Contacts of the helix formed by residues 240 - 251 (chain A) in PDB entry 3G73
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 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A TYR* 1.3 77.3 - - - +
241A TYR* 1.3 64.8 + - - +
242A MET* 3.6 15.9 + - - +
243A ALA* 3.1 24.2 + - - +
244A MET* 3.0 20.9 + - - +
9C T 3.9 20.5 + - - -
10C A 3.2 22.4 - - - -
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Residues in contact with TYR 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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236A ARG* 3.4 16.2 + - - -
240A SER* 1.3 71.2 - - - +
242A MET* 1.3 56.5 + - - +
244A MET* 3.3 14.6 + - + +
245A ILE* 2.9 38.7 + - - +
266A ILE* 6.3 0.4 - - + -
273A PHE* 3.7 24.3 - + - -
281A TRP* 3.5 32.0 - + + +
284A SER* 3.6 23.3 - - - -
285A ILE* 3.7 25.3 - - + +
288A ASN* 3.7 23.3 - - + +
10C A 3.1 35.6 + - + +
11C T 2.7 30.0 + - + -
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Residues in contact with MET 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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240A SER* 3.1 15.6 - - - +
241A TYR* 1.3 79.1 - - - +
243A ALA* 1.3 64.6 + - + +
245A ILE* 3.6 0.6 + - - -
246A GLN* 3.2 44.6 + - - +
288A ASN* 4.0 16.0 + - - +
292A HIS* 4.1 27.1 - - + +
294A MET* 4.4 11.9 - - - +
295A PHE* 3.6 28.3 - - + -
9C T 4.5 17.9 - - - +
10C A 4.6 0.4 + - - -
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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 TYR* 4.1 13.2 - - + -
240A SER* 3.1 28.1 + - - +
242A MET* 1.3 78.8 - - + +
244A MET* 1.3 57.3 + - - +
246A GLN* 3.0 16.8 + - - +
247A PHE* 3.0 43.9 + - + -
318A LEU* 6.1 3.4 - - + -
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Residues in contact with MET 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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236A ARG* 5.6 1.8 - - - +
237A PRO* 4.3 6.3 - - + -
239A TYR* 3.5 35.7 - - + +
240A SER 3.0 15.9 + - - +
241A TYR* 3.7 30.3 - - + +
243A ALA* 1.3 72.3 - - - +
245A ILE* 1.3 65.8 + - - +
247A PHE* 3.3 10.2 + - + +
248A ALA* 3.0 23.4 + - - +
265A TRP* 4.0 3.6 - - - -
266A ILE* 4.2 20.8 - - + +
270A PHE* 3.7 30.7 - - + -
273A PHE* 3.7 33.7 - - + -
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR 2.9 23.2 + - - +
243A ALA 3.3 0.2 - - - -
244A MET* 1.3 76.9 - - - +
246A GLN* 1.3 61.5 + - - +
248A ALA* 3.2 7.7 + - - +
249A ILE* 3.0 32.3 + - + +
262A ILE* 4.4 11.4 - - + -
266A ILE* 4.8 0.2 - - - -
285A ILE* 3.8 37.5 - - + +
288A ASN* 3.7 29.8 - - + -
289A LEU* 3.7 21.8 - - + -
295A PHE* 3.5 33.7 - - + -
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Residues in contact with GLN 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 MET* 3.2 38.4 + - - +
243A ALA* 3.0 17.6 + - - +
245A ILE* 1.3 75.1 - - - +
247A PHE* 1.3 59.1 + - - +
249A ILE* 3.8 0.3 - - - +
250A ASN* 2.8 43.2 + - - +
294A MET* 3.5 24.4 - - + +
295A PHE* 3.8 17.5 - - + -
310A ILE* 4.1 15.8 - - + +
314A ALA 5.4 0.5 - - - +
315A ASN* 6.0 0.2 - - - -
316A ARG* 5.4 9.4 + - - +
318A LEU* 4.1 30.1 - - + +
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Residues in contact with PHE 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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239A TYR* 4.0 35.7 - + - -
243A ALA* 3.0 28.0 + - + -
244A MET* 3.6 11.9 - - - +
246A GLN* 1.3 76.4 - - - +
248A ALA* 1.3 63.2 + - - +
250A ASN* 3.8 1.4 - - - +
251A SER* 3.1 23.7 + - - -
265A TRP* 3.4 20.8 - - + -
270A PHE* 4.3 6.1 - + - -
318A LEU* 3.6 35.9 - - + -
319A THR* 4.0 16.3 - - - -
320A LEU* 3.7 43.4 + - + +
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Residues in contact with ALA 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 MET 3.0 12.9 + - - +
245A ILE 3.4 8.7 - - - +
247A PHE* 1.3 77.7 - - - +
249A ILE* 1.3 61.9 + - - +
251A SER* 2.6 23.7 + - - -
252A THR* 4.1 0.2 - - - +
257A MET* 3.5 26.0 - - - +
262A ILE* 4.3 16.2 - - + +
265A TRP* 3.6 31.4 - - + -
266A ILE* 4.9 0.4 - - + -
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Residues in contact with ILE 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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245A ILE* 3.0 36.0 + - + +
246A GLN 4.0 2.5 - - - +
248A ALA* 1.3 75.0 - - - +
250A ASN* 1.3 62.1 + - - +
251A SER 3.2 0.2 + - - -
252A THR* 2.7 26.5 + - - -
255A LYS* 3.3 31.8 - - + +
256A ARG* 3.8 4.5 - - - +
257A MET* 4.3 10.5 - - + -
262A ILE* 4.3 13.2 - - + -
295A PHE* 4.2 4.9 - - + -
308A TRP* 3.8 31.9 - - + +
309A THR 4.2 2.9 - - - -
310A ILE* 4.1 32.1 - - + +
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Residues in contact with ASN 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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246A GLN* 2.8 27.2 + - - +
247A PHE 3.8 1.6 - - - +
249A ILE* 1.3 72.8 - - - +
251A SER* 1.3 60.5 + - - +
252A THR 3.2 1.2 + - - +
255A LYS* 3.0 29.8 + - - +
310A ILE* 3.4 11.8 - - - +
315A ASN* 2.9 43.3 + - - -
317A TYR* 3.9 5.8 - - - -
318A LEU* 3.0 36.6 + - - +
319A THR* 3.6 16.9 - - + +
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE 3.1 11.9 + - - -
248A ALA 2.6 20.0 + - - -
250A ASN* 1.3 77.7 - - - +
252A THR* 1.3 60.3 + - - +
253A GLU 4.1 0.3 + - - -
257A MET* 3.9 5.5 - - - +
265A TRP* 3.3 29.7 + - - -
319A THR* 5.1 3.8 - - - -
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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