Contacts of the helix formed by residues 273 - 283 (chain A) in PDB entry 2IG7
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A HIS* 4.2 3.3 - - - +
234A SER* 3.4 2.1 + - - +
235A PRO* 2.9 45.7 + - + +
237A VAL* 3.9 20.6 - - + -
239A CYS* 4.5 0.4 - - - -
271A ASN 3.5 1.0 + - - -
272A TYR* 1.3 72.2 - - - +
274A GLY* 1.3 62.7 + - - +
276A ASP* 3.2 13.7 + - - +
277A ILE* 3.2 23.6 + - + +
316A TYR* 3.3 38.6 + - - +
317A LEU* 4.4 13.7 - - - +
320A ALA* 5.6 2.0 - - - +
321A LYS* 5.2 9.9 - - - +
334A LEU* 6.2 2.4 - - - +
338A LEU* 3.6 18.0 - - - +
341A GLU* 2.9 32.8 + - - +
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Residues in contact with GLY 274 (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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234A SER* 3.0 16.4 + - - -
272A TYR 3.1 0.2 - - - -
273A ARG* 1.3 76.3 - - - +
275A PHE* 1.3 58.5 + - - +
277A ILE* 4.1 0.2 - - - +
278A GLY* 2.8 26.5 + - - -
341A GLU* 3.8 13.7 - - - -
342A VAL* 4.4 12.7 - - - -
345A TYR* 3.2 24.4 - - - +
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Residues in contact with PHE 275 (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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187A TRP* 4.0 16.6 - + - -
188A LEU* 3.6 29.8 - - + -
241A ASN* 3.3 43.5 - - - -
271A ASN* 3.4 14.4 - - - +
272A TYR* 2.9 13.0 + - + +
274A GLY* 1.3 74.2 - - - +
276A ASP* 1.3 63.1 + - - +
279A ASN* 2.8 40.9 + - + +
345A TYR* 3.5 18.1 - - + +
348A ALA* 3.6 17.3 - - + -
349A SER* 3.6 31.6 - - - -
352A PHE* 4.2 9.2 - + + -
353A TRP* 4.4 7.6 - - - -
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Residues in contact with ASP 276 (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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171A MSE 4.0 6.0 - - - +
175A HIS* 2.8 39.6 + - + +
239A CYS* 3.3 13.5 - - - -
240A HIS* 2.9 21.9 + - - +
241A ASN* 2.8 26.5 + - - -
243A ILE* 3.6 24.4 + - - +
272A TYR 3.6 2.0 + - - -
273A ARG 3.2 3.2 + - - +
275A PHE* 1.3 80.3 - - - +
277A ILE* 1.3 62.7 + - - +
279A ASN* 3.9 2.8 + - - +
280A HIS* 3.2 22.3 + - - +
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A MSE 3.7 22.0 - - - -
175A HIS* 4.9 0.2 - - + -
273A ARG* 3.2 33.4 + - + +
274A GLY 4.1 0.4 - - - +
276A ASP* 1.3 74.9 - - - +
278A GLY* 1.3 66.0 + - - +
280A HIS* 3.1 6.6 + - - +
281A PHE* 3.0 46.0 + - + -
312A PHE* 3.8 13.9 - - + -
313A ILE* 4.9 3.6 - - + -
316A TYR* 4.2 22.7 - - + -
338A LEU* 3.9 22.2 - - + -
342A VAL* 3.6 20.9 - - + -
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Residues in contact with GLY 278 (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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274A GLY 2.8 21.7 + - - -
277A ILE* 1.3 72.9 - - - +
279A ASN* 1.3 61.1 + - - +
281A PHE* 3.2 5.7 + - - +
282A CYS* 2.9 25.6 + - - -
342A VAL* 3.9 17.5 - - - +
346A ALA* 4.0 23.0 - - - +
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Residues in contact with ASN 279 (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 ASN 3.5 19.0 + - - -
242A ASP* 3.7 3.4 - - - +
243A ILE 3.6 21.4 - - - +
275A PHE* 2.8 32.8 + - + +
276A ASP* 3.9 4.9 + - - +
278A GLY* 1.3 73.2 - - - +
280A HIS* 1.3 62.4 + - - +
282A CYS* 3.2 4.2 + - - +
283A GLU* 3.1 33.0 + - - +
349A SER* 2.6 35.2 + - - +
353A TRP* 2.9 23.6 + - - +
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Residues in contact with HIS 280 (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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158A LEU* 4.0 26.6 + - + +
164A SER* 5.3 0.4 + - - -
167A ILE* 3.8 36.6 - - + +
171A MSE 4.0 14.4 - - + -
243A ILE* 2.8 33.2 + - + +
248A ILE* 4.4 3.8 - - + -
276A ASP 3.2 11.1 + - - +
277A ILE 3.1 9.3 + - - +
279A ASN* 1.3 78.5 - - - +
281A PHE* 1.3 68.3 + + - +
283A GLU* 3.0 15.3 + - - +
284A TRP* 3.2 31.2 + - - -
312A PHE* 3.6 27.9 - + - -
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Residues in contact with PHE 281 (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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277A ILE* 3.0 26.8 + - + -
278A GLY 3.5 7.2 - - - +
280A HIS* 1.3 84.3 - + - +
282A CYS* 1.3 62.0 + - - +
284A TRP* 3.0 31.5 + + - +
285A VAL 4.3 0.2 + - - -
303A TYR* 3.6 19.4 - - - +
304A PRO* 3.5 27.2 - - + +
308A GLN 5.3 0.2 - - - -
309A GLN* 3.6 45.3 - - + -
312A PHE* 3.6 37.9 - + + -
313A ILE* 4.7 3.8 - - + -
342A VAL* 3.6 33.0 - - + -
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Residues in contact with CYS 282 (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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278A GLY 2.9 18.2 + - - -
279A ASN* 3.2 8.9 + - - +
281A PHE* 1.3 74.5 - - - +
283A GLU* 1.3 57.3 + - + +
285A VAL* 3.0 28.9 + - - +
286A TYR* 3.5 9.2 - - - -
303A TYR* 4.0 16.4 - - - -
346A ALA* 3.7 19.5 - - - -
349A SER* 3.8 3.4 - - - +
350A HIS* 3.4 33.9 - - + -
377A ARG* 3.4 22.7 - - - +
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Residues in contact with GLU 283 (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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155A THR* 3.8 2.9 - - - +
158A LEU* 4.0 3.7 - - + +
242A ASP* 4.6 7.3 - - - +
243A ILE 4.2 4.3 - - - +
244A GLN* 3.6 34.0 + - + +
245A GLU* 3.7 5.9 - - - +
279A ASN* 3.1 26.1 + - - +
280A HIS 3.0 11.9 + - - +
282A CYS* 1.3 73.0 - - + +
284A TRP* 1.3 61.0 + - - +
285A VAL 3.0 6.9 + - - -
286A TYR* 3.4 6.7 + - - +
288A TYR* 2.7 30.9 + - - -
353A TRP* 5.1 4.2 + - - -
373A TYR* 4.3 5.1 + - - -
377A ARG* 4.4 7.8 + - - -
1024A UNX 2.4 48.3 - - - -
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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