Contacts of the helix formed by residues 114 - 124 (chain E) in PDB entry 3DUF
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 PRO 114 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E ILE* 4.2 0.6 - - - +
112E GLY 3.4 9.2 - - - +
113E LEU* 1.3 85.3 - - + +
115E LEU* 1.3 69.3 + - - +
116E TYR* 3.5 27.8 - - + -
117E GLN* 2.8 42.1 + - - +
118E ALA 3.5 5.2 + - - -
132E PRO* 4.3 10.3 - - + -
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Residues in contact with LEU 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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55E TYR* 4.0 20.0 - - + +
59E LEU* 3.9 27.4 - - + -
109E ILE* 3.8 25.7 - - + +
113E LEU 3.4 3.4 + - - -
114E PRO* 1.3 70.6 - - - +
116E TYR* 1.3 56.7 + - - +
118E ALA* 3.0 28.0 + - + +
119E PHE* 3.3 15.7 + - + -
324E GLU* 3.9 19.5 - - + +
325E ILE* 3.2 26.5 - - + -
328E ALA* 3.7 12.8 - - + -
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Residues in contact with TYR 116 (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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114E PRO* 2.9 33.4 + - + -
115E LEU* 1.3 76.5 - - - +
117E GLN* 1.3 67.4 + - + +
119E PHE* 3.5 6.9 + - - +
120E LEU* 3.2 37.4 + - + +
127E HIS* 3.0 39.1 + + - -
328E ALA* 3.5 33.4 - - + +
331E LYS* 3.5 55.2 + - + -
332E ALA* 4.2 2.1 - - - +
335E THR* 4.3 5.6 - - + -
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Residues in contact with GLN 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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113E LEU* 3.6 15.4 - - + +
114E PRO* 2.8 38.2 + - - +
116E TYR* 1.3 98.7 + - + +
118E ALA* 1.3 65.5 + - - +
119E PHE 3.1 0.4 - - - -
120E LEU* 4.1 5.2 - - + -
121E PHE* 2.9 19.9 + - - +
127E HIS* 2.7 44.2 + - + +
128E GLY* 3.4 18.6 - - - +
130E GLN 2.7 26.2 + - - +
132E PRO* 4.1 4.3 - - - +
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Residues in contact with ALA 118 (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 LEU* 6.2 1.1 - - + -
105E VAL* 4.1 19.9 - - + +
109E ILE* 3.3 29.4 - - + -
113E LEU* 4.3 7.5 - - + +
114E PRO 3.5 2.4 + - - -
115E LEU* 3.0 16.9 + - + +
117E GLN* 1.3 80.5 - - - +
119E PHE* 1.3 64.9 + - + +
121E PHE* 3.3 10.9 + - - +
122E SER* 3.2 19.2 + - - -
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Residues in contact with PHE 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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59E LEU* 4.2 7.2 - - + -
63E SER* 4.0 19.5 - - - -
66E LEU* 4.2 6.5 - - + -
72E LEU* 3.8 30.2 - - + +
115E LEU* 3.3 20.7 + - + -
116E TYR 3.7 6.5 - - - +
117E GLN 3.1 0.4 - - - -
118E ALA* 1.3 80.6 - - + +
120E LEU* 1.3 59.0 + - - +
122E SER* 3.3 5.1 + - - -
123E ARG* 3.1 32.8 + - - +
325E ILE* 3.9 39.7 - - + -
328E ALA* 3.8 37.0 - - + -
329E ILE* 4.0 12.3 - - + -
332E ALA* 4.5 9.4 - - + -
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Residues in contact with LEU 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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116E TYR* 3.2 28.2 + - + +
117E GLN* 3.1 3.6 + - - +
119E PHE* 1.3 74.9 - - - +
121E PHE* 1.3 60.7 + - - +
123E ARG* 4.5 10.1 - - - +
124E GLY 2.9 9.2 + - - -
125E HIS* 2.9 46.0 + - + +
127E HIS* 3.6 34.5 - - + -
128E GLY* 3.4 24.2 - - - +
332E ALA* 3.8 20.6 - - + +
335E THR* 3.8 24.0 - - + +
302H GLN* 5.8 0.2 - - - +
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Residues in contact with PHE 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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74E PHE* 4.4 31.4 - + - +
102E TYR* 4.9 1.6 - - + -
105E VAL* 4.3 15.7 - - + -
117E GLN 2.9 12.1 + - - +
118E ALA* 3.5 13.0 - - - +
120E LEU* 1.3 78.9 - - - +
122E SER* 1.3 66.4 + - - +
124E GLY* 3.6 9.2 + - - -
125E HIS 4.9 2.5 - - - +
128E GLY* 4.0 7.4 - - - +
129E ASN* 3.3 32.5 - - - +
139E PRO* 5.3 0.4 - - + -
140E PRO* 3.4 51.6 - - + -
142E ILE* 6.5 0.9 - - + -
125H PRO* 6.5 0.2 - - + -
126H GLU* 6.6 0.2 - - + -
300H PHE* 6.5 0.2 - + - -
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Residues in contact with SER 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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72E LEU* 3.7 18.8 - - - +
73E GLY* 3.1 19.0 + - - -
74E PHE* 2.9 49.0 + - - +
75E TYR* 4.6 7.0 - - - +
118E ALA 3.2 10.4 + - - -
119E PHE* 3.5 10.8 - - - -
120E LEU 3.2 0.4 - - - -
121E PHE* 1.3 86.2 - - - +
123E ARG* 1.3 62.4 + - - +
124E GLY* 4.5 0.3 - - - -
301H ALA* 5.6 1.2 - - - +
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Residues in contact with ARG 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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71E ARG* 3.1 29.8 + - - +
72E LEU* 4.2 11.9 - - + +
73E GLY* 4.0 8.8 - - - +
119E PHE* 3.1 16.3 + - - +
120E LEU* 4.1 11.6 - - - +
122E SER* 1.3 80.3 - - - +
124E GLY* 1.3 61.2 + - - +
125E HIS* 5.4 1.3 - - + -
329E ILE* 2.9 30.1 + - - +
332E ALA* 3.6 27.3 + - - +
333E ASP* 2.7 32.7 + - - +
123H HIS* 5.6 1.2 + - - -
301H ALA* 3.5 18.5 - - - +
302H GLN* 3.4 39.7 + - - +
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Residues in contact with GLY 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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120E LEU 2.9 8.8 + - - -
121E PHE 3.6 7.4 + - - -
122E SER 3.3 2.8 - - - -
123E ARG* 1.3 78.1 - - - +
125E HIS* 1.3 58.8 + - - -
338E GLN* 2.9 18.9 + - - -
300H PHE* 3.3 24.1 - - - +
301H ALA* 4.1 9.0 - - - -
302H GLN* 3.2 13.3 + - - +
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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