Contacts of the helix formed by residues 98 - 114 (chain A) in PDB entry 1LU9
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 GLY 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP* 5.4 2.4 + - - -
95A ASP* 3.3 24.0 + - - -
96A SER 3.1 1.0 - - - -
97A ASN* 1.3 76.6 - - - +
99A SER* 1.3 66.2 + - - +
100A ASN 3.2 3.1 - - - -
101A THR* 3.4 7.2 - - - -
102A THR* 2.8 36.4 + - - -
132A VAL* 3.8 1.7 - - - +
256A LYS* 4.1 7.6 - - - +
260A HIS* 6.1 0.2 - - - -
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 4.0 17.6 - - - +
94A LEU* 5.4 1.7 - - - +
95A ASP* 3.5 3.2 + - - -
96A SER* 3.0 36.4 + - - -
97A ASN 3.3 1.0 + - - -
98A GLY* 1.3 76.6 - - - +
100A ASN* 1.3 70.0 + - - +
103A ALA* 3.3 23.6 - - - +
131A PRO* 3.7 21.1 - - - -
132A VAL* 4.1 13.6 - - - +
135A ARG* 3.4 12.0 + - - +
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Residues in contact with ASN 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 LEU* 2.8 28.9 + - - +
95A ASP* 2.9 8.0 + - - +
99A SER* 1.3 85.1 + - - +
101A THR* 1.3 59.9 + - - +
103A ALA* 4.0 0.7 - - - +
104A ALA* 2.9 33.1 + - - +
135A ARG* 2.7 35.4 + - - +
139A LEU* 5.1 1.2 - - - +
276A ASP* 3.0 21.4 + - - +
277A ALA* 3.3 22.8 - - - +
280A ILE* 3.5 17.9 - - + -
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Residues in contact with THR 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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93A MET* 3.8 22.2 - - + -
95A ASP* 2.6 39.4 + - - +
98A GLY* 3.4 1.9 - - - -
100A ASN* 1.3 72.1 - - - +
102A THR* 1.3 63.4 + - - +
105A ALA* 3.1 24.6 + - - +
256A LYS* 2.7 31.5 + - - +
259A LEU* 3.7 8.3 - - + +
260A HIS* 3.8 18.8 - - + +
263A CYS* 4.9 0.2 - - - -
280A ILE* 4.2 17.5 - - + -
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Residues in contact with THR 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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97A ASN 4.9 0.9 + - - -
98A GLY* 2.8 27.2 + - - -
101A THR* 1.3 70.4 + - - +
103A ALA* 1.3 58.0 + - - +
105A ALA* 3.2 3.5 + - - +
106A GLY 2.9 25.5 + - - -
132A VAL* 3.9 14.8 - - + -
221A TYR* 3.4 34.3 - - + +
252A ILE* 3.9 6.6 - - + +
253A GLY* 6.4 0.7 - - - -
256A LYS* 3.4 28.9 - - + +
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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 SER 3.3 21.3 + - - +
100A ASN 3.5 1.9 + - - +
101A THR 3.5 0.2 - - - -
102A THR* 1.3 77.5 - - - +
104A ALA* 1.3 59.1 + - - +
106A GLY 3.3 0.5 + - - -
107A VAL* 2.9 34.7 + - - +
132A VAL* 3.7 8.2 - - + +
135A ARG* 3.6 21.1 - - + +
136A SER* 3.4 27.1 - - - +
139A LEU* 4.0 3.6 - - + -
221A TYR* 3.7 3.2 + - - -
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Residues in contact with ALA 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 ASN 2.9 19.2 + - - +
103A ALA* 1.3 78.7 - - - +
105A ALA* 1.3 57.6 + - - +
108A ALA* 2.9 33.1 + - - +
139A LEU* 3.5 14.7 - - + +
259A LEU* 4.0 1.8 - - + -
277A ALA* 5.3 0.9 - - - +
280A ILE* 3.8 15.0 - - + -
281A TYR* 3.7 30.2 - - - +
284A ALA* 3.6 7.0 - - + +
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Residues in contact with ALA 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 THR 3.1 19.6 + - - +
102A THR 3.6 3.8 - - - +
104A ALA* 1.3 74.9 - - - +
106A GLY* 1.3 63.0 + - - +
109A LEU* 3.1 29.6 + - - +
252A ILE* 3.7 14.8 - - + +
255A LEU* 3.7 17.6 - - + +
256A LYS* 3.7 28.7 - - + +
259A LEU* 4.2 3.0 - - + +
284A ALA* 4.5 3.6 - - - -
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Residues in contact with GLY 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 THR 2.9 11.1 + - - -
105A ALA* 1.3 77.8 - - - +
107A VAL* 1.3 62.4 + - - +
109A LEU* 3.3 3.2 + - - +
110A VAL* 3.0 28.4 + - - +
194A PHE* 4.2 3.8 - - - -
221A TYR* 3.7 17.3 - - - -
252A ILE* 3.6 25.1 - - - +
