Contacts of the helix formed by residues 224 - 237 (chain 0) 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 ASP 224 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760 LEU* 4.0 6.5 - - - +
2220 ILE* 3.4 13.7 - - - +
2230 LEU* 1.3 88.1 - - + +
2250 GLU* 1.3 56.1 + - - +
2260 SER* 2.5 38.4 + - - +
2270 HIS* 3.0 9.8 + - + +
2280 TYR 2.9 30.8 + - - -
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Residues in contact with GLU 225 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760 LEU* 3.6 13.3 - - + +
770 LYS* 2.9 37.3 - - + +
830 CYS* 3.4 25.2 - - - -
860 LYS* 6.0 2.5 - - - -
870 LEU* 3.3 29.8 - - + +
2240 ASP* 1.3 73.4 + - - +
2260 SER* 1.3 64.3 + - - +
2280 TYR* 3.3 6.6 + - - -
2290 LYS* 2.9 31.9 + - - +
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Residues in contact with SER 226 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2240 ASP* 2.5 28.5 + - - +
2250 GLU* 1.3 77.2 - - - +
2270 HIS* 1.3 61.0 + - - +
2290 LYS* 3.5 10.2 + - - +
2300 GLU* 3.1 24.1 + - - +
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Residues in contact with HIS 227 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2210 VAL* 3.1 25.1 + - + -
2220 ILE* 3.6 3.8 - - + -
2230 LEU* 3.2 43.3 + - + +
2240 ASP* 3.0 21.5 + - + +
2260 SER* 1.3 80.7 + - - +
2280 TYR* 1.3 58.4 + - - +
2300 GLU* 3.3 9.6 + - + +
2310 LEU* 3.0 40.8 + - + +
724W MET 5.3 2.7 - - - -
725W ALA* 5.6 1.6 - - - -
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Residues in contact with TYR 228 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760 LEU* 5.5 1.1 - - + -
830 CYS* 4.7 4.0 - - - -
840 THR* 3.3 49.8 - - + -
870 LEU* 3.5 30.1 - - + -
880 LEU* 3.3 24.6 - - - +
1700 ILE* 3.5 28.0 - - + +
1990 ILE* 4.0 17.3 - - + -
2010 LEU* 5.4 0.4 - - + -
2220 ILE* 3.6 29.3 - - + +
2240 ASP 2.9 7.9 + - - +
2250 GLU* 3.3 9.4 + - - +
2270 HIS* 1.3 72.9 - - - +
2290 LYS* 1.4 64.7 + - - +
2310 LEU* 3.1 4.8 + - - +
2320 LEU* 3.0 41.6 + - + +
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Residues in contact with LYS 229 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870 LEU* 3.7 33.5 - - + +
900 TYR* 4.7 18.0 - - + -
2250 GLU* 2.9 25.9 + - - +
2260 SER* 3.7 8.1 - - - +
2280 TYR* 1.4 76.1 - - - +
2300 GLU* 1.3 53.0 + - - +
2320 LEU* 4.2 4.2 - - - +
2330 THR* 2.7 47.5 + - + +
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Residues in contact with GLU 230 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2260 SER 3.1 15.7 + - - +
2270 HIS* 3.3 17.5 - - + +
2280 TYR 3.3 0.2 - - - -
2290 LYS* 1.3 75.5 - - - +
2310 LEU* 1.3 59.1 + - + +
2330 THR* 2.8 21.9 + - - -
2340 HIS* 3.0 18.2 + - - +
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Residues in contact with LEU 231 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1990 ILE* 3.8 38.8 - - + -
2200 HIS* 3.8 37.2 - - + +
2210 VAL 3.8 22.0 - - - +
2220 ILE* 4.0 9.0 - - + -
2270 HIS* 3.0 27.7 + - + +
2280 TYR* 3.1 5.6 + - - +
2300 GLU* 1.3 74.4 - - + +
2320 LEU* 1.4 64.3 + - - +
2340 HIS* 3.2 19.0 + - + +
2350 HIS* 3.2 17.5 + - - -
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Residues in contact with LEU 232 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870 LEU* 3.8 14.4 - - + +
880 LEU* 3.5 37.0 - - + -
910 PHE* 3.6 30.8 - - + -
1680 LEU* 3.8 22.4 - - + -
1700 ILE* 5.2 1.6 - - + -
1990 ILE* 3.9 15.9 - - + -
2280 TYR* 3.0 40.3 + - + +
2290 LYS* 4.2 4.3 - - - +
2310 LEU* 1.4 72.1 - - - +
2330 THR* 1.3 58.5 + - + +
2350 HIS* 2.9 20.8 + - - +
2360 VAL* 3.1 12.9 + - - +
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Residues in contact with THR 233 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910 PHE* 6.3 2.0 - - - -
940 GLU* 5.5 9.9 - - + -
2290 LYS* 2.7 33.1 + - + +
2300 GLU* 2.8 25.5 + - - -
2320 LEU* 1.3 77.0 - - + +
2340 HIS* 1.3 62.0 + - - +
2360 VAL* 3.3 27.8 + - + +
2370 SER* 3.7 6.2 + - - -
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Residues in contact with HIS 234 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2180 THR* 4.9 7.3 - - - +
2200 HIS* 4.1 28.8 + + - -
2300 GLU 3.0 13.4 + - - +
2310 LEU* 3.2 14.8 + - + +
2330 THR* 1.3 74.2 - - - +
2350 HIS* 1.4 71.8 + + - +
2370 SER* 3.1 33.4 + - - +
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Residues in contact with HIS 235 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590 ARG* 3.2 27.4 + - - -
610 LEU* 5.8 1.5 - - + +
910 PHE* 4.0 17.7 - - + -
950 TYR* 4.4 2.4 - - - -
1660 GLU* 5.5 4.4 + - - -
1680 LEU* 3.6 26.1 - - + +
1970 SER* 3.3 34.3 + - - -
1990 ILE* 4.0 14.2 - - + +
2180 THR* 4.4 13.2 - - + -
2200 HIS* 4.0 16.4 + - - -
2310 LEU 3.2 19.8 + - - -
2320 LEU* 2.9 10.6 + - - +
2340 HIS* 1.4 85.9 - + - +
2360 VAL* 1.4 63.0 - - - +
2370 SER 3.3 2.6 - - - +
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Residues in contact with VAL 236 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590 ARG* 3.1 1.4 + - - -
910 PHE* 3.7 18.4 - - + -
940 GLU* 3.7 36.6 - - + +
950 TYR* 3.9 20.2 - - - +
980 GLN* 3.8 16.1 - - + +
990 ASN* 2.8 28.1 + - - -
2320 LEU 3.1 14.0 + - - +
2330 THR* 3.3 19.9 + - + +
2350 HIS* 1.4 71.5 - - - +
2370 SER* 1.3 63.9 + - - +
2380 PRO* 3.5 2.8 - - - +
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Residues in contact with SER 237 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590 ARG* 3.1 13.0 + - - -
980 GLN* 5.0 1.3 - - - -
2330 THR 3.9 5.9 + - - -
2340 HIS* 3.1 21.9 + - - +
2350 HIS 3.3 6.2 - - - +
2360 VAL* 1.3 77.2 - - - +
2380 PRO* 1.4 72.5 - - - +
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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