Contacts of the helix formed by residues 271 - 286 (chain B) in PDB entry 3NX4
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 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A TYR* 4.5 16.2 - - + +
88B TRP* 4.8 1.6 - - + -
269B MSE 3.6 7.6 - - - +
270B THR* 1.3 92.2 - - + +
272B PRO* 1.3 76.6 - - + +
273B ALA* 3.1 5.0 + - + +
274B ARG* 3.2 13.0 + - + +
275B ARG* 2.9 19.1 + - - +
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Residues in contact with PRO 272 (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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88B TRP* 4.7 15.0 - - + -
107B ASP 5.2 7.9 - - - +
270B THR 3.6 2.4 - - - +
271B PRO* 1.3 88.4 - - + +
273B ALA* 1.3 57.7 + - - +
275B ARG* 3.3 11.4 + - + +
276B ALA* 2.8 31.8 + - - +
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Residues in contact with ALA 273 (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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271B PRO* 3.1 3.9 + - + +
272B PRO* 1.3 76.5 - - - +
274B ARG* 1.3 67.0 + - - +
276B ALA* 3.4 6.0 + - - +
277B GLU* 3.1 23.2 + - - +
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Residues in contact with ARG 274 (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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259A ASN* 6.1 2.4 - - - +
133B LEU* 4.0 25.8 + - + +
136B MSE 3.7 42.3 - - + +
137B ALA* 4.2 3.8 - - - +
140B ASP* 2.9 31.9 + - - -
270B THR* 4.2 9.4 - - + -
271B PRO* 3.2 16.2 + - + +
273B ALA* 1.3 78.5 - - - +
275B ARG* 1.3 58.4 + - - +
277B GLU* 3.2 15.2 + - - +
278B ALA* 2.9 29.2 + - - +
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Residues in contact with ARG 275 (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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86B THR* 2.9 38.0 + - - +
88B TRP* 3.3 25.4 - - - +
108B TRP 5.3 0.8 + - - -
109B LEU 5.8 0.2 - - - -
110B VAL* 3.7 28.6 - - + +
129B PHE* 3.6 27.1 - - + -
267B SER 3.1 24.4 + - - -
268B VAL 3.2 12.3 + - - -
270B THR* 3.0 43.7 + - + +
271B PRO 2.9 11.3 + - - +
272B PRO* 3.3 13.5 - - - +
273B ALA 3.2 0.2 - - - -
274B ARG* 1.3 76.9 - - - +
276B ALA* 1.3 61.2 + - - +
278B ALA* 3.3 3.8 + - - +
279B TRP* 3.2 30.5 + - + +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 5.0 10.7 - - + +
272B PRO 2.8 19.7 + - - +
273B ALA* 3.8 6.5 - - - +
275B ARG* 1.3 73.2 - - - +
277B GLU* 1.3 64.4 + - - +
279B TRP* 3.3 8.6 + - - +
280B ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 277 (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 MSE 3.2 27.0 - - + +
273B ALA 3.1 15.0 + - - +
274B ARG* 3.2 19.2 + - - +
276B ALA* 1.3 77.4 - - - +
278B ALA* 1.3 56.1 + - - +
280B ALA* 3.3 7.2 + - - +
281B ARG* 2.9 37.7 + - + +
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Residues in contact with ALA 278 (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 PHE* 3.6 24.2 - - + -
132B MSE 3.4 12.1 - - + +
133B LEU* 4.0 9.4 - - + -
136B MSE 3.8 22.9 - - - -
274B ARG 2.9 12.5 + - - +
275B ARG 3.3 8.7 + - - +
277B GLU* 1.3 75.8 - - - +
279B TRP* 1.3 58.2 + - - +
281B ARG* 3.3 0.9 + - - -
282B LEU* 3.0 33.9 + - - +
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Residues in contact with TRP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.7 35.0 - - + +
86B THR* 3.9 20.5 + - + -
110B VAL* 4.0 22.8 - - + +
113B PRO* 4.1 17.9 - - + +
116B LEU* 3.7 28.9 - - + +
121B ALA 3.7 21.8 - - - -
122B MSE 5.1 0.4 - - + -
124B ILE* 3.9 27.4 - - + -
125B GLY 4.0 5.6 - - - -
