Contacts of the helix formed by residues 107 - 117 (chain A) in PDB entry 1M9L
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LYS 3.4 19.6 + - - -
84A LYS* 4.3 0.7 - - - -
85A ILE* 3.7 37.2 + - - +
88A LEU* 4.7 5.4 - - - -
105A ILE* 4.7 2.3 - - - +
106A ALA* 1.3 74.3 - - - +
108A LEU* 1.3 60.4 + - - +
109A SER 4.6 0.2 - - - -
110A GLY* 4.1 8.1 - - - -
111A ILE* 2.9 36.2 + - - +
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Residues in contact with LEU 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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106A ALA 4.0 11.7 - - - +
107A SER* 1.3 69.2 - - - +
109A SER* 1.3 60.1 + - - +
111A ILE* 3.3 7.3 - - - +
112A GLU* 3.0 31.5 + - - +
129A ASN* 3.7 20.6 - - + +
132A GLU* 3.7 44.0 - - + +
133A ILE* 3.9 18.2 - - + -
136A LEU* 4.2 13.4 - - + +
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Residues in contact with SER 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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85A ILE* 4.1 18.3 - - - +
89A ASP* 3.4 22.4 + - - -
107A SER* 3.4 0.8 - - - -
108A LEU* 1.3 75.3 - - - +
110A GLY* 1.3 66.2 + - - +
112A GLU* 3.2 12.7 + - - +
113A LYS* 3.1 30.2 + - - +
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Residues in contact with GLY 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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85A ILE* 3.6 7.0 - - - +
88A LEU* 3.6 36.8 - - - +
89A ASP* 4.7 1.1 - - - -
107A SER* 3.6 6.1 + - - -
108A LEU 3.4 0.2 - - - -
109A SER* 1.3 80.0 - - - +
111A ILE* 1.3 61.4 + - - +
113A LYS* 3.2 1.2 + - - +
114A LEU* 2.9 33.4 + - - +
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Residues in contact with ILE 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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88A LEU* 5.0 0.4 - - - +
105A ILE* 4.2 24.9 - - + -
106A ALA 5.0 0.7 - - - -
107A SER 2.9 32.4 + - - +
108A LEU* 3.3 11.0 - - - +
110A GLY* 1.3 70.2 - - - +
112A GLU* 1.3 81.0 + - + +
114A LEU* 3.8 7.8 - - - +
115A VAL* 2.8 35.5 + - + +
127A ILE* 4.2 24.0 - - + -
133A ILE* 3.5 51.6 - - + -
136A LEU* 4.9 2.7 - - + -
137A ALA* 4.2 13.0 - - + +
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Residues in contact with GLU 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 LEU 3.0 20.8 + - - +
109A SER* 3.2 11.1 + - - +
111A ILE* 1.3 80.5 - - - +
113A LYS* 1.3 68.0 + - + +
116A ASN* 2.9 33.7 + - + +
136A LEU* 3.5 47.0 - - + +
137A ALA* 4.2 3.6 - - - +
138A ALA* 5.4 2.0 - - + +
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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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89A ASP* 3.6 43.5 + - - +
92A ALA* 3.4 22.5 - - + +
93A ASP* 6.0 1.1 - - + +
109A SER* 3.1 19.3 + - - +
110A GLY 4.1 1.6 - - - +
112A GLU* 1.3 81.3 - - + +
114A LEU* 1.3 65.4 + - - +
115A VAL 3.1 1.6 - - - -
116A ASN* 3.1 9.8 + - - +
117A LEU* 3.0 21.1 + - - +
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Residues in contact with LEU 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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82A ILE* 5.6 3.6 - - + -
88A LEU* 4.1 30.7 - - + +
91A VAL* 5.5 4.3 - - + -
92A ALA* 3.4 17.3 - - + +
98A LEU* 3.5 34.4 - - + +
100A ILE* 5.5 2.5 - - + -
105A ILE* 4.5 25.6 - - + -
110A GLY 2.9 36.9 + - - +
111A ILE* 3.8 4.3 - - - +
113A LYS* 1.3 72.7 - - - +
115A VAL* 1.3 74.0 + - + +
117A LEU* 3.1 19.3 - - - +
120A LEU* 3.9 8.5 - - + +
122A MET* 4.9 3.6 - - - -
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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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111A ILE* 2.8 35.0 + - + +
114A LEU* 1.3 89.3 - - + +
116A ASN* 1.4 61.8 + - - +
117A LEU 2.9 6.0 + - - -
120A LEU* 3.5 26.2 - - + +
122A MET* 4.6 8.5 - - + -
127A ILE* 5.0 4.9 - - + -
133A ILE* 6.3 0.7 - - + -
137A ALA* 3.9 20.6 - - + -
142A LEU* 2.9 36.8 - - + +
145A LEU* 4.9 1.1 - - + -
147A LEU* 4.6 16.6 - - + -
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Residues in contact with ASN 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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112A GLU* 2.9 25.5 + - + +
113A LYS* 3.1 8.0 + - - +
115A VAL* 1.4 74.4 - - - +
117A LEU* 1.3 65.0 + - - +
118A ARG* 4.4 6.9 + - - +
137A ALA 3.6 8.8 + - - -
138A ALA* 3.1 27.3 - - + +
141A LYS* 3.6 33.8 + - - +
142A LEU* 3.8 9.6 - - - +
143A GLU* 4.5 0.9 - - - +
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Residues in contact with LEU 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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92A ALA 3.4 26.0 - - - +
95A LEU* 3.4 34.8 - - + +
96A GLU* 3.9 8.1 - - - +
98A LEU* 3.4 44.6 - - + -
113A LYS 3.0 7.3 + - - +
114A LEU* 3.1 18.2 - - - +
115A VAL 2.9 2.8 + - - +
116A ASN* 1.3 83.6 - - - +
118A ARG* 1.3 88.8 + - - +
119A VAL 4.0 9.4 - - - +
120A LEU* 4.6 4.0 - - + -
142A LEU* 3.2 15.9 - - - +
143A GLU* 3.9 2.4 - - - +
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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