Contacts of the strand formed by residues 204 - 208 (chain W) 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 VAL 204 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53W LEU* 4.7 6.5 - - + -
70W LEU* 3.3 15.3 - - + +
72W TYR* 4.0 21.8 - - + -
87W LEU* 3.8 29.4 - - + -
91W LEU* 6.0 1.3 - - + -
104W PHE* 3.4 37.9 - - + -
105W LEU 3.1 9.3 + - - +
106W GLY* 3.7 10.1 - - - -
107W LEU 3.6 15.1 + - - +
202W ALA* 3.4 3.7 - - - +
203W ASN* 1.3 78.3 - - - +
205W VAL* 1.3 78.0 + - - +
206W VAL* 5.9 1.8 - - + -
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Residues in contact with VAL 205 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70W LEU 3.1 9.2 + - - +
71W ILE* 3.4 27.4 - - + +
72W TYR* 2.8 35.3 + - - +
107W LEU* 3.7 36.8 - - + -
199W ILE* 4.6 17.7 - - + +
202W ALA* 4.7 6.7 - - + +
204W VAL* 1.3 80.3 - - - +
206W VAL* 1.4 55.9 + - - +
207W TYR* 4.3 18.8 - - + -
221W VAL* 6.3 0.2 - - + -
225W LEU* 4.8 11.0 - - + -
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Residues in contact with VAL 206 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72W TYR* 3.4 22.2 - - + +
74W SER* 3.9 16.4 - - - +
80W ILE* 3.6 29.1 - - + +
83W VAL* 4.2 27.4 - - + -
84W ILE* 3.6 27.1 - - + -
87W LEU* 6.1 1.6 - - + -
107W LEU 3.2 9.1 + - - +
108W ALA* 3.9 0.7 - - - -
109W LEU* 2.9 28.6 + - - +
204W VAL* 5.9 1.3 - - + -
205W VAL* 1.4 71.7 - - - +
207W TYR* 1.4 63.5 + - - +
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Residues in contact with TYR 207 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71W ILE* 4.8 10.3 - - + -
72W TYR 3.0 10.8 + - - +
73W CYS* 3.5 2.0 - - - -
74W SER* 3.0 29.3 + - - -
80W ILE* 5.1 1.6 - - - -
109W LEU* 3.5 53.1 - - + +
110W SER* 3.7 17.0 - - - -
111W SER 4.4 0.4 - - - -
192W TYR* 3.1 27.4 + - - -
199W ILE* 5.1 5.8 - - + -
205W VAL* 4.3 16.6 - - + -
206W VAL* 1.4 76.4 - - - +
208W SER* 1.4 73.5 + - - +
211W TYR* 3.2 33.0 - + + -
220W LEU* 6.1 1.4 - - - +
221W VAL* 4.3 25.2 - - + +
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Residues in contact with SER 208 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73W CYS* 4.6 2.4 - - - -
74W SER 3.6 9.7 + - - -
75W ARG 5.6 1.7 + - - -
80W ILE* 6.2 0.7 - - - -
109W LEU 4.5 0.8 + - - -
110W SER* 5.1 6.7 + - - -
207W TYR* 1.4 88.0 - - - +
209W TYR* 1.3 65.6 + - - +
210W HIS* 3.0 23.2 + - - +
211W TYR* 3.6 24.3 + - - +
212W LEU* 3.4 21.7 + - - +
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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
------------------------------------------------------------
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