Contacts of the helix formed by residues 111 - 125 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105F ILE* 3.8 7.3 + - - +
106F GLU* 4.0 10.0 + - - +
109F PHE* 3.2 10.2 + - - +
110F GLY* 1.3 79.3 - - - +
112F PHE* 1.3 62.9 + - - +
113F GLU* 3.4 16.3 + - - +
114F ARG* 3.0 23.0 + - - +
115F PHE* 3.2 18.2 + - - +
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Residues in contact with PHE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F GLY 4.2 8.3 - - - -
96F GLU* 3.7 44.2 - - + +
97F PRO* 3.4 30.7 - - + -
105F ILE* 4.0 12.9 - - + +
106F GLU* 5.2 3.4 - - - +
111F SER* 1.3 72.0 - - - +
113F GLU* 1.3 67.1 + - - +
115F PHE* 3.1 20.7 + + - +
116F ARG* 2.7 66.2 + - + +
188F TRP* 4.6 5.4 - + - -
193F TRP* 3.8 22.2 - + - -
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Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F GLU* 4.7 9.6 - - - +
111F SER* 3.3 15.4 + - - +
112F PHE* 1.3 86.4 + - - +
114F ARG* 1.3 63.8 + - - +
116F ARG* 3.1 12.0 + - - +
117F LYS* 2.9 25.3 + - - +
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Residues in contact with ARG 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ALA* 3.5 27.2 + - - +
55D ARG* 3.5 11.4 - - + +
58D ASP* 3.6 30.3 + - - +
59D THR 2.7 31.7 + - - -
60D ASP* 4.8 1.4 - - - +
61D VAL* 4.8 6.9 - - - +
109F PHE* 3.0 30.5 - - + +
110F GLY 5.1 0.2 - - - -
111F SER* 3.0 15.1 + - - +
113F GLU* 1.3 77.6 - - - +
115F PHE* 1.3 64.0 + - - +
117F LYS* 3.1 26.2 + - - +
118F GLU* 2.8 55.8 + - - +
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Residues in contact with PHE 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ILE* 3.5 28.3 - - + -
109F PHE* 3.7 35.6 - + + +
111F SER 3.2 3.6 + - - +
112F PHE* 3.1 23.5 + + - +
114F ARG* 1.3 80.1 - - - +
116F ARG* 1.3 67.2 + - - +
117F LYS 3.1 0.3 + - - -
118F GLU* 3.2 0.5 + - - +
119F PHE* 2.8 57.5 + + + +
134F LEU* 4.0 27.8 - - + -
145F ILE* 4.3 2.0 - - + -
163F LEU* 4.1 14.1 - - + -
188F TRP* 3.8 20.2 - + - -
193F TRP* 3.9 17.7 - + - -
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Residues in contact with ARG 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F PHE* 2.7 46.1 + - + +
113F GLU* 3.4 10.5 - - - +
115F PHE* 1.3 80.5 - - - +
117F LYS* 1.3 54.6 + - - +
120F SER* 2.7 40.1 + - - -
185F GLU* 2.9 38.4 + - - -
188F TRP* 3.5 56.6 - - + +
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Residues in contact with LYS 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASP* 5.5 3.0 + - - -
60D ASP* 3.8 26.6 + - - +
113F GLU 2.9 15.8 + - - +
114F ARG* 3.5 29.9 - - - +
116F ARG* 1.3 76.7 - - - +
118F GLU* 1.3 60.9 + - + +
120F SER* 3.1 7.0 + - - -
121F GLN* 2.9 54.8 + - + +
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Residues in contact with GLU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 5.2 3.9 - - - +
55D ARG* 2.8 43.5 + - - +
61D VAL* 5.4 3.0 - - + +
63D ILE* 2.9 49.3 - - + +
67D LEU* 6.2 0.3 - - - +
109F PHE* 3.6 9.9 - - - -
