CYS* 3.0 44.0 - - + -
289A SER* 3.5 25.4 - - - +
290A LEU* 3.8 13.9 - - + -
293A TRP* 6.3 1.6 - - + -
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Residues in contact with VAL 105 (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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101A ASN 2.8 13.1 + - - +
102A ILE* 3.6 3.8 - - - +
104A MET* 1.3 70.8 - - + +
106A VAL* 1.3 52.9 + - - +
107A ILE 2.4 18.3 + - - -
108A GLY* 2.5 16.4 + - - +
109A VAL* 2.9 17.1 + - + +
129A CYS* 2.9 28.9 - - - -
132A VAL* 4.2 21.8 - - + -
133A LEU* 3.2 28.0 - - + -
286A CYS* 6.0 0.9 - - + +
290A LEU* 3.2 25.0 - - + +
338A GLN* 3.4 9.4 - - - +
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Residues in contact with VAL 106 (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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102A ILE* 3.0 22.6 + - + +
103A ALA* 4.3 8.3 - - - +
104A MET 3.4 0.6 - - - -
105A VAL* 1.3 75.9 - - - +
107A ILE* 1.3 57.5 + - + +
110A GLY* 3.8 13.3 + - - -
125A LEU* 4.4 18.5 - - + +
129A CYS* 3.9 8.1 - - + -
338A GLN* 3.9 19.7 - - - +
341A SER* 4.4 14.4 - - - +
342A ILE 5.1 8.5 - - - +
347A THR 5.8 2.0 - - - +
348A LYS* 5.4 17.0 - - + -
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Residues in contact with ILE 107 (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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26A SER* 4.8 10.1 - - - +
30A LEU* 3.5 35.9 - - + -
103A ALA 4.0 10.0 + - - +
104A MET* 3.1 18.5 + - + +
105A VAL 2.4 9.5 + - - -
106A VAL* 1.3 76.0 - - + +
108A GLY* 1.3 60.5 + - - +
109A VAL 3.3 1.1 - - - -
110A GLY* 3.0 15.8 + - - -
111A TYR* 2.7 44.7 + - + +
286A CYS* 5.0 1.1 - - - -
348A LYS* 4.3 32.3 - - + +
349A GLU* 3.6 15.0 - - + +
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Residues in contact with GLY 108 (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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104A MET* 3.0 11.8 + - - -
105A VAL* 2.5 13.5 + - - -
107A ILE* 1.3 72.6 - - - +
109A VAL* 1.3 60.7 + - - +
111A TYR* 3.5 12.8 + - - -
112A LEU* 4.0 2.8 + - - +
283A ALA* 3.1 27.7 - - - +
286A CYS* 4.3 20.0 - - - -
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Residues in contact with VAL 109 (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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105A VAL* 2.9 19.4 + - + +
108A GLY* 1.3 75.4 - - - +
110A GLY* 1.3 55.7 + - - +
111A TYR 3.1 0.9 - - - -
112A LEU* 2.8 33.7 + - + +
113A SER* 3.0 8.1 + - - -
120A LYS* 3.5 19.7 - - + +
125A LEU* 3.5 18.6 - - + -
128A THR* 3.4 31.9 - - + -
129A CYS* 3.7 23.8 - - - -
132A VAL* 4.4 11.2 - - + -
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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