Contacts of the strand formed by residues 216 - 219 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A TYR* 4.5 20.4 - + - -
130A TRP* 3.3 34.7 + + + -
187A LYS 3.0 7.3 + - - +
188A ARG* 3.6 25.7 + - + +
189A TYR* 2.8 31.0 + - - +
215A TYR* 1.3 75.9 - - - +
217A TYR* 1.3 70.9 + - - +
218A MET* 4.4 0.9 - - - +
238A ASN* 3.1 46.8 + - + +
240A THR* 2.9 28.7 + - - -
359A GLU* 6.1 0.9 - - + -
361A LYS* 6.4 0.7 - - - -
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Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ILE* 5.5 1.7 - - - +
189A TYR* 3.5 38.2 - + + -
191A ILE* 4.4 15.5 - - + -
201A ILE* 6.4 0.7 - - + -
202A LEU* 4.7 13.5 - - + -
205A VAL* 3.9 29.5 - - + +
211A HIS* 3.8 28.8 - - - +
215A TYR* 3.9 28.1 - + + -
216A HIS* 1.3 77.6 - - - +
218A MET* 1.3 61.6 + - - +
219A LEU* 3.9 9.9 - - + -
232A VAL* 4.7 11.7 - - + -
237A ALA* 4.7 12.6 - - + -
238A ASN 3.0 9.0 + - - +
239A ILE* 3.4 19.2 - - + +
240A THR 3.2 21.1 + - - -
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Residues in contact with MET 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.2 13.7 - - - +
124A LEU* 4.3 10.3 - - + -
125A LEU* 4.4 17.5 - - + -
128A TYR* 3.7 36.1 - - + -
130A TRP* 4.2 15.5 - - + -
189A TYR 2.8 13.6 + - - +
190A LEU* 3.4 25.5 - - + +
191A ILE 2.8 31.4 + - - -
216A HIS* 4.1 0.8 - - + -
217A TYR* 1.3 71.4 - - - +
219A LEU* 1.3 58.5 + - - +
240A THR* 3.4 19.5 - - + +
242A PHE* 3.8 29.8 - - + -
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE* 3.7 28.7 - - + -
198A ILE* 3.7 27.6 - - + -
202A LEU* 4.7 11.0 - - + -
217A TYR* 4.6 9.9 - - + +
218A MET* 1.3 69.2 - - - +
220A ALA* 1.3 57.2 + - - +
221A ASN* 2.8 18.1 + - + +
224A PHE* 4.1 19.1 - - + -
227A ILE* 3.8 18.2 - - + -
229A LEU* 3.8 30.1 - - + -
239A ILE* 4.3 11.2 - - + -
240A THR 3.2 8.7 + - - +
241A GLY* 4.3 0.9 - - - -
242A PHE* 3.1 21.1 + - - -
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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
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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