114F ARG* 2.8 52.1 + - - +
115F PHE* 3.8 4.5 - - - +
117F LYS* 1.3 79.1 - - + +
119F PHE* 1.3 62.6 + - - +
121F GLN* 3.2 7.2 + - - +
122F ALA* 2.9 3.6 + - - +
145F ILE* 4.1 11.5 - - + +
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Residues in contact with PHE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F PHE* 2.8 47.1 + + + +
116F ARG 3.9 3.4 - - - +
118F GLU* 1.3 72.9 - - - +
120F SER* 1.3 57.8 + - - +
122F ALA* 3.3 6.2 + - - +
123F ALA* 3.1 23.9 + - - +
132F ALA* 3.3 29.9 - - + +
133F VAL* 3.8 7.2 - - - -
134F LEU* 3.7 27.4 - - + -
145F ILE* 3.9 19.0 - - + +
163F LEU* 3.9 22.7 - - + -
165F LEU* 3.8 28.9 - - + -
187F PHE* 4.6 2.2 - + - -
188F TRP* 3.5 22.0 - + + -
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Residues in contact with SER 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ARG* 2.7 28.4 + - - +
117F LYS* 3.1 8.5 + - - -
119F PHE* 1.3 76.8 - - - +
121F GLN* 1.3 60.4 + - - +
123F ALA* 3.3 2.3 + - - +
124F ILE* 2.9 40.9 + - - +
184F VAL* 3.7 17.2 - - - +
185F GLU* 5.6 0.3 + - - -
188F TRP* 3.1 24.1 + - - -
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Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ASP* 5.5 5.3 - - - +
61D VAL 3.5 25.5 + - - +
63D ILE* 3.3 29.3 - - + +
117F LYS* 2.9 46.8 + - + +
118F GLU* 3.2 5.4 + - - +
120F SER* 1.3 74.1 - - - +
122F ALA* 1.3 56.2 + - - +
124F ILE* 4.4 6.3 - - + +
125F SER* 2.7 43.1 + - - -
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Residues in contact with ALA 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE* 2.8 22.8 - - + +
67D LEU* 4.0 18.8 - - + -
118F GLU 2.9 3.7 + - - +
119F PHE 3.4 11.2 - - - +
121F GLN* 1.3 76.5 - - - +
123F ALA* 1.3 61.3 + - - +
126F ALA* 3.8 1.7 + - - +
131F TRP 4.9 0.7 - - - +
132F ALA* 4.0 15.8 - - + +
145F ILE* 4.0 8.3 - - + -
147F GLN* 2.9 37.7 + - + +
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Residues in contact with ALA 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F PHE 3.1 12.6 + - - +
120F SER 3.5 7.4 - - - +
122F ALA* 1.3 78.3 - - - +
124F ILE* 1.3 67.6 + - - +
125F SER 3.4 0.5 + - - -
126F ALA* 3.5 3.0 + - - -
132F ALA* 3.9 11.2 - - + +
165F LEU* 3.8 27.8 - - + -
167F VAL* 3.6 24.7 - - + +
180F ARG* 3.4 12.5 + - - -
184F VAL* 3.8 12.8 - - + -
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Residues in contact with ILE 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F SER* 2.9 29.0 + - - +
121F GLN* 4.2 4.9 - - + +
123F ALA* 1.3 75.2 - - - +
125F SER* 1.3 62.0 + - - +
180F ARG* 2.9 30.8 + - + +
181F PRO* 3.9 41.5 - - + +
184F VAL* 3.9 22.2 - - + -
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Residues in contact with SER 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE* 4.6 0.8 - - - +
64D LYS* 3.4 37.1 + - - +
121F GLN* 2.7 26.6 + - - -
122F ALA* 4.2 0.3 - - - -
124F ILE* 1.3 78.9 - - - +
126F ALA* 1.3 64.4 + - - +
127F GLU* 3.3 5.9 + - - +
147F 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