Contacts of the helix formed by residues 246 - 257 (chain A) in PDB entry 4N0N
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A HIS* 3.4 30.2 + - - -
244A TYR 3.6 2.0 + - - -
245A PHE* 1.3 76.7 - - - +
247A PRO* 1.3 65.2 - - - +
248A VAL 3.4 2.8 + - - -
249A ASP* 3.1 19.0 + - - +
250A LEU* 3.0 25.9 + - - +
270A CYS* 3.6 20.2 - - - +
509A MG 2.6 24.9 - - - -
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Residues in contact with PRO 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A HIS 5.1 0.7 - - - +
75A LEU* 3.7 19.2 - - + +
78A HIS* 3.8 27.4 - - + +
245A PHE 3.8 1.5 - - - +
246A SER* 1.3 88.3 - - - +
248A VAL* 1.3 57.3 + - - +
250A LEU* 3.9 1.6 - - + -
251A ALA* 3.0 14.2 + - - +
276A VAL* 3.9 24.5 - - + -
277A PRO 5.8 0.4 - - - +
280A LEU* 3.9 19.3 - - + -
281A TRP* 2.9 31.6 + - + +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.0 30.3 - - + +
78A HIS* 3.8 19.1 - - + -
79A ILE* 4.5 3.4 - - + -
136A ASP* 3.5 21.1 - - - +
137A THR 3.4 27.8 - - - +
138A LEU* 4.7 6.7 - - + -
141A VAL* 4.1 11.2 - - + -
246A SER* 3.1 1.2 - - - +
247A PRO* 1.3 76.5 - - - +
249A ASP* 1.3 59.7 + - - +
251A ALA* 3.2 6.2 + - - +
252A ARG* 3.0 40.6 + - - +
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Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PRO* 3.5 21.1 - - + +
229A GLN* 3.6 14.6 - - - +
245A PHE* 3.9 19.4 - - + -
246A SER* 3.1 16.8 + - - +
248A VAL* 1.3 74.3 - - - +
250A LEU* 1.3 59.1 + - - +
252A ARG* 3.0 31.7 + - - +
253A ILE* 2.9 32.8 + - - +
509A MG 3.5 13.8 - - - -
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A VAL* 5.3 1.1 - - + -
242A VAL* 4.0 37.0 - - + +
245A PHE* 4.3 9.5 - - + +
246A SER 3.0 18.0 + - - +
247A PRO* 4.4 0.9 - - + -
249A ASP* 1.3 76.2 - - - +
251A ALA* 1.3 57.0 + - - +
253A ILE* 3.3 23.0 + - + -
254A LEU* 2.9 45.8 + - + +
259A VAL* 5.6 0.4 - - + -
281A TRP* 3.8 36.3 - - + -
282A LEU* 4.4 17.3 - - + -
285A PHE* 4.9 3.6 - - + -
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.3 3.8 - - + -
141A VAL* 3.9 24.5 - - + -
146A ALA* 3.7 6.5 - - + +
247A PRO 3.0 20.0 + - - +
248A VAL* 3.3 8.5 - - - +
249A ASP 3.2 0.2 - - - -
250A LEU* 1.3 77.2 - - - +
252A ARG* 1.3 52.6 + - - +
255A THR* 2.7 38.5 + - - -
281A TRP* 3.5 27.7 - - + +
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Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASP* 2.9 24.0 + - - -
137A THR* 2.8 25.3 + - - -
138A LEU 4.2 0.6 - - - -
139A LYS* 3.0 35.5 + - - +
140A GLY* 3.9 16.1 - - - +
141A VAL* 3.8 6.1 - - + -
226A ARG* 5.6 0.2 - - - -
228A PRO 4.5 12.8 - - - +
229A GLN* 3.4 34.7 + - - +
248A VAL* 3.0 26.6 + - - +
249A ASP* 3.0 35.3 + - - +
251A ALA* 1.3 76.8 - - - +
253A ILE* 1.3 64.4 + - - +
255A THR* 3.3 10.7 + - - -
256A GLN* 3.4 17.3 + - - +
509A MG 3.4 8.9 - - - -
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 3.6 36.1 - - + -
226A ARG* 4.6 11.2 - - - +
228A PRO* 4.1 9.4 - - + +
233A SER* 4.8 1.1 + - - +
237A THR* 5.3 0.9 - - + -
239A VAL* 4.1 17.9 - - + -
245A PHE* 3.7 28.3 - - + -
249A ASP 2.9 18.7 + - - +
250A LEU* 3.3 20.6 + - + +
252A ARG* 1.3 75.5 - - - +
254A LEU* 1.3 59.2 + - + +
256A GLN* 3.1 24.4 + - - +
257A GLY 3.4 6.1 + - - +
259A VAL* 3.8 25.5 - - + +
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ALA* 3.6 23.4 - - + +
149A ASN* 2.7 36.0 + - - +
150A ALA* 3.9 28.9 - - + +
153A SER* 3.5 24.5 - - - +
250A LEU* 2.9 27.8 + - + +
253A ILE* 1.3 74.3 - - + +
255A THR* 1.3 56.2 + - - +
257A GLY 3.3 11.8 + - - +
259A VAL* 4.0 9.0 - - + -
281A TRP* 3.9 29.6 - - + -
285A PHE* 3.9 17.3 - - + -
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Residues in contact with THR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY 3.4 22.7 + - - +
142A VAL* 3.0 50.8 + - + +
145A LYS* 3.4 25.6 + - + +
146A ALA* 3.9 8.7 - - - +
149A ASN* 3.9 0.7 + - - -
251A ALA 2.7 24.4 + - - -
252A ARG 3.5 2.9 - - - -
253A ILE 3.2 0.4 - - - -
254A LEU* 1.3 75.7 - - - +
256A GLN* 1.3 64.1 + - + +
257A GLY 3.7 0.2 + - - -
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Residues in contact with GLN 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY 6.0 0.2 - - - +
149A ASN* 4.3 0.4 - - - -
226A ARG* 4.0 12.1 - - - +
231A GLY 4.9 3.3 + - - -
232A THR* 3.2 22.8 - - - +
233A SER* 2.9 50.0 + - - +
252A ARG 3.4 13.7 + - - +
253A ILE 3.1 9.5 + - - +
255A THR* 1.3 83.0 - - - +
257A GLY* 1.3 55.4 + - - +
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASN* 3.4 17.7 - - - +
233A SER* 5.4 2.4 - - - -
237A THR* 6.1 0.7 - - - -
253A ILE 3.4 9.3 + - - +
254A LEU* 3.3 17.0 + - - +
256A GLN* 1.3 81.5 - - - +
258A ARG* 1.3 66.3 + - - -
259A VAL* 3.8 6.6 - - - +
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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