Contacts of the helix formed by residues 111 - 125 (chain E) in PDB entry 1MA1
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 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105E ILE* 3.8 6.3 - - - +
106E GLU* 4.0 9.6 + - - +
109E PHE* 3.2 9.7 + - - +
110E GLY* 1.3 78.4 - - - +
112E PHE* 1.3 63.9 + - - +
113E GLU* 3.5 15.9 + - - +
114E ARG* 3.0 24.3 + - - +
115E PHE* 3.2 16.6 + - - +
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Residues in contact with PHE 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E GLY 4.3 5.6 - - - -
96E GLU* 3.6 46.2 - - + +
97E PRO* 3.4 32.3 - - + -
105E ILE* 3.9 14.4 - - + +
106E GLU* 5.2 3.6 - - - +
111E SER* 1.3 69.9 - - - +
113E GLU* 1.3 72.1 + - - +
115E PHE* 3.1 19.2 + + - +
116E ARG* 2.7 60.0 + - + +
188E TRP* 4.6 7.4 - + - -
193E TRP* 3.7 21.3 - + - -
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Residues in contact with GLU 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E GLU* 4.5 10.4 - - - +
111E SER* 3.3 15.1 - - - +
112E PHE* 1.3 86.9 + - - +
114E ARG* 1.3 63.2 + - - +
116E ARG* 3.2 13.0 + - - +
117E LYS* 2.9 26.4 + - - +
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Residues in contact with ARG 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA* 3.6 25.4 + - - +
55C ARG* 3.5 11.7 - - + +
58C ASP* 3.8 28.9 + - - +
59C THR 2.8 30.9 + - - -
60C ASP* 4.8 0.6 - - - +
61C VAL* 4.7 10.1 - - - +
109E PHE* 3.1 30.1 - - + +
111E SER* 3.0 17.8 + - - +
113E GLU* 1.3 75.7 - - - +
115E PHE* 1.3 63.9 + - - +
117E LYS* 3.1 27.8 + - - +
118E GLU* 2.9 57.1 + - - +
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Residues in contact with PHE 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ILE* 3.6 28.5 - - + -
109E PHE* 3.7 36.9 - + + +
111E SER 3.2 3.5 + - - +
112E PHE* 3.1 23.7 + + - +
114E ARG* 1.3 79.4 - - - +
116E ARG* 1.3 64.7 + - - +
117E LYS 3.0 0.2 + - - -
118E GLU* 3.2 0.7 + - - +
119E PHE* 2.8 67.1 + + + +
134E LEU* 4.0 27.6 - - + -
145E ILE* 4.3 2.9 - - + -
163E LEU* 4.1 14.1 - - + -
188E TRP* 3.8 18.8 - + - -
193E TRP* 3.9 18.2 - + - -
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Residues in contact with ARG 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E PHE* 2.7 44.2 + - + +
113E GLU* 3.4 11.4 - - - +
115E PHE* 1.3 80.3 - - - +
117E LYS* 1.3 54.4 + - - +
120E SER* 2.6 40.2 + - - -
185E GLU* 2.9 41.2 + - - -
188E TRP* 3.5 56.1 - - + +
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Residues in contact with LYS 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASP* 5.6 2.4 + - - -
60C ASP* 3.7 25.9 + - - +
113E GLU 2.9 17.0 + - - +
114E ARG* 3.5 29.0 - - - +
115E PHE 3.0 0.2 - - - -
116E ARG* 1.3 77.7 - - - +
118E GLU* 1.3 61.5 + - + +
120E SER* 3.1 7.7 + - - -
121E GLN* 2.9 53.3 + - + +
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Residues in contact with GLU 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 5.2 3.8 - - - +
55C ARG* 2.8 46.7 + - - +
61C VAL* 5.5 3.3 - - - +
63C ILE* 2.9 49.3 - - + +
109E PHE* 3.5 11.4 - - - -
114E ARG* 2.9 48.0 + - - +
