Contacts of the strand formed by residues 118 - 129 (chain E) in PDB entry 3DOY
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 ARG 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C ASN* 5.3 2.0 - - - +
116C GLY 5.9 0.2 - - - -
118C ARG* 6.2 4.7 - - - +
34E THR* 4.1 10.7 - - - +
45E TYR* 3.3 57.0 - - + -
46E LYS 4.2 0.2 - - - -
47E ASN* 3.8 13.2 - - - +
116E GLY 4.0 0.8 + - - +
117E ASP* 1.3 72.2 - - - +
119E LEU* 1.3 61.0 + - - +
120E GLU* 3.2 43.3 + - - +
140E GLN 3.3 8.3 - - - +
141E VAL* 4.0 11.4 - - - +
142E ASP 4.7 2.5 + - - +
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Residues in contact with LEU 119 (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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45E TYR* 3.1 4.0 - - - -
46E LYS* 2.9 44.7 + - + +
48E ILE* 4.1 11.7 - - + -
65E PHE* 4.1 16.2 - - + -
70E ILE* 3.8 25.6 - - + -
113E VAL* 3.9 25.1 - - + -
117E ASP 3.7 3.0 - - - -
118E ARG* 1.3 68.2 - - - +
120E GLU* 1.3 60.9 + - - +
121E TYR* 3.8 32.8 + - + +
139E ALA* 3.9 12.3 - - + -
140E GLN 3.7 1.1 - - - +
141E VAL* 4.0 7.4 - - + -
146E VAL* 3.9 17.9 - - + -
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Residues in contact with GLU 120 (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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34E THR* 5.0 1.3 + - - +
43E VAL* 4.1 12.8 - - + +
44E ALA 3.4 12.8 - - - +
45E TYR* 3.8 2.9 - - + -
118E ARG* 3.2 36.3 + - - +
119E LEU* 1.3 72.3 - - - +
121E TYR* 1.3 60.3 + - - +
122E HIS* 2.4 39.4 + - + +
139E ALA* 3.2 3.8 - - - -
140E GLN* 2.6 55.7 + - - +
143E GLY* 5.7 2.4 + - - -
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Residues in contact with TYR 121 (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 LEU* 2.9 28.7 + - - +
30E VAL* 4.1 4.7 - - + -
42E ILE 3.8 0.5 - - - +
43E VAL* 3.3 5.5 - - - +
44E ALA* 2.6 46.9 + - + +
45E TYR* 4.0 1.8 - - - -
46E LYS* 3.6 26.8 - - + +
65E PHE* 5.0 0.7 - - - -
69E LEU 4.5 2.4 + - - -
70E ILE* 3.6 12.8 - - + -
73E GLY* 3.4 26.3 - - - -
74E MET* 3.4 19.3 - - + -
77E SER* 3.4 26.5 - - - +
119E LEU* 3.9 25.6 - - + +
120E GLU* 1.3 74.8 - - - +
122E HIS* 1.3 62.0 + - - +
123E LEU* 3.7 11.4 - - + -
138E THR 3.6 3.1 - - - -
139E ALA* 4.6 5.4 - - + -
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Residues in contact with HIS 122 (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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41E LYS* 5.7 5.1 + - - -
42E ILE 3.8 4.3 - - - -
43E VAL* 4.0 21.1 - - + +
120E GLU* 2.4 47.3 + - + -
121E TYR* 1.3 81.0 - - - +
123E LEU* 1.3 62.3 + - - +
124E GLU* 5.5 2.2 - - + -
137E GLY* 3.0 7.5 - - - -
138E THR* 2.8 41.8 + - - +
140E GLN* 3.6 29.5 + - - +
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Residues in contact with LEU 123 (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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41E LYS* 3.2 5.7 - - - +
42E ILE* 2.9 47.9 + - + +
74E MET* 3.5 46.9 - - + +
77E SER* 3.9 8.1 - - - -
78E GLY* 4.3 5.2 - - - +
81E LEU* 5.1 1.3 - - + -
121E TYR* 3.7 26.5 - - + -
122E HIS* 1.3 81.1 - - - +
124E GLU* 1.3 62.3 + - - +
135E VAL* 3.8 28.3 - - + -
136E GLY* 3.8 17.3 - - - -
149E ALA 5.2 0.9 - - - +
151E LEU* 5.3 2.2 - - + -
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Residues in contact with GLU 124 (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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40E GLN 3.2 5.8 - - - +
41E LYS* 3.8 30.6 + - + +
122E HIS* 5.5 2.0 - - + -
123E LEU* 1.3 80.0 - - - +
125E VAL* 1.3 65.1 + - - +
126E LEU* 3.3 3.3 + - + +
135E VAL* 3.3 4.6 - - - -
136E GLY 2.9 35.4 + - - +
137E GLY* 5.6 2.4 - - - -
2008E BEN 3.5 42.5 + - + +
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Residues in contact with VAL 125 (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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39E ASN 3.5 18.0 - - - +
40E GLN* 2.6 20.9 + - - +
81E LEU* 3.5 24.2 - - + -
124E GLU* 1.3 69.8 - - - +
126E LEU* 1.3 63.2 + - - +
127E LYS* 3.7 13.2 - - - +
128E HIS* 3.7 29.8 - - + -
133E TRP* 3.7 26.9 - - + -
134E GLN 3.9 5.2 - - - +
135E VAL* 4.2 5.2 - - + -
2008E BEN 3.3 22.9 + - - -
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Residues in contact with LEU 126 (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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124E GLU* 3.8 11.9 - - + +
125E VAL* 1.3 73.4 - - - +
127E LYS* 1.3 64.0 + - - +
134E GLN* 2.7 26.2 + - - +
135E VAL 3.9 4.9 - - - -
136E GLY* 3.8 24.5 - - - +
150E GLU* 4.0 26.0 - - + +
2008E BEN 3.5 50.6 + - + -
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Residues in contact with LYS 127 (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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125E VAL* 3.4 7.1 - - - +
126E LEU* 1.3 83.7 - - + +
128E HIS* 1.3 66.6 + - - +
129E LYS* 4.4 29.0 - - - +
132E ILE 4.1 0.5 - - - +
134E GLN* 2.7 53.3 + - + +
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Residues in contact with HIS 128 (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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39E ASN* 3.9 29.8 + - - +
86E LEU* 5.6 1.7 - - + +
125E VAL* 3.7 18.6 - - + -
127E LYS* 1.3 85.2 - - - +
129E LYS* 1.3 67.0 + - - +
130E GLY 4.9 3.0 + - - -
132E ILE 3.2 7.2 - - - +
133E TRP* 3.4 45.6 + + + -
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Residues in contact with LYS 129 (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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127E LYS* 4.4 26.0 - - - +
128E HIS* 1.3 78.4 - - - +
130E GLY* 1.3 66.7 + - - +
131E MET 3.2 0.5 + - - -
132E ILE* 2.9 30.7 + - + +
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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