Contacts of the helix formed by residues 98 - 113 (chain E) in PDB entry 3JCA
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 ALA 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97E GLU* 1.3 81.7 - - - +
99E THR* 1.3 58.8 + - - +
100E LYS* 4.0 21.5 - - + +
101E ASP* 2.8 36.0 + - - +
102E VAL* 3.0 11.1 + - - +
126E ALA* 6.2 0.2 - - - -
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Residues in contact with THR 99 (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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98E ALA* 1.3 73.8 - - - +
100E LYS* 1.3 53.8 + - - +
102E VAL* 3.3 8.7 + - - +
103E LEU* 2.8 31.5 + - - +
126E ALA* 5.5 1.8 - - - +
129E SER* 4.5 6.2 + - - -
131E SER* 3.4 30.4 + - - +
132E ILE* 4.1 7.4 - - + +
135E PHE* 3.8 26.1 - - + -
178F TYR* 4.2 14.6 - - + +
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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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94E ARG* 4.6 7.4 + - - +
98E ALA* 4.0 18.1 - - + +
99E THR* 1.3 76.4 - - - +
101E ASP* 1.3 72.9 + - - +
103E LEU* 4.0 3.4 - - - -
104E GLN* 2.9 23.2 + - - +
178F TYR* 3.4 58.2 - - + -
179F THR* 6.4 0.9 - - + -
182F HIS* 2.9 14.0 + - + +
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Residues in contact with ASP 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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79E HIS* 3.7 8.7 - - - +
94E ARG* 2.9 47.8 + - - +
95E THR* 4.4 4.0 + - - -
96E GLY* 3.3 37.1 + - - +
97E GLU 3.5 0.2 + - - -
98E ALA* 2.8 37.5 + - - +
100E LYS* 1.3 80.0 - - - +
102E VAL* 1.3 66.1 + - - +
104E GLN* 3.6 1.7 - - - +
105E HIS* 3.2 22.3 + - - +
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Residues in contact with VAL 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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64E MET* 4.0 14.5 - - + +
79E HIS* 3.8 23.3 - - + +
97E GLU 4.2 8.5 - - - +
98E ALA 3.0 16.4 + - - +
99E THR* 3.5 7.9 - - - +
101E ASP* 1.3 77.0 - - - +
103E LEU* 1.3 55.9 + - - +
105E HIS* 3.3 6.2 + - - +
106E LEU* 2.9 46.8 + - + +
126E ALA* 3.8 23.1 - - + +
127E TYR* 4.2 15.7 - - + -
132E ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 103 (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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99E THR 2.8 18.0 + - - +
100E LYS* 3.9 4.7 - - - +
102E VAL* 1.3 74.6 - - - +
104E GLN* 1.3 55.5 + - - +
106E LEU* 3.0 13.9 + - + +
107E ALA* 2.7 39.0 + - + +
110E PHE* 6.1 2.0 - - + -
135E PHE* 3.8 40.2 - - + -
139E TRP* 5.8 5.8 - - - +
176F LYS 5.1 7.4 - - - +
177F TYR* 5.9 2.0 - - + -
178F TYR* 3.8 23.8 - - + -
182F HIS* 3.7 22.0 - - + -
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Residues in contact with GLN 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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94E ARG* 3.5 36.4 + - - +
100E LYS 2.9 21.0 + - - +
101E ASP 3.6 5.8 - - - +
102E VAL 3.3 0.4 - - - -
103E LEU* 1.3 75.0 - - - +
105E HIS* 1.3 64.0 + - - +
107E ALA* 3.3 2.3 + - - +
108E GLN* 3.0 58.0 + - - +
179F THR* 3.2 12.6 + - - +
181F HIS* 3.7 31.7 + - - +
182F HIS* 3.2 29.5 + - - +
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Residues in contact with HIS 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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64E MET* 3.5 20.9 - - + -
79E HIS* 3.0 42.4 + - + -
80E VAL 3.7 0.8 - - - -
81E THR* 2.7 34.1 + - - -
90E PHE* 3.3 34.4 - + - -
92E THR* 2.8 31.6 + - - +
101E ASP 3.2 6.9 + - - +
102E VAL 3.4 8.1 - - - +
104E GLN* 1.3 79.5 - - - +
106E LEU* 1.3 56.8 + - + +
108E GLN* 3.2 4.1 + - - +
109E SER* 2.7 33.6 + - - -
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Residues in contact with LEU 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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62E TRP* 6.2 2.7 - - + -
64E MET* 4.0 22.0 - - - -
81E THR* 5.1 1.3 - - - +
102E VAL* 2.9 36.6 + - + +
