Contacts of the strand formed by residues 216 - 219 (chain C) in PDB entry 3P3W
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 216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C TYR* 3.7 31.1 - + - -
130C TRP* 3.7 28.9 + + + -
187C LYS* 3.6 7.7 + - - +
188C ARG* 3.4 5.1 - - + -
189C TYR* 2.8 27.4 + - - +
215C TYR* 1.3 74.4 - - - +
217C TYR* 1.3 71.8 + - - +
218C MET* 5.3 1.2 - - + +
238C ASN* 3.3 43.7 + - + +
239C ILE 4.7 0.4 - - - -
240C THR* 3.1 23.6 + - - -
361C LYS* 6.4 2.0 - - - -
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Residues in contact with TYR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C TYR* 3.6 40.4 - + + -
191C ILE* 4.6 19.3 - - + -
201C ILE* 5.5 4.7 - - + -
202C LEU* 4.7 10.3 - - + -
205C VAL* 3.8 21.9 - - + +
211C HIS* 3.2 25.9 + - - +
215C TYR* 4.1 17.8 - - + +
216C HIS* 1.3 79.3 - - - +
218C MET* 1.3 61.9 + - - +
219C LEU* 4.1 4.3 - - + -
232C VAL* 4.2 11.0 - - + -
237C ALA* 3.7 31.4 - - + -
238C ASN 2.8 12.2 + - - +
239C ILE* 3.3 21.4 - - + +
240C THR 3.2 21.3 + - - -
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Residues in contact with MET 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.7 7.6 - - - -
124C LEU* 4.1 26.0 - - + +
125C LEU* 3.7 33.2 - - + -
128C TYR* 5.0 7.0 - - + -
130C TRP* 3.7 24.2 - - + -
189C TYR 2.7 18.4 + - - +
190C LEU* 3.4 25.2 - - + +
191C ILE* 2.8 33.1 + - - +
216C HIS* 5.5 0.7 - - - +
217C TYR* 1.3 73.7 - - - +
219C LEU* 1.3 60.1 + - - +
240C THR* 4.0 21.3 - - + +
242C PHE* 4.5 14.1 - - + -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ILE* 3.7 33.2 - - + -
198C ILE* 3.6 25.8 - - + -
202C LEU* 4.5 9.4 - - + -
217C TYR* 4.1 4.5 - - + -
218C MET* 1.3 71.9 - - - +
220C ALA* 1.3 58.0 + - - +
221C ASN 3.1 12.6 + - - +
224C PHE* 5.0 2.9 - - + -
227C ILE* 3.8 43.3 - - + -
229C LEU* 4.1 6.5 - - + -
239C ILE* 3.8 26.9 - - + -
240C THR 3.1 14.1 + - - +
241C GLY* 4.2 4.4 - - - -
242C PHE* 3.3 19.9 - - - -
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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