Contacts of the helix formed by residues 203 - 221 (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 PHE 203 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1602 LEU* 4.3 10.2 - - + +
2012 PHE 3.4 2.8 + - - +
2022 GLN* 1.3 73.5 - - - +
2042 LEU* 1.3 94.0 + - + +
2052 LEU* 2.9 37.2 - - + -
2062 LEU* 3.3 22.3 + - + +
2072 ASP* 2.9 28.3 + - - +
2542 MET* 4.5 1.6 - - + -
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Residues in contact with LEU 204 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2032 PHE* 1.3 99.8 - - + +
2052 LEU* 1.3 65.6 + - + +
2072 ASP* 3.1 6.8 + - + +
2082 THR* 3.0 25.7 + - - +
2512 VAL* 3.6 13.7 - - + -
2532 GLY* 4.9 8.7 - - - +
2542 MET* 3.4 45.5 - - + +
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Residues in contact with LEU 205 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1602 LEU* 5.9 0.7 - - + -
1642 VAL* 4.5 7.1 - - + +
2032 PHE* 2.9 34.9 - - + -
2042 LEU* 1.3 76.8 - - + +
2062 LEU* 1.3 66.9 + - + +
2082 THR* 3.9 9.2 - - + -
2092 PRO* 2.8 32.4 - - - +
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Residues in contact with LEU 206 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1602 LEU* 2.9 75.6 - - + +
1632 MET* 2.9 37.0 - - + +
1642 VAL* 3.6 9.8 - - + -
1962 ILE* 4.2 2.6 - - + +
2022 GLN* 4.3 11.9 - - + -
2032 PHE* 3.3 23.5 + - + +
2052 LEU* 1.3 81.0 - - + +
2072 ASP* 1.3 63.8 + - - +
2082 THR 3.4 0.2 + - - -
2092 PRO* 3.4 2.6 - - - +
2102 ALA* 3.0 22.6 + - - +
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Residues in contact with ASP 207 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1962 ILE* 4.5 6.6 - - - +
1972 THR* 5.5 2.8 - - - +
2022 GLN* 3.4 19.6 - - - +
2032 PHE 2.9 15.5 + - - +
2042 LEU* 3.1 9.5 + - + +
2062 LEU* 1.3 76.6 - - - +
2082 THR* 1.3 63.1 + - - +
2102 ALA* 3.0 6.9 + - - +
2112 GLN* 2.7 42.0 + - + +
2422 PHE* 4.5 9.3 - - - -
2542 MET* 3.0 45.9 - - + +
2572 SER* 5.0 4.0 - - - +
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Residues in contact with THR 208 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2042 LEU 3.0 13.0 + - - +
2052 LEU* 3.3 19.7 - - + +
2072 ASP* 1.3 75.5 - - - +
2092 PRO* 1.3 83.2 - - + +
2112 GLN* 3.2 8.6 + - - +
2122 LEU* 3.0 40.9 + - - +
2572 SER* 4.6 6.5 + - - -
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Residues in contact with PRO 209 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1642 VAL* 3.3 45.5 - - + +
1672 PRO* 4.2 6.7 - - + +
1682 SER* 5.0 8.5 - - - +
1712 VAL* 4.3 2.3 - - - +
2052 LEU 2.8 24.5 - - - +
2062 LEU 4.1 2.9 - - - +
2072 ASP 3.4 0.2 - - - -
2082 THR* 1.3 93.4 - - + +
2102 ALA* 1.3 62.2 + - - +
2122 LEU* 3.7 13.9 - - + +
2132 TRP* 3.1 22.7 + - - +
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Residues in contact with ALA 210 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1672 PRO* 4.8 5.8 - - - -
1932 PRO* 4.4 7.1 - - + +
1962 ILE* 2.9 41.5 - - + +
1972 THR* 4.1 6.7 + - - +
2062 LEU 3.0 8.4 + - - +
2072 ASP* 3.0 9.2 + - - +
2092 PRO* 1.3 75.7 - - - +
2112 GLN* 1.3 72.4 + - - +
2132 TRP* 3.2 12.0 + - - +
2142 TYR* 3.2 19.9 + - - +
2612 PHE* 4.0 1.0 - - - -
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Residues in contact with GLN 211 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1972 THR* 3.6 17.7 + - - +
2072 ASP* 2.7 32.3 + - - +
2082 THR* 3.6 5.4 - - - +
2102 ALA* 1.3 80.5 - - - +
2122 LEU* 1.3 67.7 + - + +
2142 TYR* 3.1 5.9 + - - +
2152 PHE* 3.0 21.8 + - - +
2392 GLN* 4.3 7.7 - - - +
2422 PHE* 5.7 6.1 - - - -
2542 MET* 4.5 2.8 + - - +
2572 SER* 3.0 45.8 - - - +
2582 LEU* 4.1 2.2 - - - +
2602 ASN* 5.9 2.2 - - + -
2612 PHE* 2.9 39.6 - - + -
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Residues in contact with LEU 212 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1712 VAL* 3.8 12.6 - - + +
2082 THR* 3.0 39.7 + - - +
2092 PRO* 3.7 11.9 - - + +
2112 GLN* 1.3 80.4 - - + +
2132 TRP* 1.3 57.2 + - - +
2152 PHE* 3.2 10.0 + - + +
2162 MET* 2.8 31.4 + - - +
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Residues in contact with TRP 213 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1672 PRO* 4.0 10.8 - - + -
