Contacts of the helix formed by residues 96 - 110 (chain A) in PDB entry 1L1E
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 SER 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ASP* 4.7 17.7 + - - +
75A TRP* 5.6 0.2 - - - -
94A THR* 2.9 4.6 + - - -
95A LEU* 1.3 78.3 - - - +
97A GLU* 1.3 65.0 + - - +
98A ASN* 3.4 8.0 + - - +
99A GLN* 3.2 45.8 + - - +
100A ALA* 3.0 24.9 + - - +
120A LEU* 3.7 3.5 - - - +
900A SAH 3.8 4.5 + - - -
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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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95A LEU 3.8 3.8 + - - +
96A SER* 1.3 72.4 + - - +
98A ASN* 1.3 62.8 + - - +
100A ALA* 3.4 3.5 + - - +
101A GLY* 3.2 20.1 + - - -
120A LEU* 2.9 33.8 - - + +
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Residues in contact with ASN 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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17A ASP* 6.3 2.7 - - + -
18A LEU 6.0 2.0 - - - +
20A ASP* 3.3 31.3 + - - +
75A TRP* 2.9 32.0 + - + -
96A SER* 3.3 7.1 + - - +
97A GLU* 1.3 79.3 - - - +
99A GLN* 1.3 58.0 + - + +
101A GLY* 3.7 0.9 + - - -
102A HIS* 3.0 28.2 + - - +
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Residues in contact with GLN 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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33A TYR* 5.9 0.2 - - - -
74A GLY* 3.2 30.0 + - - +
75A TRP* 3.6 52.4 - - + +
94A THR* 2.9 17.2 + - + +
96A SER* 3.2 23.2 + - - +
98A ASN* 1.3 75.0 - - - +
100A ALA* 1.3 56.8 + - - +
102A HIS* 3.2 0.3 + - - +
103A VAL* 2.7 40.9 + - - +
900A SAH 2.7 34.4 + - - -
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Residues in contact with ALA 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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94A THR* 4.0 17.6 - - + +
96A SER 3.0 17.1 + - - +
97A GLU* 3.8 6.3 - - - +
99A GLN* 1.3 75.6 - - - +
101A GLY* 1.3 64.3 + - - +
103A VAL 3.4 0.2 + - - -
104A GLN* 3.0 24.3 + - - +
118A VAL* 3.8 19.0 - - + +
120A LEU* 4.3 23.3 - - + +
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Residues in contact with GLY 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 GLU 3.2 12.7 + - - -
98A ASN 4.1 0.7 - - - -
100A ALA* 1.3 79.9 - - - +
102A HIS* 1.3 62.4 + - - +
104A GLN* 3.3 5.4 + - - +
105A LYS* 3.0 24.8 + - - +
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Residues in contact with HIS 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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20A ASP* 4.9 4.9 - - - -
31A GLN* 3.9 20.8 + - + -
75A TRP* 3.5 43.8 + + + +
98A ASN* 3.0 22.1 + - - +
99A GLN 3.2 3.6 + - - +
101A GLY* 1.3 75.9 - - - +
103A VAL* 1.3 56.7 + - - +
105A LYS* 3.4 9.1 + - + +
106A MET* 3.0 40.7 + - + +
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Residues in contact with VAL 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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73A CYS* 4.6 3.6 - - - -
74A GLY 3.6 8.3 - - - +
75A TRP 3.5 32.1 - - - +
76A GLY* 3.5 7.6 - - - +
79A MET* 3.9 7.2 - - + -
99A GLN 2.7 25.4 + - - +
102A HIS* 1.3 70.6 - - - +
104A GLN* 1.3 61.0 + - - +
106A MET* 3.3 8.0 - - + +
107A PHE* 2.8 60.4 + - + -
118A VAL* 3.8 21.5 - - + -
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Residues in contact with GLN 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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100A ALA 3.0 18.3 + - - +
101A GLY* 3.8 5.8 - - - +
103A VAL* 1.3 73.6 - - - +
105A LYS* 1.3 62.5 + - - +
107A PHE* 3.1 13.7 + - - +
108A ASP* 2.8 62.3 + - - +
116A ARG 5.1 3.4 + - - +
117A ARG* 5.5 1.8 - - - +
118A VAL* 3.5 30.4 + - + +
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Residues in contact with LYS 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 GLY 3.0 17.0 + - - +
102A HIS* 3.6 9.2 - - + +
104A GLN* 1.3 75.3 - - - +
106A MET* 1.3 63.4 + - - +
108A ASP* 3.2 11.5 + - - +
109A GLN* 3.0 52.1 + - + +
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Residues in contact with MET 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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30A THR* 5.9 2.2 - - - +
75A TRP 4.2 18.4 - - - +
76A GLY* 4.2 15.7 - - - +
77A ALA* 4.6 3.8 - - - +
80A ARG* 4.0 35.7 - - + +
102A HIS* 3.0 27.3 + - + +
103A VAL* 3.3 11.7 - - - +
105A LYS* 1.3 76.8 - - - +
107A PHE* 1.3 69.6 + - - +
109A GLN* 3.1 25.0 + - - +
110A MET* 3.3 38.3 + - + +
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Residues in contact with PHE 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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76A GLY 5.6 0.4 - - - -
79A MET* 3.8 22.2 - - + -
80A ARG 5.2 2.7 - - - -
83A ILE* 4.4 7.4 - - + -
90A VAL* 3.9 18.8 - - + -
103A VAL* 2.8 40.0 + - + -
104A GLN* 3.4 18.8 - - - +
106A MET* 1.3 84.7 - - + +
108A ASP* 1.3 62.1 + - - +
109A GLN 3.3 0.7 + - - -
110A MET* 3.4 17.5 - - + +
116A ARG* 2.7 63.5 + - + +
117A ARG 3.6 32.8 - - - -
118A VAL* 3.9 4.7 - - + -
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Residues in contact with ASP 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 GLN* 2.8 50.9 + - - +
105A LYS* 3.2 8.9 + - + +
107A PHE* 1.3 72.1 - - - +
109A GLN* 1.3 62.0 + - + +
110A MET 4.1 3.6 - - - +
116A ARG* 5.1 2.5 + - - +
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Residues in contact with GLN 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 LYS* 3.0 48.4 + - + +
106A MET* 3.1 16.8 + - - +
108A ASP* 1.3 79.6 - - + +
110A MET* 1.3 62.0 + - - +
111A ASP* 4.0 0.9 + - - +
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Residues in contact with MET 110 (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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80A ARG* 2.8 54.5 - - + +
83A ILE* 4.3 26.0 - - - -
84A GLU* 5.2 3.4 - - - +
106A MET* 3.3 39.2 + - + +
107A PHE* 3.4 24.6 - - + +
108A ASP 4.1 2.6 - - - +
109A GLN* 1.3 81.6 - - - +
111A ASP* 1.3 61.6 + - - +
112A THR* 5.0 4.3 - - + -
116A ARG* 2.9 28.3 + - - +
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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