Contacts of the helix formed by residues 105 - 119 (chain A) in PDB entry 1LMU
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 ASP 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ASP* 2.9 5.3 + - - +
104A PRO* 1.3 73.6 - - - +
106A ARG* 1.3 55.3 + - - +
107A GLU* 2.7 32.5 - - - +
108A GLY* 2.7 29.8 + - - -
109A GLN* 3.0 19.2 + - - +
158A LEU* 2.8 22.0 - - - +
328A TYR* 2.7 31.5 + - - -
330A ARG* 4.2 3.2 - - - +
380A ALA* 5.0 0.2 - - - -
381A HIS* 3.3 15.0 - - + +
525A GLU* 4.6 6.7 - - - +
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Residues in contact with ARG 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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105A ASP* 1.3 71.6 - - + +
107A GLU* 1.3 72.2 + - - +
109A GLN* 3.0 13.0 + - - +
110A LEU 3.1 10.2 + - - -
158A LEU* 3.1 36.4 - - + +
161A SER* 4.1 11.3 - - - -
162A ALA* 3.1 47.4 - - + +
165A ARG* 2.8 45.1 - - - +
332A ASP* 5.6 3.8 + - - -
524A THR* 4.6 12.2 + - - +
525A GLU* 4.9 7.2 + - - +
578A LEU* 4.2 8.8 - - - +
579A THR* 4.0 23.2 + - - +
582A SER* 4.2 11.7 + - - -
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Residues in contact with GLU 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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7A GLU* 4.5 2.7 - - - +
44A HIS* 5.0 8.3 - - - +
103A ASP* 6.0 0.2 - - - +
105A ASP* 2.7 37.5 - - - +
106A ARG* 1.3 79.0 + - - +
108A GLY* 1.3 61.6 + - - +
110A LEU* 3.2 6.1 + - - +
111A LEU* 3.0 22.6 + - - +
162A ALA* 4.8 5.8 - - - -
328A TYR* 4.9 1.6 - - - +
330A ARG* 4.2 7.4 - - - +
524A THR* 5.3 1.7 - - - +
525A GLU* 3.5 23.4 - - - +
526A ALA* 3.5 27.4 - - + +
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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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7A GLU* 2.7 30.5 - - - -
100A HIS* 3.3 13.4 + - - -
102A GLY* 3.8 3.8 - - - -
103A ASP 3.6 10.8 - - - -
105A ASP* 2.7 19.2 + - - -
107A GLU* 1.3 71.2 - - - +
109A GLN* 1.3 66.5 + - - +
111A LEU* 3.4 10.3 + - - +
112A VAL 3.7 4.3 + - - -
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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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100A HIS* 2.9 39.3 + - - -
103A ASP 4.0 0.2 + - - -
105A ASP 3.0 9.2 + - - +
106A ARG 3.0 9.6 + - - +
108A GLY* 1.3 77.6 - - - +
110A LEU* 1.3 60.7 + - - +
113A ASP* 2.5 29.7 + - - +
131A ARG* 2.8 33.6 - - - +
152A ASN* 3.7 4.1 + - - +
155A PHE* 2.7 31.2 - - + +
158A LEU* 3.1 31.9 - - + -
159A CYS* 2.9 27.5 - - - +
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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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44A HIS* 5.1 7.2 - - + -
106A ARG 3.1 5.3 + - - +
107A GLU* 3.2 6.3 + - - +
109A GLN* 1.3 77.1 - - - +
111A LEU* 1.3 67.8 + - - +
113A ASP* 4.4 4.0 - - + -
114A GLU* 2.8 47.8 + - + +
159A CYS* 2.9 36.3 - - + +
162A ALA* 2.9 26.0 - - + +
163A LEU* 2.9 45.5 - - + +
166A ALA* 5.2 4.3 - - + -
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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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7A GLU* 3.6 41.5 - - + +
41A CYS* 3.7 29.5 - - + -
43A GLY* 3.1 28.3 - - - +
44A HIS* 3.3 37.2 - - + +
45A LEU* 4.5 3.5 + - - +
107A GLU 3.0 13.8 + - - +
108A GLY* 3.7 11.0 - - - +
109A GLN 3.3 0.4 - - - -
110A LEU* 1.3 78.2 - - - +
112A VAL* 1.3 62.1 + - + +
114A GLU* 4.2 4.3 - - - +
115A VAL* 3.8 13.9 + - - +
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Residues in contact with VAL 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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5A ILE* 3.8 39.5 - - + +
6A ALA 4.8 1.6 - - - +
