Contacts of the helix formed by residues 103 - 117 (chain E) in PDB entry 1CSE
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 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95E VAL 4.7 2.0 + - - +
102E GLY* 1.3 74.7 - - - -
104E TYR* 1.3 63.2 + - - +
105E SER* 2.9 13.7 + - - -
106E GLY* 2.8 36.5 + - - -
107E ILE* 3.1 17.1 + - - +
42I PRO* 4.3 2.5 - - - -
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Residues in contact with TYR 104 (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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102E GLY 4.3 0.2 + - - -
103E SER* 1.3 72.6 - - - +
105E SER* 1.3 57.2 + - - +
107E ILE* 3.3 5.6 + - + +
108E VAL* 2.8 36.7 + - + +
128E GLY* 4.6 3.7 - - - -
130E SER* 2.9 12.6 + - - -
131E GLY* 2.8 41.0 + - - -
132E SER* 4.0 24.2 - - - +
135E MET* 4.0 24.4 - - + +
167E TYR* 5.6 2.9 - - + -
40I GLY 2.6 29.4 + - - -
41I SER* 5.1 0.9 - - - -
42I PRO* 4.0 25.5 - - + +
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Residues in contact with SER 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E SER* 2.9 18.6 + - - -
104E TYR* 1.3 74.5 - - - +
106E GLY* 1.4 65.1 + - - +
108E VAL* 3.8 6.1 - - - +
109E SER* 3.0 29.0 + - - -
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Residues in contact with GLY 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PHE* 3.6 30.5 - - - +
95E VAL* 3.7 14.7 - - - +
103E SER* 2.8 19.2 + - - -
105E SER* 1.4 75.0 + - - +
107E ILE* 1.3 64.1 - - - +
109E SER* 3.4 1.8 + - - -
110E GLY 3.2 15.6 + - - -
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Residues in contact with ILE 107 (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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31E LEU* 4.3 1.9 - - + +
95E VAL* 3.9 31.9 - - + +
96E LEU* 4.6 4.9 - - + -
102E GLY 5.2 0.2 - - - -
103E SER 3.1 12.1 + - - +
104E TYR* 3.8 7.9 - - - +
106E GLY* 1.3 76.2 - - - +
108E VAL* 1.3 65.0 + - - +
110E GLY* 3.0 2.9 + - - -
111E ILE* 2.9 43.6 + - + +
124E MET* 4.0 17.7 - - - -
126E LEU* 3.8 18.2 - - + -
135E MET* 4.2 16.4 - - - -
42I PRO* 3.5 39.7 - - + -
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Residues in contact with VAL 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E TYR* 2.8 22.8 + - + +
105E SER* 3.8 7.4 - - - +
107E ILE* 1.3 75.0 - - - +
109E SER* 1.4 59.8 + - - +
111E ILE* 3.2 10.1 + - - +
112E GLU* 2.8 50.9 + - - +
132E SER* 5.1 0.9 - - - +
134E ALA* 3.9 17.7 - - + +
135E MET* 3.7 38.4 - - + +
138E ALA* 4.1 10.5 - - + +
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Residues in contact with SER 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PHE* 3.6 31.1 - - - -
105E SER* 3.0 19.5 + - - -
106E GLY* 3.7 3.3 - - - -
108E VAL* 1.4 79.5 - - - +
110E GLY* 1.3 57.6 + - - +
112E GLU* 3.4 13.3 + - - +
113E TRP* 2.8 28.9 + - - +
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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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31E LEU* 3.7 8.0 - - - +
50E PHE* 3.7 22.0 - - - -
93E VAL* 3.7 15.0 - - - +
95E VAL* 3.9 7.4 - - - -
106E GLY 3.2 6.5 + - - -
107E ILE 3.0 7.1 + - - -
109E SER* 1.3 77.7 - - - +
111E ILE* 1.3 56.7 + - - +
113E TRP* 3.3 2.6 + - - +
114E ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU* 3.6 18.2 - - + -
107E ILE* 2.9 31.2 + - + +
108E VAL* 3.5 6.7 - - - +
110E GLY* 1.3 76.3 - - - +
112E GLU* 1.3 54.9 + - - +
114E ALA* 3.4 5.7 + - - +
115E THR* 2.7 32.3 + - - +
122E ILE* 4.4 7.1 - - + +
124E MET* 4.1 11.2 - - + -
135E MET* 4.0 15.5 - - + -
138E ALA* 3.6 36.8 - - + +
139E VAL* 3.7 25.6 - - + +
142E ALA* 4.1 12.6 - - + -
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Residues in contact with GLU 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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108E VAL* 2.8 38.4 + - + +
109E SER* 3.6 11.8 + - - +
111E ILE* 1.3 73.3 - - - +
113E TRP* 1.4 66.8 + - - +
115E THR* 3.0 8.7 + - - -
116E THR* 2.9 25.8 + - - +
137E GLN* 5.7 1.2 - - - +
138E ALA* 4.7 10.1 - - + +
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Residues in contact with TRP 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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47E GLY* 4.1 22.6 + - - -
48E ALA* 3.6 22.8 - - + +
50E PHE* 3.8 18.4 - + + -
91E TYR* 4.0 25.4 - + + -
93E VAL* 3.6 30.5 - - + -
109E SER 2.8 20.3 + - - +
110E GLY 3.5 3.6 - - - +
112E GLU* 1.4 72.4 - - - +
114E ALA* 1.4 64.6 + - - +
116E THR* 3.2 3.0 + - - +
117E ASN* 2.7 76.4 + - + +
119E MET* 4.2 16.8 - - + -
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Residues in contact with ALA 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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29E ALA* 4.5 4.7 - - + -
31E LEU* 4.9 1.8 - - + -
110E GLY 3.0 17.4 + - - +
111E ILE* 3.6 5.6 - - - +
112E GLU 3.0 0.2 - - - -
113E TRP* 1.4 90.8 - - + +
115E THR* 1.3 60.7 - - - +
118E GLY 3.4 2.4 + - - -
119E MET* 3.0 41.0 + - + +
122E ILE* 3.5 33.9 - - + -
145E ARG* 3.7 1.3 + - - -
147E VAL* 5.4 0.7 - - - -
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Residues in contact with THR 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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111E ILE* 2.7 19.7 + - - +
112E GLU* 3.0 10.6 + - - -
114E ALA* 1.3 78.2 - - - +
116E THR* 1.3 62.0 + - - +
118E GLY* 3.8 0.9 + - - -
138E ALA 4.9 0.3 + - - -
141E ASN* 4.4 7.1 - - + +
142E ALA* 3.4 28.9 + - - +
145E ARG* 3.0 66.0 + - + +
147E VAL* 4.7 3.1 - - - -
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Residues in contact with THR 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLU* 2.9 16.2 + - - +
113E TRP* 4.0 4.3 - - - -
115E THR* 1.3 82.2 - - - +
117E ASN* 1.3 68.3 + - - +
118E GLY 3.4 0.9 + - - -
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Residues in contact with ASN 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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27E LYS* 4.4 5.0 - - - +
113E TRP* 2.7 78.1 + - + +
115E THR 3.4 0.2 - - - -
116E THR* 1.3 91.9 - - - +
118E GLY* 1.3 62.8 + - - +
119E MET* 3.3 14.2 - - + +
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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