Contacts of the helix formed by residues 238 - 250 (chain A) in PDB entry 1GOT
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 ARG 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA* 5.3 3.3 - - - +
38A GLY 4.3 6.4 + - - -
39A GLU* 3.8 37.8 + - - +
143A GLN* 2.7 27.7 + - - -
225A ASP* 3.5 40.4 + - + +
228A LEU* 2.9 31.4 + - - +
229A VAL 2.9 28.2 + - - -
230A LEU* 3.7 18.5 - - + +
231A ALA* 4.3 9.7 - - - +
236A MSE 3.5 0.4 + - - -
237A ASN* 1.3 71.9 + - - +
239A MSE 1.3 58.0 + - - +
241A GLU* 3.5 8.4 + - - +
242A SER* 3.0 26.0 + - - -
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Residues in contact with MSE 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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221A VAL* 3.8 21.1 - - + -
222A ALA 3.4 25.8 - - - +
223A LEU* 3.9 12.8 - - - +
225A ASP* 4.0 4.9 + - + +
226A TYR* 4.1 24.5 - - - +
237A ASN* 2.7 18.1 + - - +
238A ARG* 1.3 72.4 - - - +
240A HIS* 1.3 58.3 + - - +
242A SER* 3.3 6.6 + - - +
243A MSE 2.9 28.7 + - + +
282A CYS* 3.5 12.6 - - - -
283A TYR* 3.7 25.6 - - - +
299A ILE* 3.8 23.3 - - + -
303A PHE* 4.2 7.0 - - + -
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Residues in contact with HIS 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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237A ASN* 3.3 31.6 + - + +
239A MSE 1.3 76.3 - - - +
241A GLU* 1.3 57.6 + - - +
243A MSE 3.1 18.1 + - - +
244A LYS* 2.9 47.2 + - - +
281A ILE 5.3 1.8 - - - -
282A CYS* 3.0 44.0 + - - -
283A TYR* 5.1 3.6 - + - -
284A PRO* 5.9 0.9 - - + -
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Residues in contact with GLU 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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37A ALA* 5.6 1.3 - - - -
230A LEU* 3.8 25.7 - - + +
236A MSE 3.1 33.1 - - - +
237A ASN 3.1 8.7 + - - +
238A ARG* 3.5 12.1 - - - +
240A HIS* 1.3 79.4 - - - +
242A SER* 1.3 57.2 + - - +
244A LYS* 3.3 28.5 + - - +
245A LEU* 3.0 26.5 + - - +
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Residues in contact with SER 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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37A ALA* 4.6 18.2 + - - +
219A PHE* 3.9 7.4 - - - -
220A CYS 4.8 1.4 + - - -
221A VAL* 4.0 17.5 - - - +
222A ALA 6.1 0.7 - - - -
225A ASP* 5.9 2.0 - - - -
238A ARG 3.0 14.4 + - - -
239A MSE 3.4 11.9 - - - -
240A HIS 3.2 0.2 - - - -
241A GLU* 1.3 74.0 - - - +
243A MSE 1.3 59.6 + - - +
245A LEU* 3.3 8.2 + - - +
246A PHE* 3.0 27.4 + - - +
303A PHE* 3.5 19.4 - - - -
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Residues in contact with MSE 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 MSE 2.9 18.8 + - - +
240A HIS* 3.1 19.3 + - - +
242A SER* 1.3 75.4 - - - +
244A LYS* 1.3 60.5 + - + +
246A PHE 3.2 0.3 + - - -
247A ASP* 2.9 31.1 + - - +
283A TYR* 3.4 29.8 - - + -
302A GLN* 3.8 35.9 - - + +
303A PHE* 3.5 26.5 - - + -
306A LEU* 3.4 22.4 - - + +
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Residues in contact with LYS 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 MSE 4.7 10.7 - - - +
240A HIS* 2.9 29.4 + - - +
241A GLU* 3.3 35.8 + - - +
243A MSE 1.3 75.5 - - + +
245A LEU* 1.3 63.7 + - - +
247A ASP* 3.4 7.6 + - - +
248A SER* 3.0 25.7 + - - -
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Residues in contact with LEU 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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35A LEU* 5.6 3.1 - - + -
36A GLY* 3.5 17.9 - - - +
37A ALA* 3.5 34.1 - - + +
204A ARG* 3.6 38.4 - - - +
219A PHE* 3.7 11.7 - - + -
241A GLU 3.0 13.8 + - - +
242A SER* 3.5 9.0 - - - +
244A LYS* 1.3 76.8 - - - +
246A PHE* 1.3 56.7 + - - +
248A SER* 3.4 3.6 + - - -
249A ILE* 3.0 35.9 + - + +
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Residues in contact with PHE 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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219A PHE* 3.6 37.0 - + + -
242A SER 3.0 16.9 + - - +
243A MSE 3.7 3.8 - - - +
245A LEU* 1.3 74.0 - - - +
247A ASP* 1.3 57.7 + - - +
249A ILE* 4.5 2.2 - - + +
250A CYS* 2.7 63.4 + - + +
260A ILE* 4.1 17.5 - - + -
262A LEU* 4.0 20.2 - - + -
303A PHE* 3.1 45.8 - + + -
304A LEU* 4.9 1.8 - - + -
306A LEU* 4.0 12.1 - - + -
307A ASN 4.9 0.9 - - - -
315A ILE* 4.1 24.7 - - + -
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Residues in contact with ASP 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 MSE 2.9 17.3 + - - +
244A LYS* 3.6 8.8 - - - +
246A PHE* 1.3 74.1 - - - +
248A SER* 1.3 64.8 + - - +
250A CYS* 4.8 0.2 - - - -
251A ASN* 2.8 50.6 + - - +
306A LEU* 3.8 26.5 - - + +
308A MSE 5.7 0.5 - - - +
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Residues in contact with SER 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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204A ARG* 2.9 31.3 + - - -
244A LYS 3.0 17.9 + - - -
245A LEU 3.5 4.3 - - - -
247A ASP* 1.3 79.5 - - - +
249A ILE* 1.3 61.5 + - - +
251A ASN 4.0 1.0 - - - -
252A ASN* 3.3 25.6 + - - +
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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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35A LEU* 3.7 34.1 - - + -
204A ARG* 3.9 22.4 - - - +
208A ILE* 4.0 20.6 - - + -
217A ILE* 4.1 21.5 - - + -
219A PHE* 4.6 9.0 - - + -
245A LEU* 3.0 33.6 + - + +
246A PHE* 3.8 6.5 - - + +
248A SER* 1.3 75.8 - - - +
250A CYS* 1.3 68.3 + - - +
252A ASN* 3.2 19.0 + - + +
255A PHE* 3.5 13.8 - - + +
260A ILE* 5.1 3.1 - - + -
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Residues in contact with CYS 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 PHE* 2.7 40.8 + - + +
247A ASP* 4.2 1.6 - - - +
249A ILE* 1.3 75.8 - - - +
251A ASN* 1.3 60.3 + - - +
252A ASN 3.6 2.6 + - - +
255A PHE 4.4 4.9 - - - +
260A ILE* 4.1 12.6 - - + -
306A LEU 5.1 0.2 - - - +
307A ASN* 3.3 46.9 - - - -
309A ARG* 3.1 31.1 + - - -
315A ILE* 3.8 16.4 - - - -
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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
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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