Contacts of the helix formed by residues 242 - 253 (chain E) in PDB entry 4IG9
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 THR 242 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241E ASN* 1.3 85.2 - - + +
243E ILE* 1.3 63.9 + - - +
244E GLU* 3.3 20.6 + - - +
245E ASP* 3.1 41.1 + - - +
246E ALA 3.3 7.8 + - - -
476E VAL* 3.6 6.1 - - - +
644F PHE* 5.5 4.0 - - + -
647F PRO 5.2 3.4 - - - +
650F TYR* 3.2 14.6 - - - +
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Residues in contact with ILE 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E THR* 1.3 70.9 - - - +
244E GLU* 1.3 87.4 + - - +
246E ALA* 3.1 8.2 + - + +
247E VAL* 3.0 22.1 + - - +
476E VAL* 4.6 2.7 - - - -
478E LEU* 4.1 16.4 - - + -
485E ILE* 6.0 0.2 - - + -
488E GLU* 4.4 4.5 - - + -
489E LEU* 4.2 20.9 - - + -
492E ARG* 3.8 35.0 - - - +
642F TYR* 5.2 3.1 - - + +
650F TYR* 3.1 32.2 + - + -
652F PHE* 4.1 26.2 - - + -
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Residues in contact with GLU 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E THR* 3.3 23.6 - - - +
243E ILE* 1.3 89.8 - - - +
245E ASP* 1.3 62.7 + - - +
247E VAL* 3.3 10.3 + - - +
248E LYS* 3.1 22.2 + - - +
492E ARG* 3.1 26.6 + - - +
642F TYR* 5.1 3.6 + - - -
650F TYR* 4.2 1.9 + - - -
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Residues in contact with ASP 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E ASP 3.8 13.5 - - - +
240E ILE* 4.1 17.5 - - + -
241E ASN* 3.2 20.1 + - - +
242E THR* 3.1 27.5 + - - +
244E GLU* 1.3 77.7 - - - +
246E ALA* 1.3 63.8 + - - +
248E LYS* 3.4 12.9 + - - +
249E LEU* 3.1 29.4 + - + +
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Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E THR 3.3 6.0 + - - +
243E ILE* 3.1 20.5 + - + +
245E ASP* 1.3 80.2 - - - +
247E VAL* 1.3 60.5 + - - +
249E LEU* 3.4 6.5 + - - +
250E LEU* 3.2 29.6 + - + +
462E ILE* 3.7 30.8 - - + +
476E VAL* 4.4 13.9 - - + +
478E LEU* 5.1 2.0 - - + -
489E LEU* 5.0 7.2 - - + -
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Residues in contact with VAL 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E ILE 3.0 15.3 + - - +
244E GLU* 3.6 9.9 - - - +
245E ASP 3.2 0.2 - - - -
246E ALA* 1.3 74.5 - - - +
248E LYS* 1.3 64.9 + - - +
250E LEU* 3.0 19.6 + - + +
251E GLN* 3.2 27.1 + - - +
489E LEU* 4.1 15.3 - - + +
492E ARG* 3.9 45.1 - - + +
493E LEU* 3.9 17.9 - - + -
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Residues in contact with LYS 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E GLU 3.1 13.5 + - - +
245E ASP* 3.4 15.3 + - - +
247E VAL* 1.3 76.0 - - - +
249E LEU* 1.3 67.4 + - + +
251E GLN* 3.2 14.9 + - - +
252E GLU* 3.1 53.2 + - + +
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Residues in contact with LEU 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E ILE* 4.0 26.7 - - + -
245E ASP* 3.1 19.3 + - + +
246E ALA* 3.6 7.4 - - - +
247E VAL 3.2 0.2 - - - -
248E LYS* 1.3 81.7 - - + +
250E LEU* 1.3 57.7 + - - +
252E GLU* 4.6 6.3 - - + +
253E CYS* 3.0 47.8 + - - +
435E LEU* 3.7 19.7 - - + +
460E PRO* 3.7 34.5 - - + -
462E ILE* 4.3 10.5 - - + -
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Residues in contact with LEU 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246E ALA* 3.2 17.6 + - + +
247E VAL* 3.0 12.6 + - - +
249E LEU* 1.3 77.1 - - - +
251E GLN* 1.3 59.7 + - - +
253E CYS 4.2 8.8 - - - +
256E ILE* 4.2 13.2 - - + +
329E PHE* 4.4 17.7 - - + -
338E LYS* 4.2 14.2 + - - +
435E LEU* 4.0 11.0 - - + -
437E ILE* 3.6 31.0 - - + -
462E ILE* 5.5 2.9 - - + -
489E LEU* 4.4 28.3 - - + -
493E LEU* 3.9 31.3 - - + +
497E TYR* 5.3 3.1 + - - -
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Residues in contact with GLN 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E VAL* 3.2 29.3 + - - +
248E LYS* 3.6 18.1 - - - +
249E LEU 3.2 0.4 - - - -
250E LEU* 1.3 79.8 - - - +
252E GLU* 1.3 64.2 + - + +
253E CYS 3.7 1.7 - - - +
338E LYS* 4.3 16.1 + - - +
492E ARG 4.4 8.3 + - - -
493E LEU* 3.7 24.1 + - + +
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Residues in contact with GLU 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E LYS* 3.1 46.4 + - + +
249E LEU* 4.6 7.6 - - + +
251E GLN* 1.3 84.4 - - + +
253E CYS* 1.3 66.1 + - - +
254E LYS* 3.8 14.4 + - - +
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Residues in contact with CYS 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E LEU* 3.0 42.9 + - - +
250E LEU 4.2 5.9 - - - +
251E GLN 4.7 1.2 - - - +
252E GLU* 1.3 81.7 + - - +
254E LYS* 1.3 59.3 + - - +
256E ILE* 4.1 9.8 - - + +
338E LYS* 4.2 16.8 - - - +
434E ASP* 3.3 40.6 - - - +
435E LEU* 3.7 21.8 - - + -
460E PRO* 5.8 0.4 - - - -
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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