Contacts of the strand formed by residues 218 - 222 (chain P) in PDB entry 5IYB
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 LYS 218 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172P VAL 3.9 5.6 - - - +
173P ASN* 4.2 21.1 - - + +
174P LEU* 5.3 0.2 - - - -
213P ILE* 3.8 1.2 - - - +
214P PHE* 2.8 45.4 + - + +
216P SER* 3.5 7.5 + - - +
217P GLY* 1.3 82.1 - - - +
219P MET* 1.3 62.8 + - - +
220P VAL* 6.0 0.2 - - + -
16X A 3.6 33.0 + - - +
17X G 3.1 35.3 + - - +
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Residues in contact with MET 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171P THR* 3.5 4.5 - - - -
172P VAL* 2.7 64.0 + - + +
174P LEU* 3.7 29.2 - - + -
211P ALA* 4.0 10.5 - - + -
212P LEU 3.1 14.8 - - - +
213P ILE* 3.4 29.4 - - + -
217P GLY 4.0 0.2 + - - -
218P LYS* 1.3 76.9 - - - +
220P VAL* 1.3 73.5 + - - +
221P CYS* 5.7 1.3 - - + -
234P ALA* 4.4 8.7 - - + +
237P TYR* 3.9 32.1 - - + -
238P ALA 4.7 0.2 - - - +
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Residues in contact with VAL 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169P VAL* 4.7 3.6 - - + -
170P SER 3.2 17.7 - - - +
171P THR* 3.7 18.6 - - + -
210P THR 4.0 0.3 - - - +
211P ALA* 3.1 5.7 - - - +
212P LEU* 2.7 55.2 + - + +
214P PHE* 4.3 20.0 - - + -
218P LYS* 6.0 0.2 - - + -
219P MET* 1.3 81.7 - - - +
221P CYS* 1.3 60.0 + - - +
222P THR* 4.3 13.8 + - + +
15X A 4.1 28.9 - - + +
16X A 4.5 7.4 - - - +
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Residues in contact with CYS 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168P ILE 4.0 1.0 - - - +
169P VAL* 3.9 0.2 - - - -
170P SER* 2.8 47.9 + - - +
171P THR* 4.5 0.8 - - - +
172P VAL* 5.4 3.1 - - + +
209P THR* 4.5 5.8 - - - -
210P THR 3.7 5.8 - - - -
211P ALA* 4.9 3.4 - - + -
219P MET* 4.5 2.7 + - + -
220P VAL* 1.3 73.7 - - - +
222P THR* 1.3 69.5 + - - +
224P ALA* 5.8 0.7 - - - -
230P SER* 4.4 14.8 - - - +
233P ALA* 4.0 26.0 - - - -
234P ALA* 4.5 13.7 - - + -
237P TYR* 4.1 18.8 - - + -
253P PHE* 6.1 0.4 - - + -
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Residues in contact with THR 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ILE 3.5 6.3 - - - -
169P VAL* 3.8 32.1 - - + -
209P THR* 3.4 7.8 - - - -
210P THR* 3.0 39.2 + - - +
212P LEU* 6.0 3.9 - - + +
220P VAL* 4.4 11.0 - - + -
221P CYS* 1.3 80.3 - - - +
223P GLY* 1.3 59.5 + - - +
224P ALA* 3.5 2.9 - - - -
14X A 4.6 2.5 - - + -
15X A 5.5 0.4 - - + -
78Y T 3.8 20.3 + - - +
79Y T 3.6 25.1 + - - +
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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