Contacts of the helix formed by residues 239 - 248 (chain 2) in PDB entry 5IY8
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 GLN 239 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1942 PRO* 5.3 8.1 - - + +
1972 THR* 3.1 38.4 + - + +
1982 SER* 5.6 1.1 - - - +
2112 GLN* 4.3 3.6 - - - +
2142 TYR* 4.9 0.7 - - - -
2352 SER 4.4 3.9 - - - +
2362 PHE* 2.7 51.9 + - + +
2382 PHE* 1.3 79.2 - - + +
2402 LEU* 1.3 54.2 + - - +
2412 SER 3.1 0.2 - - - -
2422 PHE* 2.7 31.9 + - + +
2432 SER* 2.9 10.4 + - - -
2582 LEU* 3.3 13.4 - - + +
2612 PHE* 2.7 39.4 - - - -
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Residues in contact with LEU 240 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2362 PHE* 3.8 20.6 - - + +
2372 LEU* 2.7 45.5 - - + +
2382 PHE 3.2 1.2 - - - -
2392 GLN* 1.3 74.6 - - - +
2412 SER* 1.3 63.7 + - - +
2432 SER* 2.6 28.7 + - - +
2442 THR* 2.9 11.3 + - - -
2582 LEU* 5.0 3.6 - - + -
2622 LEU* 5.1 5.8 - - + -
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Residues in contact with SER 241 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1982 SER* 5.1 1.2 + - - -
2382 PHE* 3.5 26.9 + - - -
2392 GLN 3.1 0.2 - - - -
2402 LEU* 1.3 76.8 - - - +
2422 PHE* 1.3 61.9 + - - +
2442 THR* 3.0 14.2 + - - -
2452 LEU* 2.7 34.7 + - - +
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Residues in contact with PHE 242 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962 ILE 5.6 0.4 - - - -
1972 THR* 3.1 25.8 - - + +
1982 SER* 2.8 28.5 - - - +
1992 ALA 3.2 22.9 - - - -
2002 GLY* 3.6 14.4 - - - -
2072 ASP* 4.5 9.2 - - - -
2112 GLN* 5.7 5.8 - - - -
2382 PHE 5.3 0.2 - - - +
2392 GLN* 2.7 22.4 + - + +
2412 SER* 1.3 79.7 + - - +
2432 SER* 1.3 52.8 + - - -
2452 LEU* 2.5 40.9 - - + +
2462 GLY* 5.3 2.0 - - - -
2542 MET* 3.5 48.5 - - + -
2582 LEU* 5.7 6.1 - - + -
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Residues in contact with SER 243 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2392 GLN 2.9 6.2 + - - -
2402 LEU* 2.6 25.1 + - - +
2422 PHE* 1.3 76.1 - - - +
2442 THR* 1.3 59.1 + - - +
2452 LEU 2.5 18.9 - - - +
2472 LYS* 3.2 15.6 + - - +
2552 SER* 5.7 7.9 - - - +
2582 LEU* 2.9 44.7 - - - +
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Residues in contact with THR 244 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2402 LEU* 2.9 14.5 + - - +
2412 SER* 3.2 12.8 + - - -
2432 SER* 1.3 72.1 + - - +
2452 LEU* 1.3 71.0 + - + +
2472 LYS* 3.1 7.6 - - + +
2482 ASP* 3.0 41.4 + - - +
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Residues in contact with LEU 245 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002 GLY* 6.1 2.7 - - - -
2412 SER* 2.7 32.9 + - - +
2422 PHE* 2.5 30.1 - - + +
2432 SER* 2.5 15.1 - - - +
2442 THR* 1.3 80.7 - - + +
2462 GLY* 1.3 61.5 + - - +
2472 LYS 2.9 1.8 - - - -
2482 ASP* 3.7 17.9 - - - +
2492 TYR* 4.4 18.8 - - + -
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Residues in contact with GLY 246 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2422 PHE* 4.2 3.6 - - - -
2452 LEU* 1.3 73.9 - - - +
2472 LYS* 1.3 52.2 + - - -
2482 ASP 3.3 0.8 - - - +
2492 TYR* 2.5 44.1 - - - +
2512 VAL* 3.1 34.1 + - - +
2542 MET* 4.8 14.6 - - - -
2552 SER* 5.7 2.7 - - - -
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Residues in contact with LYS 247 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2432 SER 3.2 11.7 + - - +
2442 THR* 3.1 14.6 - - + +
2452 LEU 2.6 8.1 + - - -
2462 GLY* 1.3 67.2 - - - -
2482 ASP* 1.3 64.3 + - - +
2492 TYR 2.7 14.0 - - - +
2502 SER* 4.9 0.2 - - - -
2512 VAL 5.5 0.2 - - - -
2552 SER* 5.4 13.9 - - - -
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Residues in contact with ASP 248 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2442 THR* 3.0 30.7 + - - +
2452 LEU* 3.7 18.1 - - + +
2472 LYS* 1.3 81.8 - - - +
2492 TYR* 1.3 73.0 + - + +
2502 SER* 4.0 1.0 + - - -
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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