41A CYS* 4.6 6.1 - - - -
100A HIS* 3.0 44.6 - - + +
102A GLY* 3.7 19.5 - - - +
108A GLY 3.7 2.3 + - - +
110A LEU 3.3 0.2 - - - -
111A LEU* 1.3 79.1 - - + +
113A ASP* 1.3 61.1 + - - +
115A VAL* 2.7 32.2 - - + +
116A LEU* 3.2 18.8 + - + +
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Residues in contact with ASP 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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100A HIS* 3.2 10.2 + - - -
109A GLN* 2.5 33.1 + - - +
110A LEU* 3.2 5.8 + - + +
112A VAL* 1.3 78.1 - - - +
114A GLU* 1.3 63.2 + - - +
116A LEU* 3.0 12.0 + - - +
117A ASP* 2.9 32.2 + - - +
152A ASN* 3.0 24.1 + - - -
156A VAL* 6.1 0.5 - - - +
159A CYS* 2.9 30.3 - - + -
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Residues in contact with GLU 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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44A HIS* 3.1 32.1 + - - +
46A LEU* 3.6 18.9 + - + +
48A GLN* 5.1 4.2 + - - -
75A LEU* 3.4 26.8 - - + +
110A LEU* 2.8 43.3 + - + +
111A LEU 4.2 4.0 - - - +
113A ASP* 1.3 75.0 - - - +
115A VAL* 1.3 58.0 + - - +
117A ASP* 3.2 9.6 + - - +
118A TYR* 2.8 30.3 + - - +
163A LEU* 4.6 15.6 - - + +
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Residues in contact with VAL 115 (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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5A ILE* 5.2 2.7 - - + -
41A CYS* 5.0 6.3 - - - -
45A LEU* 4.9 14.8 - - + -
46A LEU* 4.3 9.4 - - + -
85A LEU* 3.0 37.0 - - + -
88A ILE* 4.5 12.3 - - + -
111A LEU 3.8 7.2 + - - +
112A VAL* 2.7 32.9 + - + +
114A GLU* 1.3 80.9 - - - +
116A LEU* 1.3 64.7 + - + +
118A TYR* 3.3 0.5 + - - +
119A LEU* 2.7 50.0 + - + +
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Residues in contact with LEU 116 (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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5A ILE* 5.2 10.3 - - + -
88A ILE* 5.4 1.1 - - + -
92A LEU* 3.2 30.3 - - + -
98A ILE* 4.0 26.7 - - + -
100A HIS* 5.3 3.6 - - + -
112A VAL* 3.7 24.7 - - + +
113A ASP* 3.0 18.4 + - - +
115A VAL* 1.3 91.0 - - + +
117A ASP* 1.3 63.2 + - - +
119A LEU* 3.5 3.8 + - + +
120A GLN 3.2 15.8 + - - -
121A LEU* 3.3 23.9 + - + +
126A ARG* 6.4 1.6 - - + -
129A VAL* 4.2 13.9 - - + -
152A ASN* 4.9 4.3 - - - +
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Residues in contact with ASP 117 (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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113A ASP* 2.9 25.9 + - - +
114A GLU* 3.6 10.6 - - - +
116A LEU* 1.3 75.5 - - - +
118A TYR* 1.3 64.6 + - - +
120A GLN* 3.0 18.8 + - - +
126A ARG* 4.5 16.7 + - - +
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Residues in contact with TYR 118 (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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46A LEU* 3.1 39.5 - - + -
75A LEU* 3.7 29.2 + - + -
77A PRO* 3.7 32.4 - - + +
85A LEU* 4.4 6.3 - - + -
89A LYS* 5.5 3.1 - - - -
114A GLU 2.8 7.6 + - - +
115A VAL* 3.7 3.6 - - + +
117A ASP* 1.3 76.4 - - - +
119A LEU* 1.3 74.2 + - + +
120A GLN* 3.1 13.2 + - - +
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Residues in contact with LEU 119 (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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85A LEU* 3.8 13.7 - - + -
88A ILE* 3.3 35.0 - - + -
89A LYS* 2.9 44.1 - - + +
92A LEU* 3.4 27.8 - - + +
93A HIS* 4.9 10.7 + - - +
115A VAL* 2.7 31.7 + - + +
116A LEU 3.7 5.4 - - - +
118A TYR* 1.3 81.9 - - + +
120A GLN* 1.3 70.3 + - - +
121A LEU* 4.6 0.2 - - - -
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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