115E PHE* 3.8 3.6 - - - +
117E LYS* 1.3 77.8 - - + +
119E PHE* 1.3 62.4 + - - +
121E GLN* 3.2 8.5 + - - +
122E ALA* 2.9 3.6 + - - +
145E ILE* 4.2 11.5 - - + +
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Residues in contact with PHE 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E PHE* 2.8 42.5 + + + +
116E ARG 3.9 3.6 - - - +
118E GLU* 1.3 73.1 - - - +
120E SER* 1.3 57.1 + - - +
122E ALA* 3.3 5.4 + - - +
123E ALA* 3.1 24.1 + - - +
132E ALA* 3.3 33.9 - - + +
133E VAL* 3.8 3.1 - - - -
134E LEU* 3.7 25.1 - - + -
145E ILE* 3.9 19.4 - - + +
163E LEU* 3.9 25.1 - - + -
165E LEU* 3.8 30.7 - - + -
187E PHE* 4.5 2.5 - + - -
188E TRP* 3.5 27.4 - + + -
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Residues in contact with SER 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ARG* 2.6 26.6 + - - +
117E LYS* 3.4 7.6 - - - -
119E PHE* 1.3 75.9 - - - +
121E GLN* 1.3 59.4 + - - +
123E ALA* 3.3 2.6 + - - +
124E ILE* 2.9 41.9 + - - +
184E VAL* 3.8 18.0 - - - +
188E TRP* 3.1 24.4 + - - -
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Residues in contact with GLN 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASP* 5.6 4.4 - - - +
61C VAL* 3.5 25.4 + - - +
62C ASP* 5.3 0.2 - - - +
63C ILE* 3.3 30.8 - - + +
117E LYS* 2.9 45.9 + - + +
118E GLU* 3.6 4.7 - - - +
120E SER* 1.3 73.7 - - - +
122E ALA* 1.3 60.5 + - - +
124E ILE* 4.4 5.6 - - - +
125E SER* 2.7 39.8 + - - +
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Residues in contact with ALA 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ILE* 2.9 23.9 - - + +
67C LEU* 3.9 7.9 - - + -
118E GLU 2.9 3.5 + - - +
119E PHE 3.4 10.1 - - - +
120E SER 3.2 0.2 - - - -
121E GLN* 1.3 75.5 - - - +
123E ALA* 1.3 62.5 + - - +
126E ALA* 3.8 2.1 + - - +
131E TRP 4.9 0.3 - - - +
132E ALA* 3.9 10.4 - - + +
145E ILE* 3.9 25.4 - - + -
147E GLN* 2.9 37.6 + - + +
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Residues in contact with ALA 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E PHE 3.1 12.9 + - - +
120E SER 3.6 7.2 - - - +
122E ALA* 1.3 77.3 - - - +
124E ILE* 1.3 66.8 + - - +
125E SER 3.3 0.5 + - - -
126E ALA 3.5 2.3 + - - -
132E ALA* 3.8 11.8 - - + +
165E LEU* 3.8 20.4 - - + -
167E VAL* 3.5 24.2 - - + +
180E ARG* 3.3 14.6 + - - -
184E VAL* 3.8 20.4 - - + -
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Residues in contact with ILE 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E SER* 2.9 31.6 + - - +
121E GLN* 4.2 4.3 - - - +
123E ALA* 1.3 73.1 - - - +
125E SER* 1.3 60.5 + - - +
126E ALA 4.1 0.3 - - - +
180E ARG* 3.0 27.9 + - + +
181E PRO* 4.0 43.5 - - + +
184E VAL* 3.9 23.1 - - + -
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Residues in contact with SER 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ILE* 4.8 0.7 - - - +
64C LYS* 3.5 36.7 + - - +
121E GLN* 2.7 26.0 + - - -
122E ALA* 4.2 0.2 - - - -
124E ILE* 1.3 77.8 - - - +
126E ALA* 1.3 64.6 + - - +
127E GLU* 3.3 5.4 + - - +
147E GLN* 3.1 14.4 + - - -
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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