Contacts of the strand formed by residues 223 - 230 (chain A) in PDB entry 3F00
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 THR 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A LEU* 3.3 5.9 - - - -
186A LEU* 2.7 49.8 + - + +
221A GLY 4.8 2.1 + - - -
222A LYS* 1.3 80.2 + - - +
224A LEU* 1.3 64.1 + - - +
225A VAL* 3.8 3.6 + - + +
244A LYS* 3.8 36.1 - - + -
245A VAL 3.7 13.0 - - - +
246A PRO* 3.9 14.4 - - + +
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Residues in contact with LEU 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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147A TYR* 5.1 0.9 - - + -
149A LEU* 4.2 20.9 - - + -
158A LEU* 5.0 1.8 - - + -
160A VAL* 3.9 24.2 - - + -
183A VAL* 3.9 21.5 - - + -
184A PHE 3.5 16.4 - - - +
185A LEU* 3.9 16.2 - - + +
212A PHE* 4.1 13.2 - - + -
223A THR* 1.3 72.8 - - - +
225A VAL* 1.3 60.8 + - - +
226A MET* 3.8 25.7 + - + +
244A LYS* 3.4 3.3 - - - -
245A VAL* 2.7 48.2 + - + +
247A MET* 3.9 12.0 - - + +
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Residues in contact with VAL 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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182A LYS 3.6 0.7 - - - +
183A VAL* 3.4 6.8 - - - +
184A PHE* 2.9 63.5 + - + -
186A LEU* 3.7 27.4 - - + -
223A THR* 4.2 3.4 - - + +
224A LEU* 1.3 78.6 - - - +
226A MET* 1.3 72.1 + - - +
227A ALA* 4.2 5.6 - - + +
242A GLU* 4.8 4.0 - - + -
243A PHE 3.7 9.0 - - - +
244A LYS* 3.6 35.4 - - + +
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Residues in contact with MET 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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145A LEU* 4.0 17.7 - - + -
147A TYR* 3.7 26.5 - - + -
160A VAL* 4.5 1.3 - - - -
162A ILE* 3.6 31.9 - - + -
181A VAL* 4.3 2.0 - - + -
182A LYS 3.4 3.1 - - - -
183A VAL* 4.2 11.0 - - + -
224A LEU* 3.8 29.6 + - + +
225A VAL* 1.3 77.7 - - - +
227A ALA* 1.3 61.1 + - - +
228A VAL* 5.5 0.7 - - - -
242A GLU* 3.3 3.1 - - - +
243A PHE* 3.0 70.7 + - + -
245A VAL* 3.8 13.7 - - + -
262A LEU* 5.2 0.5 - - - +
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Residues in contact with ALA 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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181A VAL* 3.3 3.4 - - - +
182A LYS* 2.8 41.8 + - + +
184A PHE* 4.9 4.7 - - + -
225A VAL* 4.2 7.8 - - + -
226A MET* 1.3 74.6 - - - +
228A VAL* 1.3 63.8 + - - +
229A TYR* 3.7 27.2 - - + +
239A ILE* 4.0 4.9 - - + -
241A GLY 3.6 4.3 - - - -
242A GLU* 3.8 13.9 - - + -
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Residues in contact with VAL 228 (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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145A LEU* 4.5 14.1 - - + -
168A LEU* 4.5 10.5 - - + -
179A PRO* 4.1 15.7 - - + -
180A TYR 3.4 11.4 - - - +
181A VAL* 4.2 18.4 - - + -
206A PHE* 5.3 1.8 - - + -
226A MET 5.5 0.2 - - - -
227A ALA* 1.3 75.3 - - - +
229A TYR* 1.3 57.9 + - - +
239A ILE* 3.2 6.8 - - - +
240A ILE* 2.8 49.0 + - + -
241A GLY 2.8 10.5 + - - -
262A LEU* 3.7 35.9 - - + -
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Residues in contact with TYR 229 (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 ASP 3.7 0.5 - - - +
179A PRO* 3.2 6.9 - - - +
180A TYR* 2.9 55.7 + + + +
182A LYS* 3.4 44.0 + - + +
184A PHE* 6.3 0.2 - + - -
192A LYS* 6.1 0.5 - - - -
227A ALA* 3.7 23.6 - - + +
228A VAL* 1.3 73.9 - - - +
230A ASP* 1.3 58.9 + - - +
231A PHE 3.8 0.2 - - - -
237A HIS* 3.7 20.4 - - + -
238A ASP 3.5 6.7 - - - -
239A ILE* 3.5 40.0 - - + +
240A ILE* 4.0 5.9 - - - +
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Residues in contact with ASP 230 (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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171A LEU* 3.5 19.4 - - - +
177A SER* 3.4 21.2 - - - -
178A ASP* 2.9 25.6 + - - +
180A TYR* 4.4 0.2 - - - -
229A TYR* 1.3 70.7 - - - +
231A PHE* 1.3 70.0 + - - +
232A ASP* 3.4 3.7 + - - +
237A HIS* 3.4 20.9 - - - +
238A ASP* 2.9 26.5 + - + +
240A ILE* 4.2 15.6 - - + +
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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