Contacts of the helix formed by residues 86 - 106 (chain A) in PDB entry 1LDJ
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 LEU 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 2.4 27.2 + - - +
85A GLY* 1.3 72.3 - - - +
87A GLU* 1.3 63.2 + - - +
88A LEU 2.9 1.4 + - - -
89A TYR* 3.0 19.9 + - + +
90A LYS* 3.2 37.9 + - + +
144A TRP* 3.1 41.9 + - + +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 5.8 1.7 - - - -
52A TYR* 3.4 19.3 + - + -
84A VAL 3.9 3.4 + - - +
85A GLY* 2.8 4.8 + - - +
86A LEU* 1.3 78.1 - - - +
88A LEU* 1.3 53.7 + - - +
90A LYS* 2.6 50.6 + - + +
91A ARG* 2.6 57.9 + - + +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 4.7 4.7 - - + -
24A LEU* 4.1 13.9 - - + -
49A VAL* 3.3 34.3 - - + -
52A TYR* 3.4 44.3 - - + +
53A CYS* 3.4 17.5 - - - -
85A GLY 2.8 20.6 + - - +
87A GLU* 1.3 73.4 - - - +
89A TYR* 1.3 64.9 + - - +
91A ARG* 2.9 11.3 + - + +
92A LEU* 2.8 36.9 + - + +
140A LEU* 3.6 12.6 - - + -
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.0 12.5 + - + +
88A LEU* 1.3 77.6 - - - +
90A LYS* 1.3 57.0 + - + +
92A LEU* 2.8 19.1 + - + -
93A LYS* 2.7 44.1 + - + +
140A LEU* 4.7 19.8 - - + +
144A TRP* 4.8 13.0 - + + +
157A TYR* 3.5 64.7 - + + -
158A GLU 3.6 2.5 + - - -
159A ILE* 5.1 5.8 - - + -
162A LEU* 2.8 56.7 - - + +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.2 33.5 - - + +
87A GLU* 2.6 42.5 + - + +
89A TYR* 1.3 74.0 - - + +
91A ARG* 1.3 58.1 + - + -
93A LYS* 4.2 6.8 - - - +
94A GLU* 3.3 24.7 + - - +
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Residues in contact with ARG 91 (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 LEU 5.4 0.2 - - - -
18A ASP* 3.8 30.7 + - - +
21A TRP* 3.1 50.0 - - + +
25A ARG* 4.0 11.0 + - - +
52A TYR* 3.3 14.2 + - + +
87A GLU* 2.6 52.2 + - + +
88A LEU* 3.1 9.4 - - + +
90A LYS* 1.3 72.0 - - - +
92A LEU* 1.3 55.4 + - - +
94A GLU* 3.1 14.0 + - - +
95A PHE* 2.8 33.8 + - - +
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Residues in contact with LEU 92 (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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21A TRP* 4.0 11.0 - - + -
24A LEU* 5.2 2.0 - - + -
28A ILE* 3.5 31.6 - - + -
49A VAL* 6.1 0.4 - - + -
88A LEU* 2.8 35.9 + - + +
89A TYR* 2.8 18.1 + - + +
91A ARG* 1.3 74.1 - - - +
93A LYS* 1.3 68.1 + - - +
95A PHE* 2.8 9.0 + - + +
96A LEU* 2.8 33.6 + - + +
133A LEU* 4.1 14.1 - - + -
137A CYS* 3.6 25.4 - - + -
140A LEU* 5.1 5.2 - - + -
159A ILE* 4.5 11.7 - - + -
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Residues in contact with LYS 93 (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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89A TYR* 2.7 34.1 + - + +
90A LYS* 4.2 6.5 - - - +
92A LEU* 1.3 71.9 - - - +
94A GLU* 1.3 53.0 + - - +
96A LEU* 3.2 2.5 + - - +
97A LYS* 2.6 64.0 + - + +
157A TYR* 4.4 15.3 + - - +
162A LEU* 3.7 34.7 - - + +
165A VAL* 6.2 2.0 - - - -
166A THR* 4.7 2.4 + - - +
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Residues in contact with GLU 94 (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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25A ARG* 4.1 21.6 + - - +
90A LYS 3.3 14.5 + - - +
91A ARG* 3.1 16.5 + - - +
92A LEU 3.1 0.2 - - - -
93A LYS* 1.3 80.3 - - - +
95A PHE* 1.3 64.0 + - - +
97A LYS* 3.0 20.2 + - - +
98A ASN* 2.9 29.3 + - + +
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Residues in contact with PHE 95 (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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21A TRP* 4.2 13.9 - + + -
25A ARG* 4.3 31.6 - - + +
28A ILE* 3.1 44.2 - - + -
29A GLN* 3.4 31.2 - - + -
32A TYR* 4.4 6.7 - + - -
91A ARG 2.8 15.4 + - - +
92A LEU* 2.8 11.6 + - + +
94A GLU* 1.3 73.1 - - - +
96A LEU* 1.3 81.8 + - + +
98A ASN* 3.2 9.1 + - - +
99A TYR* 2.9 43.3 + + + +
133A LEU* 5.4 0.4 - - + -
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Residues in contact with LEU 96 (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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32A TYR* 3.4 27.6 - - + +
92A LEU* 2.8 38.5 + - + +
93A LYS 3.5 2.9 - - - +
95A PHE* 1.3 81.2 - - + +
97A LYS* 1.3 62.8 + - - +
98A ASN 2.8 5.8 + - - -
99A TYR* 2.9 8.1 + - + -
100A LEU* 2.7 28.9 - - + +
