Contacts of the helix formed by residues 111 - 121 (chain A) in PDB entry 2M3L
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PRO 3.9 1.2 + - - -
110A LEU* 1.3 74.2 - - - +
112A PRO* 1.3 76.1 - - - +
113A GLU 3.4 2.0 - - - -
114A GLU* 2.7 24.8 + - - -
115A LYS* 3.0 22.0 + - - +
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Residues in contact with PRO 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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97A TYR* 3.9 37.5 - - + +
111A GLY* 1.3 80.9 - - - +
113A GLU* 1.3 57.6 + - - +
115A LYS* 3.2 11.2 + - + +
116A GLN* 3.0 33.8 + - + +
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Residues in contact with GLU 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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111A GLY 3.4 0.4 - - - -
112A PRO* 1.3 80.2 - - - +
114A GLU* 1.3 55.4 + - + +
116A GLN* 3.2 11.7 + - + +
117A LYS* 2.6 80.4 + - - +
137A ALA* 4.8 2.4 - - + +
141A GLN* 3.4 14.0 + - - -
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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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109A PRO 4.2 2.9 - - - +
110A LEU* 3.6 11.1 - - + -
111A GLY* 2.7 36.5 + - - +
113A GLU* 1.3 82.2 - - + +
115A LYS* 1.3 60.5 + - - +
117A LYS* 3.5 7.6 + - - +
118A LEU* 3.4 21.0 - - - +
135A GLN 4.0 3.8 - - - +
136A CYS* 3.0 15.7 - - - +
137A ALA* 2.8 26.8 + - + +
138A ASN* 2.7 53.2 + - - -
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Residues in contact with LYS 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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96A LEU* 3.0 30.1 + - + +
97A TYR* 2.7 30.1 + - - -
98A ASP 4.0 1.8 + - - -
99A LEU 2.7 29.2 + - - +
100A SER* 4.4 2.6 - - - +
101A ILE* 4.9 7.9 - - + +
109A PRO* 6.1 0.4 - - - -
110A LEU* 3.1 44.2 - - + +
111A GLY 3.0 13.1 + - - +
112A PRO* 3.5 9.2 - - + +
114A GLU* 1.3 75.3 - - - +
116A GLN* 1.3 65.9 + - + +
118A LEU* 3.4 15.7 + - - +
119A VAL* 3.6 15.3 + - - +
125A PHE* 3.8 7.0 - - + -
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Residues in contact with GLN 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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96A LEU* 4.3 17.9 - - - +
97A TYR* 5.9 3.5 + - - +
112A PRO* 3.0 21.0 + - + +
113A GLU* 3.4 19.5 - - + +
115A LYS* 1.3 79.4 - - - +
117A LYS* 1.3 50.6 + - - +
119A VAL* 3.0 15.2 + - - +
120A ASP* 2.6 41.3 + - + +
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Residues in contact with LYS 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 GLU* 2.6 65.7 + - - +
114A GLU* 3.8 6.1 - - - +
115A LYS 3.3 0.8 - - - -
116A GLN* 1.3 71.6 - - - +
118A LEU* 1.3 57.7 + - - +
120A ASP* 2.7 32.3 + - - -
121A GLU* 2.8 61.3 + - - +
137A ALA* 4.2 13.0 - - + -
140A TRP* 3.5 19.2 - - + -
141A GLN* 3.8 8.3 - - - +
144A ARG* 3.8 13.0 - - - +
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Residues in contact with LEU 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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110A LEU* 3.8 17.3 - - + -
114A GLU 3.4 16.4 - - - +
115A LYS 3.6 4.7 - - - +
116A GLN 3.1 0.2 - - - -
117A LYS* 1.3 77.5 - - - +
119A VAL* 1.3 59.1 + - - +
122A LYS 3.1 5.0 + - - -
123A LYS* 2.6 52.5 + - + +
124A ARG 5.3 3.6 - - - +
125A PHE* 3.4 39.9 - - + -
134A GLY* 4.3 3.1 - - - -
135A GLN* 3.8 28.7 - - + +
140A TRP* 3.6 25.6 - - + -
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Residues in contact with VAL 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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84A TYR* 3.0 39.0 + - + +
85A GLY* 4.1 7.2 - - - +
86A THR* 5.5 1.8 - - - +
96A LEU* 3.6 32.8 - - + -
115A LYS 3.7 4.7 - - - +
116A GLN* 3.0 14.0 + - - +
118A LEU* 1.3 76.3 - - - +
120A ASP* 1.3 61.1 + - - +
122A LYS* 2.9 20.5 + - - +
125A PHE* 3.6 28.3 - - + -
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Residues in contact with ASP 120 (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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116A GLN* 2.6 25.5 + - + +
117A LYS* 2.7 36.2 + - - +
119A VAL* 1.3 74.8 - - - +
121A GLU* 1.3 59.2 + - - +
122A LYS* 2.7 27.5 + - - +
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Residues in contact with GLU 121 (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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117A LYS* 2.8 34.4 + - - +
120A ASP* 1.3 79.4 - - + +
122A LYS* 1.3 70.0 + - - +
123A LYS* 2.7 42.7 + - + +
140A TRP* 3.3 11.4 - - - -
144A ARG* 2.7 47.3 + - - -
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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