Contacts of the strand formed by residues 218 - 222 (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 THR 218 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1950 ARG* 4.2 20.2 + - - +
1960 VAL 3.6 5.0 + - - -
1970 SER* 2.6 34.5 + - - +
1980 VAL 2.8 31.7 + - - +
2120 ALA* 3.7 10.3 + - - +
2160 GLY 4.9 0.3 - - - -
2170 GLY* 1.4 77.1 + - - +
2190 TYR* 1.4 53.0 + - - +
2200 HIS* 4.0 27.9 + - + +
2340 HIS* 4.9 7.4 - - - +
2350 HIS* 4.4 6.1 - - + -
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Residues in contact with TYR 219 (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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1710 PHE* 3.9 19.6 - - - -
1980 VAL* 3.4 33.7 - - + -
2000 GLY* 4.5 3.2 - - - -
2030 ALA 2.6 31.5 + - - -
2040 GLU* 4.0 15.4 - - + -
2050 VAL 4.3 0.7 + - - -
2080 CYS* 3.8 10.0 - - + +
2090 THR* 3.4 59.2 - - + +
2120 ALA* 4.2 6.2 - - + +
2130 ARG* 5.5 4.9 - - + +
2170 GLY 4.0 2.2 + - - -
2180 THR* 1.4 73.1 - - - +
2200 HIS* 1.3 79.0 + - - +
2210 VAL* 5.3 3.6 - - + -
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Residues in contact with HIS 220 (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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1980 VAL 2.9 8.1 + - - +
1990 ILE* 3.4 8.3 - - + +
2000 GLY* 2.7 32.7 + - - -
2170 GLY 5.2 0.8 + - - -
2180 THR* 4.0 35.7 + - + +
2190 TYR* 1.3 87.3 - - - +
2210 VAL* 1.4 52.9 + - - +
2310 LEU* 3.8 35.4 - - + +
2340 HIS* 4.1 27.4 + + - -
2350 HIS* 4.0 13.9 + - - -
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Residues in contact with VAL 221 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2000 GLY* 3.4 9.9 - - - +
2020 SER 3.9 17.0 - - - +
2030 ALA 4.1 12.6 - - - +
2190 TYR* 5.6 2.9 - - + -
2200 HIS* 1.4 73.6 - - - +
2220 ILE* 1.4 62.4 + - - +
2270 HIS* 3.1 27.2 + - + -
2310 LEU* 3.8 5.5 - - - +
724W MET* 3.9 48.2 - - + +
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Residues in contact with ILE 222 (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* 4.2 20.0 - - + -
1990 ILE* 3.3 26.9 - - + -
2000 GLY 2.9 28.5 + - - +
2010 LEU* 3.8 20.3 - - + +
2020 SER* 3.9 18.0 + - - -
2210 VAL* 1.4 73.4 - - - +
2230 LEU* 1.3 60.3 + - - +
2240 ASP* 3.4 33.7 - - - +
2270 HIS* 3.6 4.5 - - + +
2280 TYR* 3.6 30.1 - - + +
2310 LEU* 4.0 6.5 - - + -
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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