Contacts of the helix formed by residues 98 - 115 (chain A) in PDB entry 1LBA
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASP* 3.8 22.2 - - - +
54A GLY* 3.6 4.7 - - - -
96A THR* 3.2 11.9 - - + +
97A PRO* 1.3 76.8 - - - +
99A GLN* 1.3 64.4 + - - +
101A GLN* 3.6 9.3 + - - +
102A SER* 3.1 26.5 + - - -
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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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50A ILE* 3.2 32.0 - - + +
51A LYS 3.1 20.2 - - - +
52A ARG* 3.6 25.1 - - - +
54A GLY* 4.2 1.5 - - - -
81A LEU* 4.1 9.7 - - + +
82A VAL 2.9 23.9 + - - +
95A PHE* 3.3 16.4 - - - +
96A THR* 3.1 38.9 + - + +
98A ALA* 1.3 77.2 - - - +
100A MET* 1.3 62.4 + - - +
102A SER* 3.3 3.1 + - - -
103A LEU* 3.0 28.4 + - - +
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Residues in contact with MET 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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81A LEU* 4.4 7.6 - - - -
95A PHE* 3.5 29.6 - - - -
96A THR 3.2 13.3 + - - +
97A PRO* 3.2 8.7 + - + +
99A GLN* 1.3 78.6 - - - +
101A GLN* 1.4 57.4 + - - +
103A LEU* 3.3 21.0 + - + +
104A ARG* 3.0 25.5 + - - +
133A PHE* 3.9 19.5 - - + -
138A TRP* 3.3 48.6 - - + +
142A ASN* 5.9 0.2 - - - +
144A LEU* 4.0 26.5 - - + -
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Residues in contact with GLN 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 PRO* 3.0 27.6 + - + +
98A ALA* 3.8 8.7 - - - +
100A MET* 1.4 75.2 - - - +
102A SER* 1.4 65.6 + - - +
103A LEU 3.4 0.2 + - - -
104A ARG* 3.5 6.8 + - - +
105A SER* 3.4 20.8 + - - -
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Residues in contact with SER 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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50A ILE* 4.3 10.8 - - - -
54A GLY* 2.8 28.7 + - - -
56A VAL* 4.3 13.5 - - - +
98A ALA 3.1 13.8 + - - -
99A GLN 3.3 3.3 + - - -
101A GLN* 1.4 76.2 - - - +
103A LEU* 1.3 67.2 + - - +
105A SER* 3.4 6.1 + - - -
106A LEU* 3.1 24.1 + - - +
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Residues in contact with LEU 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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16A VAL* 4.4 12.1 - - + -
50A ILE* 3.6 26.0 - - + +
79A VAL* 4.0 16.6 - - + -
81A LEU* 4.1 20.2 - - + -
99A GLN 3.0 17.0 + - - +
100A MET* 3.6 24.9 - - + +
101A GLN 3.2 0.4 - - - -
102A SER* 1.3 76.5 - - - +
104A ARG* 1.3 58.7 + - - +
106A LEU* 3.2 4.6 + - + +
107A LEU* 2.9 53.3 + - + +
133A PHE* 4.3 7.0 - - + -
138A TRP* 3.8 24.2 - - + -
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Residues in contact with ARG 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 MET 3.0 16.3 + - - +
101A GLN* 3.9 7.0 - - - +
102A SER 3.3 0.2 - - - -
103A LEU* 1.3 77.1 - - - +
105A SER* 1.3 60.6 + - - +
107A LEU* 4.0 1.0 - - - +
108A VAL* 3.2 32.6 + - + +
138A TRP* 2.9 45.5 + - + +
139A TRP* 2.5 55.9 + - + +
140A GLU 5.1 0.2 - - - -
142A ASN* 2.6 37.5 + - - +
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Residues in contact with SER 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 GLN 3.4 12.2 + - - -
102A SER* 3.4 6.6 + - - -
104A ARG* 1.3 74.9 - - - +
106A LEU* 1.4 64.6 + - - +
108A VAL* 3.9 6.3 - - - +
109A THR* 2.8 32.4 + - - -
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Residues in contact with LEU 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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48A PHE* 3.9 44.6 - - + -
50A ILE* 4.3 12.1 - - + -
56A VAL* 4.4 17.9 - - + -
79A VAL* 4.1 18.8 - - + -
102A SER 3.1 14.2 + - - +
