Contacts of the helix formed by residues 133 - 145 (chain D) in PDB entry 6NFJ
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 PHE 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D SER 4.4 5.4 - - - +
129D ASP* 2.9 37.0 + - + +
130D SER 4.2 4.5 - - - -
132D ILE* 1.3 99.4 - - + +
134D LEU* 1.3 60.4 + - - +
135D GLU* 3.4 3.4 - - - +
136D LYS* 3.5 45.7 + - + +
137D ASP* 3.0 28.0 + - - +
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D SER 4.0 3.7 + - - +
131D TYR 5.3 0.7 - - - +
132D ILE 3.5 4.4 + - - -
133D PHE* 1.3 74.7 - - - +
135D GLU* 1.3 66.2 + - - +
136D LYS 3.1 0.4 - - - -
137D ASP* 3.1 11.6 + - + +
138D LEU* 3.0 44.0 + - + +
149D TYR* 6.3 0.4 - - + -
174D TYR* 3.8 36.8 - - + +
177D THR* 4.2 14.1 - - + +
178D LEU* 3.7 57.7 - - + +
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LYS* 3.2 32.2 - - + +
133D PHE* 3.4 1.0 - - - +
134D LEU* 1.3 78.7 - - - +
136D LYS* 1.3 61.5 + - + +
138D LEU* 3.4 10.0 - - - +
139D SER* 3.1 26.4 + - - +
185D ARG* 3.1 27.1 + - - -
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Residues in contact with LYS 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PHE* 3.5 56.5 + - + +
134D LEU 3.1 0.6 - - - -
135D GLU* 1.3 80.1 - - + +
137D ASP* 1.3 66.3 + - - +
138D LEU 3.3 0.2 - - - -
139D SER* 3.6 6.7 + - - -
140D ALA* 3.3 20.1 + - - +
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Residues in contact with ASP 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D SER* 3.1 32.9 + - - +
133D PHE* 3.0 17.4 - - - +
134D LEU* 3.1 17.4 + - + +
136D LYS* 1.3 79.9 - - - +
138D LEU* 1.3 65.4 + - - +
140D ALA* 3.2 9.4 + - - +
141D LEU* 3.0 31.2 + - + +
149D TYR* 5.1 10.2 + - + +
174D TYR* 5.4 0.2 + - - -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LEU* 3.0 32.3 + - + +
135D GLU* 3.4 24.7 - - - +
136D LYS 3.3 0.2 - - - -
137D ASP* 1.3 77.7 - - - +
139D SER* 1.3 62.7 + - - +
141D LEU* 3.2 20.9 + - + +
142D ASP* 3.1 18.7 + - - +
178D LEU* 4.4 12.3 - - + -
181D ALA* 3.6 25.6 - - + -
182D LEU* 4.1 26.0 - - + -
185D ARG* 3.5 32.9 - - - +
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D GLU* 3.1 15.9 + - - +
136D LYS* 3.9 9.6 - - - -
137D ASP 3.3 0.4 - - - -
138D LEU* 1.3 78.7 - - - +
140D ALA* 1.3 61.8 + - - +
142D ASP* 3.3 14.3 + - - +
143D PHE* 3.2 18.5 + - - +
185D ARG* 5.0 3.8 + - - +
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LYS 3.3 11.5 + - - +
137D ASP* 3.2 13.3 + - - +
139D SER* 1.3 77.2 - - - +
141D LEU* 1.3 64.3 + - - +
143D PHE* 3.2 21.1 + - - +
144D ILE* 3.4 13.0 + - - +
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ILE* 3.9 9.0 - - + -
137D ASP* 3.0 22.3 + - + +
138D LEU* 3.2 19.3 + - + +
140D ALA* 1.3 77.2 - - - +
142D ASP* 1.3 57.7 + - - +
144D ILE* 3.4 4.8 + - - +
145D GLY* 2.8 27.0 + - - -
146D VAL* 3.7 26.9 + - + +
149D TYR* 3.7 41.3 - - + -
182D LEU* 3.9 28.0 - - + -
185D ARG* 6.0 0.4 - - - -
187D ILE* 4.0 15.4 - - + +
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Residues in contact with ASP 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU 3.1 11.1 + - - +
139D SER* 3.6 12.1 - - - +
140D ALA 3.3 0.4 - - - -
141D LEU* 1.3 74.8 - - - +
143D PHE* 1.3 67.3 + - - +
145D GLY* 3.5 10.4 + - - +
185D ARG* 2.9 46.5 + - - +
187D ILE* 4.9 4.0 - - - +
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Residues in contact with PHE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D SER 3.2 10.1 + - - +
140D ALA* 3.2 15.4 + - - +
141D LEU 3.2 0.4 - - - -
142D ASP* 1.3 79.9 - - - +
144D ILE* 1.3 77.3 + - + +
145D GLY* 4.5 0.2 - - - -
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Residues in contact with ILE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ILE* 5.1 17.7 - - + -
140D ALA 3.4 13.2 + - - +
141D LEU* 4.2 4.3 - - - +
143D PHE* 1.3 92.5 - - + +
145D GLY* 1.3 63.2 + - - +
146D VAL* 3.6 25.8 - - + -
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Residues in contact with GLY 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D TRP* 5.5 3.6 - - - +
141D LEU 2.8 15.0 + - - -
142D ASP* 4.0 9.0 - - - -
143D PHE 3.3 2.6 - - - -
144D ILE* 1.3 80.8 - - - +
146D VAL* 1.3 61.0 + - - +
147D SER* 4.0 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