Contacts of the helix formed by residues 103 - 114 (chain A) in PDB entry 4EA3
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 THR 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LEU 3.5 16.6 - - - +
100A VAL* 2.7 20.2 + - - +
102A LEU* 1.3 76.0 - - + +
104A LEU* 1.3 60.6 + - - +
105A PRO* 3.3 2.9 - - - -
106A PHE* 3.0 12.7 + - - +
107A GLN* 2.8 50.8 + - - +
126A VAL* 4.4 24.0 - - + +
129A ILE* 3.9 29.2 - - + -
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Residues in contact with LEU 104 (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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58A TYR* 3.7 40.7 - - + +
61A VAL* 3.8 30.5 - - + -
62A CYS* 4.2 5.8 - - + +
100A VAL 3.9 11.0 - - - +
101A LEU* 3.6 22.0 - - + +
103A THR* 1.3 80.3 + - - +
105A PRO* 1.3 59.9 - - + +
107A GLN* 4.4 3.8 - - - +
108A GLY* 2.7 34.5 + - - -
309A TYR* 3.7 44.4 - - + -
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Residues in contact with PRO 105 (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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59A LEU* 5.2 15.7 - - + -
62A CYS* 3.7 21.1 - - + -
101A LEU 3.4 6.7 - - - +
102A LEU* 3.4 14.4 - - - +
103A THR 3.3 3.1 - - - -
104A LEU* 1.3 96.7 - - + +
106A PHE* 1.3 65.2 + - + +
108A GLY* 3.6 1.7 + - - -
109A THR* 2.9 28.9 + - - +
1503A OLA 4.2 6.1 - - + +
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Residues in contact with PHE 106 (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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102A LEU 3.6 21.8 - - - -
103A THR* 3.0 10.2 + - - +
105A PRO* 1.3 83.7 - - + +
107A GLN* 1.3 65.0 + - - +
108A GLY 3.1 1.3 - - - -
109A THR* 3.2 20.3 + - - -
110A ASP* 3.4 5.5 + - - +
116A TRP* 4.1 17.8 - + + -
118A PHE* 3.6 44.3 - + + -
122A LEU* 3.4 30.5 - - + -
126A VAL* 4.8 8.1 - - + -
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Residues in contact with GLN 107 (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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58A TYR* 4.3 11.8 + - + -
100A VAL* 5.2 1.0 - - - +
103A THR* 2.8 42.0 + - - +
104A LEU* 4.0 4.8 - - - +
106A PHE* 1.3 71.7 - - + +
108A GLY* 1.3 62.4 + - - +
110A ASP* 3.2 10.0 + - - +
111A ILE* 3.1 27.7 + - + +
116A TRP* 4.7 1.3 - - + -
126A VAL* 4.2 15.0 - - + +
130A ASP* 5.3 3.2 + - - +
309A TYR* 3.2 36.6 + - - -
1501A 0NN 3.2 51.0 + - + +
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Residues in contact with GLY 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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55A VAL* 3.3 35.1 - - - +
58A TYR* 4.0 15.8 - - - -
104A LEU 2.7 22.3 + - - -
105A PRO 3.9 2.2 - - - -
106A PHE 3.1 0.4 - - - -
107A GLN* 1.3 74.0 - - - +
109A THR* 1.3 60.1 + - - +
111A ILE* 3.5 2.4 + - - +
112A LEU* 3.3 11.4 + - - +
1503A OLA 4.2 4.7 - - - -
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Residues in contact with THR 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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105A PRO 2.9 20.6 - - - +
106A PHE 3.2 2.2 + - - +
108A GLY* 1.3 74.4 - - - +
110A ASP* 1.3 64.2 + - - +
112A LEU* 3.0 6.9 + - - +
113A LEU* 2.8 34.9 + - - +
117A PRO* 4.4 5.5 - - - +
118A PHE* 3.1 35.0 - - + -
1503A OLA 3.6 44.4 - - + -
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Residues in contact with ASP 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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106A PHE 3.4 4.1 + - - +
107A GLN 3.2 10.0 + - - +
109A THR* 1.3 82.3 + - - +
111A ILE* 1.3 58.8 + - - +
114A GLY* 2.8 28.8 + - - -
115A PHE* 3.4 32.7 + - - +
116A TRP* 3.3 36.0 - - + +
117A PRO* 5.2 0.2 - - + -
199A GLU* 5.4 1.0 - - - +
200A CYS 4.8 4.7 + - - -
302A ARG* 5.6 3.3 + - - -
1501A 0NN 3.9 24.9 - - + +
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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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51A LYS* 3.3 39.1 + - + +
54A ILE* 3.7 26.9 - - + -
55A VAL* 4.4 8.7 - - + -
58A TYR* 3.8 27.1 - - + +
107A GLN* 3.1 11.9 + - + +
108A GLY* 3.5 7.9 - - - +
109A THR 3.2 0.2 - - - -
110A ASP* 1.3 81.2 - - - +
112A LEU* 1.3 62.2 + - - +
114A GLY* 3.9 4.4 + - - -
302A ARG* 4.1 38.8 - - + +
1501A 0NN 5.4 4.3 - - + -
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Residues in contact with LEU 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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48A LEU 5.4 0.2 - - - +
51A LYS* 3.2 40.2 + - + -
52A VAL* 4.4 7.9 - - + -
55A VAL* 3.7 16.6 - - + -
108A GLY 3.3 11.2 + - - +
109A THR* 3.0 6.8 + - - +
111A ILE* 1.3 74.0 - - - +
113A LEU* 1.3 67.7 + - + +
1503A OLA 3.5 32.8 - - + -
63B VAL* 3.8 24.7 - - + -
67B LEU* 4.0 42.2 - - + +
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Residues in contact with LEU 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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109A THR* 2.8 24.5 + - - +
112A LEU* 1.3 75.2 - - - +
114A GLY* 1.3 61.7 + - - +
115A PHE* 3.4 34.4 - - + +
117A PRO* 3.4 32.8 - - + -
197A GLU* 5.7 0.3 - - - +
1503A OLA 3.6 49.6 - - + -
67B LEU* 3.8 20.2 - - + -
71B LEU* 5.5 4.5 - - + -
333B PHE* 5.3 12.3 - - + +
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Residues in contact with GLY 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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51A LYS* 5.5 2.2 - - - -
110A ASP* 2.8 15.1 + - - -
111A ILE* 4.4 4.5 - - - -
112A LEU 3.2 3.7 - - - -
113A LEU* 1.3 78.0 - - - +
115A PHE* 1.3 59.9 + - - +
197A GLU* 2.6 31.5 - - - +
198A ILE 4.8 0.2 - - - +
199A GLU* 6.0 0.3 - - - +
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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