Contacts of the strand formed by residues 223 - 228 (chain A) in PDB entry 3F6K
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 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.5 29.9 - - + +
204A ASN* 3.0 33.3 + - - +
206A LEU* 3.8 11.9 - - + -
220A HIS* 3.8 28.0 - - + +
222A ALA* 1.3 77.7 - - - +
224A CYS* 1.3 64.8 + - - +
225A LEU 3.6 18.4 - - - +
226A ALA* 4.4 1.3 - - + -
236A PHE* 3.7 29.4 - - + -
237A THR 3.4 11.0 - - - +
238A THR* 4.0 1.1 - - + -
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Residues in contact with CYS 224 (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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200A LEU* 3.6 14.0 - - - +
204A ASN* 4.9 1.3 + - - +
223A VAL* 1.3 74.1 - - - +
225A LEU* 1.3 63.9 + - + +
237A THR* 3.1 17.5 + - - +
239A TYR* 3.3 19.1 - - - -
244A CYS* 2.1 53.9 - - + -
251A LEU* 4.3 20.6 - - + -
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Residues in contact with LEU 225 (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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188A MET* 6.3 0.4 - - + -
200A LEU* 4.4 3.1 - - - -
223A VAL* 3.6 3.1 - - - +
224A CYS* 1.3 80.5 - - + +
226A ALA* 1.3 66.7 + - - +
227A LYS* 4.1 22.9 - - - +
236A PHE* 3.1 5.9 - - - +
237A THR* 3.1 34.7 + - + +
272A SER* 4.1 13.5 - - - +
273A PHE* 3.7 41.1 - - + +
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Residues in contact with ALA 226 (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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188A MET* 3.3 26.4 - - + +
198A LEU* 4.0 13.0 - - + -
200A LEU* 4.7 6.1 - - + +
206A LEU* 3.9 28.0 - - + -
223A VAL* 4.4 3.1 - - + -
225A LEU* 1.3 79.5 - - - +
227A LYS* 1.3 69.3 + - - +
234A ILE* 4.5 1.1 - - + -
235A PHE 3.3 6.1 - - - +
236A PHE* 3.7 14.6 - - + -
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Residues in contact with LYS 227 (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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188A MET* 4.8 7.0 - - - -
198A LEU* 4.5 7.4 - - - -
225A LEU* 4.1 24.8 - - - +
226A ALA* 1.3 76.7 - - - +
228A TRP* 1.3 66.9 + - - +
229A GLY 3.8 0.2 + - - -
234A ILE* 3.5 3.5 - - - +
235A PHE* 2.9 32.1 + - - +
273A PHE* 3.3 40.2 + - + +
275A LEU* 4.5 10.3 - - + -
11N TYR* 2.8 49.2 + - + +
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Residues in contact with TRP 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A MET* 2.9 34.8 + - + -
189A TYR 3.2 17.3 - - - -
190A SER* 3.3 30.2 - - - +
191A PRO* 3.8 20.1 - - + +
196A TYR* 3.8 27.8 - - + -
197A LEU 3.9 11.4 - - - -
198A LEU* 3.7 19.2 - - + +
208A VAL* 4.7 2.5 - - + -
227A LYS* 1.3 74.2 - - - +
229A GLY* 1.3 59.5 + - - +
232A ASN* 3.7 20.9 - - + -
233A THR 3.3 23.1 - - - -
234A ILE* 3.6 20.0 - - + -
259A LEU* 3.6 22.7 - - + -
275A LEU* 3.5 15.3 - - - +
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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