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Residues in contact with VAL 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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103A ALA 2.9 22.2 + - - +
106A GLY* 1.3 71.7 - - - -
108A ALA* 1.3 56.9 + - - +
110A VAL* 3.3 0.7 + - - +
111A VAL* 2.9 37.6 + - + +
136A SER* 3.8 30.7 - - - +
139A LEU* 3.9 18.2 - - + +
140A LEU* 4.0 22.2 - - + +
143A GLU* 4.9 0.2 - - + -
194A PHE* 4.2 15.5 - - + -
221A TYR* 4.0 0.6 + - - -
281A TYR* 3.5 28.5 - - + +
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Residues in contact with ALA 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 ALA 2.9 20.7 + - - +
105A ALA* 4.0 3.1 - - - +
107A VAL* 1.3 75.8 - - - +
109A LEU* 1.3 63.4 + - - +
111A VAL* 4.0 1.5 - - - +
112A LYS* 3.0 25.5 + - - +
255A LEU* 5.0 0.2 - - + -
281A TYR* 3.6 16.5 - - + -
284A ALA* 3.8 32.8 - - + +
285A LYS* 3.9 9.3 - - - +
288A ALA* 4.1 7.4 - - + +
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Residues in contact with LEU 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 ALA 3.1 22.8 + - - +
106A GLY 3.8 3.1 - - - +
108A ALA* 1.3 77.9 - - - +
110A VAL* 1.3 58.2 + - - +
112A LYS* 3.4 8.8 + - + +
113A ALA* 2.9 29.8 + - - +
237A LYS* 3.8 22.7 - - - -
247A PHE* 3.8 29.6 - - + -
251A GLY 4.2 7.4 - - - +
252A ILE* 3.9 31.4 - - + -
255A LEU* 3.6 22.0 - - + -
288A ALA* 4.0 20.6 - - + +
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Residues in contact with VAL 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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106A GLY 3.0 20.6 + - - +
107A VAL 3.7 3.4 - - - +
109A LEU* 1.3 73.5 - - - +
111A VAL* 1.3 62.0 + - + +
113A ALA* 3.2 5.1 + - - -
114A ALA* 2.9 27.1 + - + +
118A VAL* 6.4 1.3 - - + -
140A LEU* 5.4 3.1 - - + -
192A PHE* 4.1 27.1 - - + -
194A PHE* 3.6 35.2 - - + -
217A ILE* 3.6 21.4 - - + +
218A VAL 5.4 0.2 - - - -
219A ALA* 3.9 16.6 - - + -
247A PHE* 4.5 8.1 - - + -
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Residues in contact with VAL 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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107A VAL* 2.9 31.8 + - + +
108A ALA* 4.1 3.4 - - - +
110A VAL* 1.3 73.4 - - + +
112A LYS* 1.3 55.0 + - - +
114A ALA* 3.3 12.3 + - - +
115A GLY 3.4 0.3 + - - -
116A GLY* 2.7 56.5 + - - +
117A SER* 4.1 4.0 - - - +
118A VAL* 4.1 16.2 - - + +
140A LEU* 5.2 4.0 - - + -
143A GLU* 4.0 24.9 - - + +
281A TYR* 3.5 17.7 - - - +
285A LYS* 4.5 9.0 - - - -
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Residues in contact with LYS 112 (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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108A ALA 3.0 19.9 + - - +
109A LEU* 3.6 7.9 - - + +
111A VAL* 1.3 78.8 - - - +
113A ALA* 1.3 58.6 + - - +
115A GLY* 3.0 20.3 + - - -
116A GLY* 3.8 5.0 + - - +
288A ALA* 2.7 50.2 + - + +
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Residues in contact with ALA 113 (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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109A LEU 2.9 17.9 + - - +
110A VAL 3.2 4.2 + - - +
112A LYS* 1.3 77.1 - - - +
114A ALA* 1.3 56.0 + - - +
115A GLY* 3.1 2.1 + - - -
217A ILE* 3.8 9.9 - - + -
245A ARG* 2.7 49.4 + - - +
247A PHE* 3.7 27.6 - - + -
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Residues in contact with ALA 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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110A VAL* 2.9 16.9 + - + +
111A VAL* 3.6 9.2 - - - +
112A LYS 3.1 0.8 - - - -
113A ALA* 1.3 76.6 - - - +
115A GLY* 1.3 59.2 + - - +
117A SER 3.8 21.2 - - - +
118A VAL* 5.3 0.7 - - + -
121A LYS* 5.3 5.4 + - - +
192A PHE* 3.9 27.8 - - + -
216A GLU* 5.0 4.8 - - - +
217A ILE* 4.0 4.5 - - + -
245A ARG* 4.7 2.7 - - - +
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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