1702 ALA* 2.9 40.6 - - + -
1712 VAL* 2.9 46.4 - - + +
1742 ASP* 2.7 34.3 - - - -
1792 LEU* 4.6 6.1 - - + -
1842 LEU* 5.2 6.7 - - + -
1892 GLU* 5.4 6.5 - - + -
1902 PRO* 4.7 19.9 - - + +
1932 PRO* 3.3 39.1 - - + +
1942 PRO* 5.5 1.0 - - + +
2092 PRO 3.1 11.1 + - - +
2102 ALA* 3.4 7.0 - - - +
2112 GLN 3.2 0.2 - - - -
2122 LEU* 1.3 76.1 - - - +
2142 TYR* 1.3 64.5 + + + +
2162 MET 3.2 1.2 + - - -
2172 LEU* 2.8 52.6 + - + +
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Residues in contact with TYR 214 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1932 PRO* 5.9 1.6 - - + -
1942 PRO* 5.5 12.6 - - + -
2102 ALA 3.2 4.1 + - - +
2112 GLN 3.1 2.0 + - - -
2132 TRP* 1.3 87.5 - + + +
2152 PHE* 1.3 70.1 + - - +
2172 LEU* 3.1 7.5 + - + +
2182 GLN* 3.0 35.5 + - + +
2332 ILE* 2.8 58.9 + - + +
2352 SER* 6.0 0.7 - - - -
2362 PHE* 3.5 16.0 - - + +
2392 GLN* 4.9 1.1 - - - -
2612 PHE* 2.9 64.8 - + + -
2642 HIS* 5.1 0.4 - - + -
2652 LEU* 3.1 19.4 - - - +
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Residues in contact with PHE 215 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2112 GLN 3.0 12.5 + - - +
2122 LEU* 3.4 15.7 - - + +
2142 TYR* 1.3 81.1 - - + +
2162 MET* 1.3 71.7 + - + +
2192 TYR* 2.9 35.4 + + + -
2602 ASN* 4.1 22.9 - - + -
2612 PHE* 6.0 0.7 - - + -
2632 GLN* 6.3 0.9 - - + -
2642 HIS* 2.9 69.5 + + + -
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Residues in contact with MET 216 (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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1712 VAL* 2.9 57.7 - - + +
1742 ASP* 3.6 3.1 - - + +
1752 LEU* 3.1 50.7 - - + +
2122 LEU 2.8 8.5 + - - +
2132 TRP 3.8 2.0 - - - +
2152 PHE* 1.3 86.2 - - + +
2172 LEU* 1.3 59.7 + - - +
2192 TYR* 3.1 12.2 + - + +
2202 LEU* 2.8 28.4 + - - +
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Residues in contact with LEU 217 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1742 ASP* 3.2 24.8 + - - +
1812 GLN* 4.7 5.9 - - - +
1842 LEU* 4.1 20.9 - - + -
1902 PRO* 5.0 14.1 - - + -
2132 TRP* 2.8 38.0 + - + +
2142 TYR* 3.1 11.8 + - + +
2162 MET* 1.3 75.6 - - - +
2182 GLN* 1.3 64.4 + - - +
2202 LEU* 3.2 18.4 + - + +
2212 GLN* 3.5 5.9 + - - +
2292 ASP* 4.1 15.7 - - + +
2322 GLU* 6.2 2.0 - - + -
2332 ILE* 2.9 31.8 - - + +
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Residues in contact with GLN 218 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2142 TYR* 3.0 37.4 + - - +
2152 PHE 3.8 0.2 - - - +
2172 LEU* 1.3 74.0 - - - +
2192 TYR* 1.3 64.2 + - - +
2212 GLN* 3.1 23.7 + - - +
2302 LEU* 4.1 3.7 - - + +
2332 ILE* 4.2 13.7 - - + +
2642 HIS* 3.0 19.4 + - + +
2652 LEU* 2.6 61.8 - - - +
2682 PHE* 2.7 32.5 - - + +
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Residues in contact with TYR 219 (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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1752 LEU* 5.1 16.6 - - + -
1772 GLN* 3.7 18.0 + - + -
2152 PHE* 2.9 22.3 + + + +
2162 MET* 3.3 18.4 - - + +
2182 GLN* 1.3 73.1 - - - +
2202 LEU* 1.3 69.0 + - - +
2212 GLN 3.2 7.3 + - - +
2222 THR* 4.3 4.7 + - - -
2642 HIS* 2.7 28.2 + + + +
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Residues in contact with LEU 220 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1742 ASP* 2.7 40.2 - - + +
1772 GLN* 2.8 70.4 + - - +
1792 LEU* 4.6 16.4 - - + +
1812 GLN* 3.2 28.9 - - + +
1842 LEU* 5.6 0.4 - - + -
2162 MET 2.8 11.1 + - - +
2172 LEU* 3.2 14.8 - - + +
2192 TYR* 1.3 78.6 - - - +
2212 GLN* 1.3 62.8 + - - +
2222 THR* 3.2 6.2 + - - +
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Residues in contact with GLN 221 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1812 GLN* 2.7 28.2 + - - +
2172 LEU 3.5 4.7 + - - +
2182 GLN* 3.1 13.7 + - - +
2192 TYR 3.5 4.1 - - - +
2202 LEU* 1.3 81.7 - - - +
2222 THR* 1.3 54.2 + - - +
2232 ALA* 4.0 2.5 - - + +
2242 GLN* 2.7 29.3 - - - +
2262 ARG 5.3 0.7 - - - +
2272 GLY* 3.1 17.4 - - - +
2292 ASP* 4.1 1.0 - - - +
2302 LEU* 2.9 37.1 - - - +
2332 ILE* 4.6 2.4 - - - +
2682 PHE* 2.7 57.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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