Contacts of the helix formed by residues 130 - 142 (chain B) in PDB entry 3NT2
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 ASP 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B MET 3.7 1.8 + - - -
127B ARG* 3.0 14.3 + - - +
129B TYR* 1.3 78.0 - - - +
131B SER* 1.3 54.6 + - - +
132B GLY* 2.6 33.8 + - - -
133B TYR* 3.2 10.6 + - + +
134B VAL* 2.8 35.8 + - - +
250B LEU* 4.6 2.1 - - - +
275B ARG* 3.4 17.1 + - - +
276B PHE* 3.2 39.6 - - + -
279B ALA* 4.4 5.7 - - + +
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Residues in contact with SER 131 (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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129B TYR 3.6 3.8 + - - -
130B ASP* 1.3 74.4 + - - +
132B GLY* 1.3 54.1 + - - +
134B VAL* 3.6 9.7 - - - +
135B GLN* 2.8 51.9 + - - +
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Residues in contact with GLY 132 (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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130B ASP* 2.6 18.8 + - - -
131B SER* 1.3 75.4 + - - +
133B TYR* 1.3 56.6 + - - -
135B GLN* 3.0 11.4 + - - +
136B LEU* 2.9 27.7 + - - +
250B LEU* 3.7 16.8 - - - -
251B PRO* 4.2 18.5 - - - +
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Residues in contact with TYR 133 (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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127B ARG* 3.2 71.0 + - + +
130B ASP* 3.2 15.2 + - + +
132B GLY* 1.3 74.7 - - - +
134B VAL* 1.3 57.6 + - - +
136B LEU* 3.1 15.7 + - + +
137B LYS* 2.9 29.3 + - - +
177B GLU* 5.3 1.6 - - - +
180B VAL* 3.6 33.1 - - + +
181B LEU* 5.3 0.4 - - + +
183B TRP* 4.3 7.4 - - + -
184B LEU* 3.8 20.4 - - + +
237B ILE* 3.7 12.0 - - - +
238B GLN 5.3 0.2 + - - -
239B CYS* 4.3 15.4 - - + +
250B LEU* 4.0 25.5 - - + +
276B PHE* 4.2 10.1 - + - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG 3.5 21.5 - - - +
129B TYR* 4.2 6.1 - - - +
130B ASP 2.8 28.1 + - - +
131B SER* 3.6 9.2 - - - +
133B TYR* 1.3 73.6 - - - +
135B GLN* 1.3 59.4 + - + +
137B LYS* 3.4 7.5 + - - +
138B GLU* 3.0 29.4 + - + +
183B TRP* 4.8 4.3 - - + -
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Residues in contact with GLN 135 (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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131B SER* 2.8 39.0 + - - +
132B GLY* 3.0 8.4 + - - +
134B VAL* 1.3 74.4 - - + +
136B LEU* 1.3 64.7 + - + +
138B GLU* 3.4 8.5 + - - +
139B ALA* 3.1 23.4 + - - +
251B PRO* 4.5 16.8 - - - +
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Residues in contact with LEU 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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132B GLY 2.9 12.1 + - - +
133B TYR* 3.4 24.7 - - + +
135B GLN* 1.3 77.0 - - + +
137B LYS* 1.3 61.9 + - - +
139B ALA* 3.2 4.8 + - - +
140B LEU* 3.0 26.6 + - - +
184B LEU* 3.9 16.4 - - + -
239B CYS* 4.7 11.0 - - - +
241B ILE* 4.7 7.4 - - + -
248B ILE* 3.7 37.7 - - + +
249B LYS* 4.1 19.3 - - - +
250B LEU* 3.7 33.2 - - + +
251B PRO* 6.0 0.2 - - + -
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Residues in contact with LYS 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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133B TYR 2.9 16.5 + - - +
134B VAL* 3.6 5.2 - - - +
136B LEU* 1.3 74.3 - - - +
138B GLU* 1.3 53.7 + - - +
140B LEU* 3.3 3.9 + - - +
141B ASP* 2.8 68.2 + - - +
183B TRP* 2.9 65.0 + - + +
184B LEU* 3.5 27.6 + - + +
186B ASN* 5.1 6.9 - - - +
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Residues in contact with GLU 138 (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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134B VAL* 3.0 19.2 + - + +
135B GLN* 3.5 9.0 - - - +
137B LYS* 1.3 77.9 - - - +
139B ALA* 1.3 59.0 + - + +
141B ASP* 3.4 7.7 + - - +
142B ASN* 3.0 49.3 + - - +
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Residues in contact with ALA 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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135B GLN 3.1 13.3 + - - +
136B LEU* 3.2 7.6 + - - +
138B GLU* 1.3 75.6 - - - +
140B LEU* 1.3 65.7 + - - +
142B ASN* 3.2 1.7 + - - -
143B HIS 3.2 3.5 + - - -
144B VAL* 3.1 49.9 + - + +
145B ILE* 4.8 0.8 + - - -
248B ILE* 4.1 22.4 - - + -
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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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136B LEU 3.0 21.2 + - - +
137B LYS 3.6 3.8 - - - +
139B ALA* 1.3 76.8 - - - +
141B ASP* 1.3 63.4 - - - +
143B HIS* 3.2 17.9 + - - +
145B ILE* 4.2 17.5 - - + -
146B GLY 5.1 3.6 - - - +
148B PRO* 3.9 27.6 - - + -
184B LEU* 3.7 40.4 - - + +
185B VAL* 4.8 4.0 - - + -
241B ILE* 3.8 27.4 - - + -
248B ILE* 3.9 15.9 - - + -
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Residues in contact with ASP 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 LYS* 2.8 60.3 + - - +
138B GLU* 3.8 7.3 + - - +
139B ALA 3.3 0.2 - - - -
140B LEU* 1.3 75.8 - - - +
142B ASN* 1.3 61.8 + - - +
143B HIS* 3.3 19.0 + - - -
184B LEU 5.1 0.9 - - - +
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Residues in contact with ASN 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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138B GLU* 3.0 43.2 + - - +
139B ALA* 3.2 4.5 + - - +
140B LEU 3.1 0.4 - - - -
141B ASP* 1.3 80.3 - - - +
143B HIS* 1.3 77.5 + - - +
144B VAL* 3.2 13.7 + - + +
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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