Contacts of the helix formed by residues 98 - 110 (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 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E GLU 5.1 1.1 - - - -
97E PRO* 1.3 76.1 - - - +
99E GLY* 1.3 68.0 + - - +
100E LYS 3.8 0.5 + - - -
101E LEU 4.0 0.7 + - - -
102E ALA* 3.5 13.6 + - - -
194E LYS* 5.4 3.1 + - - -
197E GLU* 3.0 34.4 + - - +
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Residues in contact with GLY 99 (chain E).
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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38A GLN* 6.0 1.3 - - - -
98E SER* 1.3 77.2 + - - +
100E LYS* 1.3 65.6 + - - -
102E ALA* 3.1 12.7 + - - +
103E GLU* 3.1 21.0 + - - +
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Residues in contact with LYS 100 (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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34A GLN 5.1 3.6 - - - +
38A GLN* 3.3 38.9 + - - +
42A ASP* 3.7 15.3 + - - -
98E SER 3.8 0.2 + - - -
99E GLY* 1.3 70.8 - - - -
101E LEU* 1.3 53.4 + - - +
103E GLU* 2.9 21.2 + - - +
104E TYR* 2.7 45.0 + - + -
200E PHE* 3.9 15.3 - - + -
201E GLU* 4.7 27.7 + - + +
204E LEU* 5.1 17.6 + - - +
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Residues in contact with LEU 101 (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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97E PRO* 3.7 20.6 - - + -
98E SER 4.0 7.8 + - - +
99E GLY 3.3 0.2 - - - -
100E LYS* 1.3 78.4 - - - +
102E ALA* 1.3 57.8 + - - +
104E TYR* 3.2 1.4 + - - -
105E ILE* 2.9 47.0 + - + +
134E LEU* 4.5 12.3 - - + -
143E LEU* 4.4 11.2 - - + -
162E LEU* 5.1 1.1 - - + -
193E TRP* 3.8 11.9 - - + -
196E VAL* 3.6 27.8 - - + -
197E GLU* 4.1 18.1 - - + +
200E PHE* 3.7 34.0 - - + -
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Residues in contact with ALA 102 (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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97E PRO* 3.4 32.9 - - + +
98E SER* 3.5 11.9 + - - -
99E GLY 3.1 11.5 + - - +
101E LEU* 1.3 78.8 - - - +
103E GLU* 1.3 63.1 + - + +
105E ILE* 3.4 4.5 + - - +
106E GLU* 3.1 27.2 + - - +
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Residues in contact with GLU 103 (chain E).
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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10A LEU* 3.8 19.7 - - - +
17A TYR* 3.9 2.3 + - - -
33A HIS* 4.6 0.9 - - - -
34A GLN* 2.6 64.6 + - - +
38A GLN* 4.7 0.7 - - - +
99E GLY* 3.3 13.2 - - - +
100E LYS* 2.9 28.9 + - - +
102E ALA* 1.3 78.2 - - + +
104E TYR* 1.3 65.6 + - + +
106E GLU* 3.4 12.4 + - - +
107E LYS* 3.1 23.8 + - - +
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Residues in contact with TYR 104 (chain E).
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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35A LYS* 3.0 29.0 + - - -
100E LYS* 2.7 34.0 + - + +
101E LEU 3.7 1.8 - - - +
103E GLU* 1.3 74.8 - - + +
105E ILE* 1.3 60.1 + - - +
107E LYS* 3.7 17.5 - - - -
108E ASP* 2.9 50.5 + - - +
136E TYR* 3.9 14.0 + + - -
141E ASP* 2.6 43.3 + - - -
143E LEU* 3.6 18.8 - - + -
200E PHE* 3.4 30.3 - + + -
204E LEU 4.8 9.1 + - - -
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Residues in contact with ILE 105 (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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97E PRO* 3.8 28.0 - - + -
101E LEU* 2.9 31.2 + - + +
102E ALA* 3.8 5.2 - - - +
104E TYR* 1.3 76.1 - - - +
106E GLU* 1.3 59.1 + - - +
109E PHE* 2.9 32.7 + - + +
110E GLY 3.6 0.2 + - - -
111E SER 3.8 8.9 - - - +
112E PHE* 3.9 15.9 - - + +
115E PHE* 3.6 51.6 - - + -
134E LEU* 5.1 1.1 - - + -
143E LEU* 3.7 19.1 - - + -
193E TRP* 4.8 2.9 - - + -
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Residues in contact with GLU 106 (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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17A TYR* 5.1 11.1 - - - -
34A GLN* 5.5 1.4 + - - -
102E ALA 3.1 15.5 + - - +
103E GLU* 3.5 14.3 - - - +
105E ILE* 1.3 79.0 - - - +
107E LYS* 1.3 57.9 + - - +
110E GLY* 2.6 47.7 + - - +
111E SER* 4.3 8.6 - - - +
112E PHE 5.2 1.8 - - - +
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Residues in contact with LYS 107 (chain E).
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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5C LYS* 2.8 27.5 + - + +
103E GLU 3.1 12.8 + - - +
104E TYR* 3.3 27.8 + - - +
106E GLU* 1.3 80.3 - - + +
108E ASP* 1.3 89.8 + - - +
110E GLY* 4.5 1.2 + - - -
140E THR 5.2 0.2 + - - -
141E ASP* 2.8 34.8 + - - -
142E ARG* 4.2 3.6 - - - +
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Residues in contact with ASP 108 (chain E).
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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5C LYS* 4.2 12.2 + - - +
55C ARG* 2.9 31.3 + - - +
104E TYR* 2.9 22.3 + - - +
107E LYS* 1.3 112.0 + - - +
109E PHE* 1.3 72.9 + - + +
142E ARG* 3.5 16.3 + - - +
143E LEU* 2.8 38.5 + - + +
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Residues in contact with PHE 109 (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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55C ARG* 3.5 32.3 - - - +
105E ILE* 2.9 26.4 + - - +
108E ASP* 1.3 80.1 - - + +
110E GLY* 1.3 57.8 + - - +
111E SER 3.2 13.5 - - - +
114E ARG* 3.1 24.8 - - + +
115E PHE* 3.7 42.4 - + + +
118E GLU* 3.5 28.9 - - - -
134E LEU* 4.6 0.9 - - + -
143E LEU* 4.0 39.7 - - + -
145E ILE* 3.8 27.4 - - + -
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Residues in contact with GLY 110 (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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55C ARG* 5.7 3.1 - - - -
106E GLU* 2.6 36.8 + - - +
107E LYS 4.4 1.4 + - - -
108E ASP 3.7 1.0 - - - -
109E PHE* 1.3 71.8 - - - +
111E SER* 1.3 60.0 + - - +
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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