103E LEU* 3.0 22.2 + - + +
105E HIS* 1.3 77.7 - - + +
107E ALA* 1.3 51.3 + - - +
109E SER* 2.6 25.8 + - - +
110E PHE* 2.7 45.1 + - + -
119E ILE* 4.8 12.6 - - + -
132E ILE* 5.4 4.5 - - + -
135E PHE* 4.6 15.3 - - + -
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Residues in contact with ALA 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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103E LEU* 2.7 25.1 + - + +
104E GLN* 3.6 6.7 - - - +
106E LEU* 1.3 71.9 - - - +
108E GLN* 1.3 63.1 + - - +
110E PHE* 3.2 20.7 + - - +
111E ALA* 3.2 10.2 + - - +
139E TRP* 6.2 0.7 - - - -
182F HIS* 4.3 20.0 - - + +
185F ALA* 3.9 26.4 - - + +
186F HIS* 4.8 6.7 - - + +
189F PHE* 5.2 0.2 - - - +
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Residues in contact with GLN 108 (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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90E PHE* 3.6 16.3 - - + -
91E ALA 5.0 0.2 - - - +
92E THR* 2.7 37.8 + - - +
94E ARG* 5.5 0.8 - - - +
104E GLN* 3.0 43.7 + - - +
105E HIS 3.5 6.1 - - - +
107E ALA* 1.3 79.1 - - - +
109E SER* 1.3 50.3 + - - +
111E ALA* 3.2 5.8 + - - +
112E TYR* 2.7 34.8 + - - +
112F TYR* 3.6 14.6 + - - +
181F HIS* 5.3 5.9 + - - +
185F ALA* 4.4 11.4 - - + -
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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
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62E TRP* 3.9 13.6 - - - -
81E THR* 4.7 2.6 + - - -
90E PHE* 3.5 22.4 - - - -
105E HIS* 2.7 23.9 + - - -
106E LEU* 2.6 30.1 + - - +
108E GLN* 1.3 69.8 - - - +
110E PHE* 1.3 63.5 + - - +
112E TYR* 4.0 2.9 - - - -
113E MET* 2.7 41.7 + - - +
114E GLY 3.2 4.9 + - - -
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Residues in contact with PHE 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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62E TRP* 5.1 4.7 - + - -
103E LEU* 6.1 2.2 - - + -
106E LEU* 2.7 52.1 + - + -
107E ALA* 3.6 10.5 - - - +
108E GLN 3.2 0.2 - - - -
109E SER* 1.3 79.7 - - - +
111E ALA* 1.3 59.2 + - - +
114E GLY* 2.9 45.6 + - - +
115E ILE* 3.9 11.2 - - + -
116E PRO* 4.6 3.1 - - + -
139E TRP* 3.5 58.1 - + + -
141E ILE* 3.9 25.6 - - + -
186F HIS* 6.5 0.2 - - - -
189F PHE* 3.0 30.9 - + + -
193F HIS* 3.7 0.9 + - - -
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Residues in contact with ALA 111 (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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107E ALA 3.2 8.9 + - - +
108E GLN* 3.2 10.4 + - - +
110E PHE* 1.3 80.9 - - - +
112E TYR* 1.3 59.3 + - - +
88F PHE* 5.2 5.2 - - - -
112F TYR* 4.0 18.9 - - + -
185F ALA* 4.0 19.5 - - + +
188F LEU* 4.8 10.3 - - + -
189F PHE* 3.9 8.8 - - - +
193F HIS* 2.7 28.9 + - - -
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Residues in contact with TYR 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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88E PHE* 3.5 31.9 - + - -
89E THR 3.2 22.0 + - - -
90E PHE* 3.4 42.8 - + + -
108E GLN 2.7 21.5 + - - +
109E SER* 4.0 3.8 - - - -
111E ALA* 1.3 76.8 - - - +
113E MET* 1.3 61.4 + - + +
188E LEU* 3.7 19.2 + - + +
192E ASN* 2.9 19.3 + - - +
193E HIS* 4.7 0.2 + - - -
111F ALA* 3.2 40.7 + - + -
112F TYR* 3.6 30.3 - + + +
193F HIS* 4.9 0.2 - - - -
208F TRP* 4.7 10.4 - - - -
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Residues in contact with MET 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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59E ARG* 3.2 14.9 + - - -
62E TRP* 3.4 34.1 - - + -
81E THR* 3.7 29.2 - - + +
82E VAL 3.8 4.9 - - - -
83E ASP* 3.3 35.7 - - + +
88E PHE* 3.6 25.4 - - + +
90E PHE* 4.0 10.1 - - + -
109E SER* 2.7 19.1 + - - +
112E TYR* 1.3 92.8 - - + +
114E GLY* 1.3 56.7 + - - +
207E HIS* 2.9 22.4 + - + +
193F HIS* 4.6 1.8 - - - -
208F TRP* 4.2 1.6 - - - -
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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