Contacts of the helix formed by residues 249 - 260 (chain A) in PDB entry 1N3Y
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ALA* 4.1 2.2 - - - -
243A LYS* 4.1 10.3 + - - +
246A ASP 5.2 1.7 - - - +
247A SER 4.9 3.6 - - - +
248A LEU* 1.3 79.4 - - - +
250A TYR* 1.3 61.0 + - - +
251A LYS* 3.0 35.6 + - + +
252A ASP* 2.7 43.1 + - - +
253A VAL* 3.5 8.3 + - - +
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Residues in contact with TYR 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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209A THR* 3.4 17.4 - - + -
210A ALA* 4.1 18.6 - - + -
213A ILE* 4.1 14.4 - - + -
243A LYS* 3.7 22.2 - - + +
249A ASP* 1.3 73.9 - - - +
251A LYS* 1.3 57.4 + - - +
252A ASP 3.0 0.4 + - - -
253A VAL* 3.1 4.7 + - + -
254A ILE* 2.8 52.3 + - + +
281A GLU* 2.5 40.2 + - - -
284A ASP* 3.7 33.0 - - + -
285A ILE* 3.4 29.5 - - + +
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Residues in contact with LYS 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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249A ASP* 3.0 34.2 + - + +
250A TYR* 1.3 78.2 - - - +
252A ASP* 1.3 69.9 + - - +
253A VAL 3.4 0.2 - - - -
254A ILE* 5.2 0.7 - - - -
255A PRO* 3.3 26.9 - - + +
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Residues in contact with ASP 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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214A GLN* 5.0 3.2 - - - +
247A SER 4.9 0.9 - - - +
248A LEU* 3.8 16.4 - - + +
249A ASP* 2.7 49.1 + - - +
251A LYS* 1.3 94.3 - - - +
253A VAL* 1.3 64.8 + - + +
255A PRO* 4.4 2.2 - - - +
256A MET* 5.1 11.1 - - - +
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Residues in contact with VAL 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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210A ALA* 3.6 32.3 - - - +
213A ILE* 4.3 10.6 - - + +
214A GLN* 3.7 33.2 - - + +
217A VAL* 5.3 3.3 - - - +
218A HIS* 5.8 1.6 + - - -
248A LEU* 4.2 9.6 - - + -
249A ASP 4.0 10.8 - - - +
250A TYR* 3.5 14.6 - - + +
252A ASP* 1.3 85.8 - - + +
254A ILE* 1.3 77.8 + - + +
255A PRO* 3.5 2.2 - - - -
256A MET* 3.5 10.1 + - - +
257A ALA* 3.3 17.5 + - - +
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Residues in contact with ILE 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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213A ILE* 4.4 14.4 - - + -
250A TYR* 2.8 33.8 + - + +
251A LYS* 5.2 0.2 - - - -
253A VAL* 1.3 80.1 - - + +
255A PRO* 1.3 69.5 - - + +
257A ALA* 3.0 4.4 + - + +
258A ASP* 2.9 28.7 + - - +
264A ARG* 3.6 42.4 - - - +
284A ASP 3.4 26.7 - - - +
285A ILE* 4.0 8.3 - - - +
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Residues in contact with PRO 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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251A LYS* 3.3 31.9 - - + +
252A ASP 4.4 1.3 - - - -
253A VAL* 3.6 3.6 - - - +
254A ILE* 1.3 94.6 - - + +
256A MET* 1.3 59.5 + - + +
258A ASP* 3.3 11.2 + - + +
259A ALA* 3.0 25.1 + - - +
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Residues in contact with MET 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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217A VAL* 4.7 5.7 - - + +
218A HIS* 3.4 42.0 - - + +
252A ASP 5.1 10.3 - - - +
253A VAL* 3.5 9.0 + - - +
254A ILE 3.2 0.6 - - - -
255A PRO* 1.3 77.6 - - + +
257A ALA* 1.3 66.5 + - - +
259A ALA* 3.1 8.6 + - - +
260A ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 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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213A ILE* 5.1 1.3 - - + -
217A VAL* 4.0 29.3 - - + +
253A VAL 3.3 10.6 + - - +
254A ILE* 3.0 13.3 + - + +
256A MET* 1.3 78.4 - - - +
258A ASP* 1.3 62.9 + - - +
260A ALA* 3.3 1.7 + - - +
261A GLY 3.2 3.6 + - - -
262A ILE* 3.0 32.0 + - + +
264A ARG* 3.7 27.8 - - - +
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Residues in contact with ASP 258 (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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254A ILE* 2.9 19.2 + - - +
255A PRO* 3.5 12.4 - - + +
257A ALA* 1.3 76.2 - - - +
259A ALA* 1.3 65.5 + - - +
261A GLY* 3.0 15.5 + - - -
262A ILE 5.2 0.2 - - - -
264A ARG* 2.9 33.8 + - - +
287A SER* 4.9 1.6 + - - -
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Residues in contact with ALA 259 (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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255A PRO 3.0 13.0 + - - +
256A MET* 3.1 13.2 + - + +
258A ASP* 1.3 76.4 - - - +
260A ALA* 1.3 59.6 + - - +
261A GLY* 3.1 1.3 + - - -
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Residues in contact with ALA 260 (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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217A VAL* 5.0 4.3 - - + -
233A LYS* 4.8 8.3 - - - +
256A MET 3.0 15.7 + - - +
257A ALA 3.7 5.2 - - - +
258A ASP 3.2 0.4 - - - -
259A ALA* 1.3 75.4 - - - +
261A GLY* 1.3 60.6 + - - +
262A ILE* 3.4 22.6 + - + +
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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