129B PHE* 3.4 29.5 - + + -
275B ARG* 3.2 30.0 + - + +
276B ALA 3.8 6.5 - - - +
278B ALA* 1.3 76.6 - - - +
280B ALA* 1.3 64.1 + - - +
282B LEU* 3.2 26.9 + - + +
283B VAL* 3.3 16.1 + - - +
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Residues in contact with ALA 280 (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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113B PRO* 4.8 7.1 - - + +
276B ALA 3.0 13.7 + - - +
277B GLU* 3.3 10.1 + - - +
279B TRP* 1.3 77.2 - - - +
281B ARG* 1.3 62.1 + - + +
283B VAL* 3.3 22.1 + - - +
284B LYS* 3.5 19.0 + - - +
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Residues in contact with ARG 281 (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 MSE 3.8 29.7 - - + +
136B MSE 4.2 13.5 - - - +
139B GLU* 2.9 41.0 + - - -
170B LEU* 4.0 11.1 - - - +
277B GLU* 2.9 34.7 + - + +
278B ALA 3.6 4.7 - - - +
279B TRP 3.3 0.2 - - - -
280B ALA* 1.3 72.8 - - + +
282B LEU* 1.3 62.6 + - - +
284B LYS* 3.0 29.2 + - - +
285B ASP* 2.8 62.5 + - - +
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Residues in contact with LEU 282 (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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116B LEU* 5.5 1.6 - - + -
124B ILE* 3.8 28.7 - - + -
128B GLY 4.1 8.3 - - - +
129B PHE* 4.2 7.9 - - + -
132B MSE 3.7 33.4 - - + -
162B THR* 4.8 0.4 - - + -
166B LEU* 4.3 10.3 - - + -
278B ALA 3.0 21.2 + - - +
279B TRP* 3.2 34.7 + - + +
281B ARG* 1.3 72.8 - - - +
283B VAL* 1.3 66.7 + - - +
285B ASP 4.5 0.2 - - - +
286B LEU* 3.2 48.8 + - + +
291B TYR* 4.3 4.8 + - - -
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Residues in contact with VAL 283 (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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113B PRO* 4.1 10.1 - - + -
114B ALA 3.9 16.2 - - - +
115B GLY* 3.6 29.9 - - - +
116B LEU* 3.9 28.0 - - + -
279B TRP 3.3 13.6 + - - +
280B ALA* 3.5 9.4 - - - +
281B ARG 3.2 0.4 - - - -
282B LEU* 1.3 78.5 - - - +
284B LYS* 1.3 67.1 + - + +
286B LEU 4.4 6.4 - - - +
291B TYR* 5.6 0.7 - - - -
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Residues in contact with LYS 284 (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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169B LYS* 3.6 16.2 + - - +
280B ALA* 3.7 19.3 + - - +
281B ARG* 3.0 36.7 + - - +
283B VAL* 1.3 84.4 - - + +
285B ASP* 1.3 67.4 + - - +
286B LEU 3.7 1.5 - - - +
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Residues in contact with ASP 285 (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 MSE 4.1 4.5 - - - +
166B LEU* 3.7 22.4 - - + +
169B LYS* 2.9 54.7 + - + +
170B LEU* 3.7 19.2 - - + +
281B ARG* 2.8 58.0 + - - +
284B LYS* 1.3 81.0 - - - +
286B LEU* 1.3 60.1 + - - +
287B PRO* 3.5 1.4 - - - +
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Residues in contact with LEU 286 (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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124B ILE* 3.7 24.2 - - + -
162B THR* 4.3 8.7 - - + -
165B ALA* 4.0 11.9 - - + -
166B LEU* 3.7 23.3 - - + +
282B LEU* 3.2 27.4 + - + +
283B VAL 4.4 6.2 - - - +
284B LYS 5.1 1.4 - - - +
285B ASP* 1.3 78.5 - - - +
287B PRO* 1.3 73.7 - - + +
288B GLU 3.7 0.9 + - - -
290B PHE* 3.6 44.0 - - + -
291B TYR* 3.6 25.4 + - + +
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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
------------------------------------------------------------
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