Contacts of the helix formed by residues 238 - 248 (chain A) in PDB entry 3NTY
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A TYR* 2.6 36.7 + - + +
234A VAL 3.8 1.2 + - - -
235A LEU 3.1 18.8 + - - +
236A LEU 3.2 2.1 - - - +
237A GLU* 1.3 76.4 - - - +
239A PRO* 1.4 74.7 - - - +
240A VAL* 2.9 32.0 + - - +
241A LEU* 3.1 19.4 + - + +
242A CYS* 3.0 21.0 + - - +
299A LEU* 3.6 19.7 - - - +
301A ARG* 5.3 0.2 + - - -
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Residues in contact with PRO 239 (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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196A TYR* 5.1 0.4 - - - +
237A GLU 3.3 7.8 - - - +
238A ASP* 1.4 91.3 - - - +
240A VAL* 1.3 60.2 + - + +
242A CYS* 3.4 7.5 + - + +
243A ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 240 (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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238A ASP* 2.9 13.9 + - - +
239A PRO* 1.3 74.6 - - + +
241A LEU* 1.3 67.6 + - - +
243A ALA* 3.9 6.0 - - + +
244A LEU* 2.9 43.8 + - + +
295A ALA* 4.6 18.6 - - + +
299A LEU* 3.8 30.1 - - + -
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Residues in contact with LEU 241 (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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195A PRO* 4.1 21.1 - - + -
235A LEU* 3.7 29.8 - - + +
236A LEU* 4.8 3.6 - - + -
238A ASP* 3.1 19.5 + - + +
240A VAL* 1.3 76.8 - - - +
242A CYS* 1.3 56.4 + - - +
244A LEU* 4.4 2.7 - - + -
245A ALA* 2.9 28.1 + - - +
252A PRO* 3.9 27.2 - - + +
255A ILE* 3.7 29.8 - - + +
256A ALA* 4.5 7.0 - - + +
296A ILE* 4.4 15.7 - - + -
299A LEU* 3.8 18.4 - - + -
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Residues in contact with CYS 242 (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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236A LEU 5.6 0.4 - - - +
237A GLU 5.4 3.4 - - - +
238A ASP 3.0 13.6 + - - +
239A PRO* 3.6 11.4 - - + +
240A VAL 3.2 0.2 - - - -
241A LEU* 1.3 75.4 - - - +
243A ALA* 1.3 59.9 + - - +
245A ALA* 3.3 3.0 + - - +
246A LYS* 3.0 56.7 + - - +
252A PRO* 4.0 17.6 - - + +
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Residues in contact with ALA 243 (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 PRO 2.9 17.3 + - - +
240A VAL* 4.0 6.1 - - + +
242A CYS* 1.3 74.9 - - - +
244A LEU* 1.3 58.8 + - + +
246A LYS* 3.3 11.8 + - - +
247A LYS* 3.0 30.2 + - - +
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Residues in contact with LEU 244 (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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240A VAL* 2.9 35.6 + - + +
241A LEU* 3.9 4.0 - - - +
243A ALA* 1.3 78.0 - - + +
245A ALA* 1.3 60.4 + - - +
247A LYS* 3.5 4.4 + - + -
248A HIS* 2.4 41.5 + - + +
255A ILE* 3.7 19.0 - - + +
288A LEU* 4.8 2.0 - - + -
292A GLU* 3.9 41.5 - - + +
295A ALA* 5.1 3.4 - - + -
296A ILE* 3.5 39.7 - - + -
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Residues in contact with ALA 245 (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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241A LEU 2.9 20.2 + - - +
242A CYS* 3.4 6.7 - - - +
243A ALA 3.3 0.2 - - - -
244A LEU* 1.3 77.2 - - - +
246A LYS* 1.3 60.8 + - + +
248A HIS 3.2 2.3 + - - -
249A LYS 3.1 4.3 + - - -
250A ARG* 2.8 45.4 + - - +
251A THR* 3.4 20.9 - - - -
252A PRO* 3.6 7.4 - - + -
255A ILE* 3.6 9.3 - - - +
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Residues in contact with LYS 246 (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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242A CYS* 3.0 43.6 + - - +
243A ALA* 3.6 9.9 - - - +
245A ALA* 1.3 74.2 - - + +
247A LYS* 1.3 63.7 + - - +
248A HIS 3.2 1.2 + - - -
249A LYS* 3.3 27.5 + - - +
250A ARG 4.6 0.9 - - - +
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Residues in contact with LYS 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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243A ALA 3.0 17.8 + - - +
244A LEU* 3.8 4.0 - - + +
245A ALA 3.3 0.2 - - - -
246A LYS* 1.3 75.5 - - - +
248A HIS* 1.3 74.4 + - + +
249A LYS* 3.5 3.3 + - - +
292A GLU* 3.6 23.8 + - - +
324A ZN 4.6 4.3 - - - -
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Residues in contact with HIS 248 (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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244A LEU* 2.4 42.7 + - + +
245A ALA 3.2 1.8 + - - +
246A LYS 3.1 0.6 - - - -
247A LYS* 1.3 90.0 - - + +
249A LYS* 1.3 72.3 + - - +
250A ARG* 2.9 26.3 + - + +
255A ILE* 4.3 7.0 - - + +
286A PHE* 4.5 13.5 - + + +
287A GLN 4.1 12.6 - - - -
288A LEU* 4.1 10.1 - - + +
292A GLU* 3.1 22.2 + - - -
324A ZN 2.1 31.6 - - - -
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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