Contacts of the strand formed by residues 219 - 222 (chain C) in PDB entry 4UQJ
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 HIS 219 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C TYR* 3.8 28.5 - + - -
130C TRP* 3.2 35.6 - + + +
190C ARG 2.8 9.1 + - - -
191C ARG* 3.4 12.1 - - + +
192C VAL 2.9 27.4 + - - +
217C GLY 5.4 0.4 - - - +
218C TYR* 1.3 73.6 - - - +
220C TYR* 1.3 71.0 + - - +
221C ILE* 4.2 2.5 - - + -
241C GLU* 3.2 41.6 + - + +
243C SER* 3.3 27.3 + - - -
362C GLU* 5.4 0.8 + - - -
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Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C PHE* 4.6 6.4 - + - -
192C VAL* 3.2 42.7 - - + +
194C LEU* 4.7 14.1 - - + -
204C ILE* 5.8 0.2 - - + -
208C VAL* 3.2 34.4 - - + +
213C LYS* 2.7 37.1 + - - +
214C HIS* 4.6 1.3 - - + -
218C TYR* 3.9 19.8 - + + -
219C HIS* 1.3 75.7 + - - +
221C ILE* 1.3 65.9 + - - +
222C ILE* 4.2 7.6 - - + -
235C ILE* 6.1 2.9 - - + -
240C ALA* 4.4 14.1 - - + -
241C GLU 2.9 7.3 + - - -
242C VAL* 3.4 21.6 - - + -
243C SER 2.8 26.4 + - - -
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Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 5.0 4.9 - - + -
124C LEU* 3.9 31.4 - - + -
125C ILE* 5.0 7.6 - - + -
128C TYR* 4.4 11.0 - - + -
130C TRP* 3.6 38.6 - - + -
192C VAL 3.0 10.2 + - - +
193C ILE* 3.5 21.3 - - + +
194C LEU 2.8 26.8 + - - +
219C HIS* 4.0 7.9 - - + +
220C TYR* 1.3 79.0 - - - +
222C ILE* 1.3 63.2 + - - +
223C ALA* 3.2 5.0 + - - +
243C SER* 3.3 9.9 - - - +
245C PHE* 4.2 15.3 - - + -
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Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 3.7 22.9 - - + +
196C CYS 5.6 0.2 - - - +
201C VAL* 4.0 34.5 - - + -
205C VAL* 5.1 5.2 - - + -
220C TYR* 5.1 4.7 - - + -
221C ILE* 1.3 72.0 - - - +
223C ALA* 1.3 59.0 + - - +
224C ASN* 2.9 42.0 + - - +
226C GLY 5.1 1.8 - - - +
227C PHE* 4.2 21.5 - - + +
232C LEU* 6.1 4.3 - - + -
242C VAL* 4.2 12.3 - - + -
243C SER 2.9 15.6 + - - +
244C GLY* 3.6 5.2 - - - -
245C PHE* 3.5 15.8 - - - -
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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