126A TYR* 4.5 12.8 - - + +
133A LEU* 3.8 11.2 - - + -
159A ILE* 3.9 15.7 - - + -
162A LEU* 3.3 27.1 - - + -
163A ALA* 4.6 5.2 - - + -
166A THR* 3.4 18.6 - - + +
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Residues in contact with LYS 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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93A LYS* 2.6 46.3 + - + +
94A GLU* 3.0 26.3 + - - +
96A LEU* 1.3 73.6 - - - +
98A ASN* 1.3 50.3 + - - +
100A LEU* 4.7 2.2 - - - +
101A THR* 2.5 32.3 + - - +
166A THR* 3.9 14.8 - - + +
169A ASP* 5.4 12.1 - - + +
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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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25A ARG* 6.1 1.2 - - - +
94A GLU* 2.9 19.0 + - + +
95A PHE* 3.5 9.5 + - - +
96A LEU 2.8 1.2 + - - -
97A LYS* 1.3 78.0 - - - +
99A TYR* 1.3 60.7 + - - +
100A LEU 3.2 2.0 - - - -
101A THR* 2.9 17.4 + - - -
102A ASN* 2.4 46.1 + - - +
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Residues in contact with TYR 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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29A GLN* 5.2 15.0 - - - +
32A TYR* 3.3 50.6 - + + +
33A THR* 4.6 8.5 + - - -
95A PHE* 2.9 42.4 + + + +
96A LEU* 2.9 6.7 + - + +
98A ASN* 1.3 73.6 - - - +
100A LEU* 1.3 60.2 + - + +
102A ASN* 3.0 16.7 + - + +
103A LEU* 2.7 57.3 + - + +
122A GLN* 5.0 4.3 + - - -
126A TYR* 5.2 4.9 - + - -
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Residues in contact with LEU 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 LEU* 2.7 33.0 - - - +
97A LYS 4.7 2.5 - - - +
98A ASN 3.2 0.4 - - - -
99A TYR* 1.3 79.9 - - + +
101A THR* 1.3 56.2 + - - +
103A LEU* 2.7 14.6 + - + +
104A LEU* 2.6 36.1 + - - +
126A TYR* 3.6 33.0 - - + +
166A THR* 2.8 42.0 - - + +
167A TRP* 3.4 28.0 - - + +
169A ASP 4.9 8.1 - - - +
170A CYS* 4.5 9.6 - - + +
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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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97A LYS* 2.5 26.7 + - - +
98A ASN* 2.9 11.4 + - - -
100A LEU* 1.3 78.0 - - - +
102A ASN* 1.3 64.7 + - - +
104A LEU* 3.5 17.5 + - + +
105A LYS* 3.3 16.8 + - - +
169A ASP 5.5 4.3 + - - -
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Residues in contact with ASN 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 ASN* 2.4 54.2 + - - +
99A TYR* 3.1 16.5 - - + +
100A LEU 3.0 0.2 - - - -
101A THR* 1.3 77.0 - - - +
103A LEU* 1.3 63.1 + - - +
105A LYS* 2.9 29.5 - - + +
106A ASP* 3.5 4.5 + - - +
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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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99A TYR* 2.7 36.4 + - + +
100A LEU* 2.7 24.1 + - + +
102A ASN* 1.3 72.2 - - - +
104A LEU* 1.3 48.4 + - - +
106A ASP* 2.8 39.2 + - + +
118A PHE* 3.6 11.2 - - + -
122A GLN* 2.8 58.8 - - + +
126A TYR* 5.0 6.5 - - + -
167A TRP* 4.2 16.6 - - + -
170A CYS* 6.0 3.4 - - - -
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Residues in contact with LEU 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 LEU 2.6 14.5 + - - +
101A THR* 3.5 19.1 - - + +
103A LEU* 1.3 69.3 - - - +
105A LYS* 1.3 67.1 + - - +
106A ASP 2.8 10.6 - - - +
108A GLU* 2.9 34.2 - - + +
118A PHE* 5.9 2.0 - - - -
169A ASP 5.6 3.1 - - - +
170A CYS* 5.3 21.0 - - - +
173A ARG* 4.3 27.4 - - + -
174A PRO* 4.0 28.3 - - + -
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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 THR 3.3 7.3 + - - +
102A ASN* 2.9 25.5 + - + +
104A LEU* 1.3 79.1 - - - +
106A ASP* 1.3 55.2 + - - +
107A GLY 3.8 0.2 + - - -
108A GLU* 2.9 37.6 + - - +
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Residues in contact with ASP 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 ASN 3.5 2.9 + - - +
103A LEU* 2.8 27.5 + - + +
104A LEU* 2.8 9.5 - - - +
105A LYS* 1.3 76.7 - - - +
107A GLY* 1.3 63.4 + - - +
108A GLU 2.8 4.4 + - - -
118A PHE* 4.1 21.3 - - - -
122A GLN* 5.2 2.8 + - - -
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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
------------------------------------------------------------
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