103A LEU 3.6 7.9 - - - +
105A SER* 1.4 73.0 - - - +
107A LEU* 1.3 59.2 + - + +
109A THR* 3.1 12.2 + - + -
110A LEU* 2.8 59.9 + - + +
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Residues in contact with LEU 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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14A ILE* 3.8 29.8 - - + -
16A VAL* 4.3 11.7 - - + -
79A VAL* 4.4 7.2 - - + -
103A LEU* 2.9 45.0 + - + +
104A ARG 4.0 0.2 - - - +
106A LEU* 1.3 73.2 - - + +
108A VAL* 1.3 65.9 + - - +
110A LEU* 3.0 6.2 + - + -
111A LEU* 2.8 34.4 + - + +
119A LEU* 3.8 24.2 - - + -
135A LEU* 5.1 1.1 - - + -
138A TRP* 4.4 6.1 - - + -
139A TRP* 3.8 30.5 - - + -
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Residues in contact with VAL 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 ARG* 3.2 25.6 + - + +
105A SER* 3.9 7.0 - - - +
107A LEU* 1.3 72.6 - - - +
109A THR* 1.3 62.4 + - - +
111A LEU* 3.5 5.6 + - - +
112A ALA* 3.3 23.1 + - + +
139A TRP* 4.0 19.7 - - + -
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Residues in contact with THR 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 SER* 2.8 16.7 + - - -
106A LEU* 3.2 13.9 - - + +
108A VAL* 1.3 76.3 - - - +
110A LEU* 1.3 70.3 + - + +
112A ALA* 3.4 6.2 + - - +
113A LYS* 3.1 30.1 + - + +
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Residues in contact with LEU 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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14A ILE* 4.0 39.0 - - + -
48A PHE* 4.3 13.2 - - + -
62A GLU* 4.6 9.6 - - - +
77A ILE* 4.2 15.9 - - + -
79A VAL* 4.2 5.8 - - + -
106A LEU* 2.8 52.8 + - + +
107A LEU* 3.6 6.5 - - + +
109A THR* 1.3 76.7 - - + +
111A LEU* 1.3 63.9 + - - +
112A ALA 3.0 5.0 + - - -
113A LYS* 3.1 17.7 + - + -
114A TYR* 3.2 28.2 + - + +
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Residues in contact with LEU 111 (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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14A ILE* 4.0 20.6 - - + -
107A LEU* 2.8 27.5 + - + +
108A VAL* 4.0 4.5 - - - +
110A LEU* 1.3 72.1 - - - +
112A ALA* 1.3 59.9 + - - +
114A TYR 4.0 13.9 - - - +
115A GLU* 4.6 2.3 + - - -
116A GLY 5.1 1.7 + - - -
117A ALA 3.8 22.9 - - - +
119A LEU* 4.2 28.7 - - + +
139A TRP* 3.9 29.6 - - + -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A VAL* 3.3 15.8 + - + +
109A THR* 3.6 7.2 - - - +
110A LEU 3.0 0.8 - - - -
111A LEU* 1.3 84.1 - - - +
113A LYS* 1.3 62.1 - - + +
114A TYR 3.4 0.6 + - - -
115A GLU* 4.4 6.1 + - - +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.0 30.9 + - - +
109A THR* 3.1 24.7 + - + +
110A LEU* 3.1 8.2 + - + +
112A ALA* 1.3 78.1 - - - +
114A TYR* 1.3 89.4 + - + +
115A GLU* 3.5 7.7 + - - +
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Residues in contact with TYR 114 (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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8A ARG* 4.6 0.2 + - - -
11A THR* 3.7 35.2 - - + -
14A ILE* 4.8 1.8 - - + -
62A GLU* 2.8 34.3 + - + +
63A MET* 3.8 26.5 - - + -
77A ILE* 4.1 22.4 - - + -
110A LEU* 3.2 21.8 + - + +
111A LEU 4.0 7.4 - - - +
112A ALA 3.4 0.2 - - - -
113A LYS* 1.3 109.4 + - + +
115A GLU* 1.3 72.4 - - + +
116A GLY 3.2 0.5 + - - -
117A ALA* 2.8 32.4 + - + +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A THR 4.8 3.3 - - - +
111A LEU 4.9 2.5 - - - -
112A ALA 4.4 5.8 + - - +
113A LYS 3.5 6.5 - - - +
114A TYR* 1.3 78.8 - - + +
116A GLY* 1.3 60.0 + - - +
117A ALA 3.3 0.5 + - - -
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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