Contacts of the helix formed by residues 135 - 146 (chain B) in PDB entry 2NUE
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 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B LEU* 3.3 55.6 - - + -
86B LYS* 5.2 4.9 - - + -
87B LEU* 3.9 17.7 - - + -
109B PHE* 3.9 19.7 - + - -
113B TRP* 3.5 27.8 - + - -
131B PHE* 3.0 44.4 - + + +
132B TYR 3.4 0.4 + - - -
134B LEU* 1.3 100.6 - - + +
136B LYS* 1.3 59.7 + - - +
137B GLU* 2.7 10.6 + - - -
138B ASP* 2.7 30.5 + - - +
139B ILE* 2.7 20.0 + - + +
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU* 4.1 22.7 - - + +
58B TYR* 4.5 23.5 + - + +
132B TYR* 2.9 52.8 + - + +
133B LYS* 5.9 0.7 - - - +
135B PHE* 1.3 77.3 - - - +
137B GLU* 1.3 62.5 + - - +
139B ILE* 3.4 1.7 + - - +
140B LEU* 2.9 31.8 + - + +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B TYR 4.0 4.0 - - - +
133B LYS 3.8 13.6 - - - +
134B LEU* 3.3 2.5 - - - -
135B PHE 2.7 25.2 + - - -
136B LYS* 1.3 79.4 - - - +
138B ASP* 1.3 93.2 + - - +
140B LEU* 3.9 6.6 - - - +
141B SER* 3.0 26.9 + - - -
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 4.1 7.2 - - + -
82B LEU* 6.1 0.6 - - + +
83B LEU* 4.1 17.0 - - + +
86B LYS* 2.6 43.1 + - - +
134B LEU 4.2 5.0 - - - +
135B PHE* 2.7 23.6 + - - +
137B GLU* 1.3 104.7 - - - +
139B ILE* 1.3 56.2 + - - +
141B SER* 2.7 19.4 + - - -
142B ALA* 3.7 6.6 + - - +
147B ARG* 4.7 2.4 + - - -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 4.6 17.0 - - + +
54B LEU* 3.7 28.3 - - + -
74B LEU* 3.7 31.0 - - + -
79B PHE* 3.8 24.2 - - + -
83B LEU* 5.0 1.6 - - + -
131B PHE* 3.9 29.4 - - + -
135B PHE* 2.7 26.7 + - + +
136B LYS 3.7 3.6 - - - +
138B ASP* 1.3 71.6 - - + +
140B LEU* 1.3 57.2 + - - +
141B SER 2.9 4.3 - - - -
142B ALA* 2.7 26.9 + - - +
143B ILE* 3.1 15.9 + - + +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU* 4.8 1.5 - - + +
58B TYR* 3.3 63.7 - - + +
136B LYS* 2.9 23.4 + - + +
137B GLU* 4.1 5.6 - - - +
139B ILE* 1.3 73.3 - - - +
141B SER* 1.3 55.8 + - - +
143B ILE* 3.4 11.3 + - + -
144B LYS* 2.9 52.9 + - + +
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLU 3.0 14.7 + - - -
138B ASP* 2.7 25.9 + - - -
139B ILE 2.9 0.4 - - - -
140B LEU* 1.3 74.6 - - - +
142B ALA* 1.3 59.5 + - - +
143B ILE 3.0 1.6 - - - -
144B LYS* 3.2 8.1 + - - +
145B GLU* 2.8 36.7 + - - +
147B ARG* 3.8 14.7 + - - -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 5.2 0.4 - - - -
73B TYR* 3.8 14.6 - - + -
74B LEU* 4.0 14.6 - - + -
79B PHE* 4.1 6.1 - - + -
138B ASP 4.1 0.9 - - - +
139B ILE 2.7 13.7 + - - +
141B SER* 1.3 77.1 + - - +
143B ILE* 1.3 57.2 + - - +
145B GLU 3.6 0.2 + - - -
146B GLY 2.9 22.0 + - - -
147B ARG* 2.9 52.0 + - + +
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU* 4.8 3.8 - - + +
55B LEU* 3.5 39.7 - - + -
58B TYR* 3.3 28.7 - - + +
59B SER* 4.2 2.7 - - - +
60B PRO* 4.2 21.9 - - + +
70B LEU* 4.2 16.5 - - + +
74B LEU* 4.3 10.8 - - + -
139B ILE* 3.1 18.4 + - + +
140B LEU* 3.5 20.2 - - + +
141B SER 3.0 0.4 - - - -
142B ALA* 1.3 72.5 - - - +
144B LYS* 1.3 69.3 + - - +
145B GLU 3.0 0.9 - - - -
146B GLY* 2.8 17.8 + - - -
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PRO* 6.2 1.6 - - - -
140B LEU* 2.9 45.3 + - + +
141B SER* 3.7 8.1 - - - +
143B ILE* 1.3 75.1 - - - +
145B GLU* 1.3 61.8 + - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B SER 2.8 16.6 + - - +
142B ALA 3.6 4.0 - - - +
144B LYS* 1.3 80.3 - - - +
146B GLY* 1.3 59.4 + - - +
147B ARG* 3.1 42.1 + - + +
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Residues in contact with GLY 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 4.7 5.2 - - - -
142B ALA 2.9 1.4 + - - -
143B ILE 2.8 18.5 + - - -
145B GLU* 1.3 75.9 - - - +
147B ARG* 1.3 68.8 + - - +
148B VAL* 3.2 19.5 + - - +
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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