Contacts of the strand formed by residues 226 - 231 (chain A) in PDB entry 4FDI
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 PHE 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASN* 3.2 50.8 + - + -
33A ILE 2.8 36.6 + - - -
34A LEU* 4.3 13.5 - - + -
133A TYR* 3.7 5.4 - - - -
134A VAL 3.4 8.7 - - - +
216A PHE* 3.9 15.5 - + + -
217A ILE* 3.8 39.5 - - + -
220A GLN* 3.8 31.0 - - + -
221A ALA* 4.6 9.4 - - + -
224A HIS 4.6 1.6 - - - -
225A PRO* 1.3 75.2 - - - +
227A PHE* 1.3 55.9 + - - +
228A LEU* 4.1 12.3 - - + -
272A LEU* 3.9 19.1 - - + -
277A VAL* 5.1 0.7 - - + -
281A THR* 4.2 2.5 - - + -
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Residues in contact with PHE 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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33A ILE* 3.2 22.9 - - + -
35A LEU* 3.6 32.8 - - + -
87A LEU* 5.0 3.6 - - + -
124A LEU* 3.7 20.0 - - + -
125A PRO* 4.1 14.1 - - + -
128A LEU* 3.6 22.7 - - + -
133A TYR* 3.9 6.4 - - + -
134A VAL 2.9 7.8 + - - +
135A SER* 3.2 30.4 - - - +
136A LYS 3.0 25.8 + - - +
156A PHE* 3.6 25.6 - + - -
216A PHE* 3.7 3.5 - - - -
226A PHE* 1.3 73.4 - - - +
228A LEU* 1.3 64.6 + - - +
229A TYR* 4.0 16.6 - + + -
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Residues in contact with LEU 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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33A ILE 2.9 9.5 + - - +
34A LEU* 3.5 31.1 - - + -
35A LEU* 2.8 33.3 + - - +
136A LYS* 3.6 15.7 - - + +
138A VAL* 3.8 27.4 - - + -
213A ALA* 3.8 31.6 - - + +
216A PHE* 4.0 22.0 - - + -
217A ILE* 4.1 15.3 - - + -
226A PHE* 4.1 6.1 - - + -
227A PHE* 1.3 75.6 - - - +
229A TYR* 1.3 62.4 + - - +
230A TRP* 4.5 4.7 - - + +
268A ILE* 5.5 0.7 - - + -
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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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35A LEU* 3.7 16.6 - - + -
37A LEU* 3.3 37.5 - - + +
83A ARG* 3.8 22.5 + - - +
86A LEU* 4.2 19.3 - - + +
87A LEU* 4.4 22.6 - - + +
136A LYS 2.9 8.2 + - - +
137A ILE* 3.4 36.7 - - + -
138A VAL 2.8 29.3 + - - +
140A LYS 4.4 2.9 + - - -
141A TRP* 5.2 2.3 + + - -
156A PHE* 3.7 29.8 - + + -
227A PHE* 4.0 11.8 - + + -
228A LEU* 1.3 72.7 - - - +
230A TRP* 1.3 59.8 + - - +
231A ALA* 3.5 12.9 + - + -
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Residues in contact with TRP 230 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.6 0.2 - - + -
35A LEU 2.8 16.5 + - - +
36A LEU* 3.6 26.6 - - + -
37A LEU* 3.0 25.4 + - - +
38A MET* 4.3 6.2 - - + +
138A VAL* 3.5 24.6 - - + +
206A THR* 4.7 4.9 - - + -
209A TYR* 3.0 21.9 + - + -
210A LEU* 4.0 18.2 - - - -
213A ALA* 3.7 15.4 - - + +
228A LEU* 3.8 10.1 + - + -
229A TYR* 1.3 70.0 - - - +
231A ALA* 1.3 58.6 + - - +
232A VAL* 3.5 37.5 + - + -
261A ILE* 4.3 6.3 - - + -
264A SER* 3.8 24.9 - - - -
265A ILE* 3.6 25.1 - - + -
268A ILE* 3.9 17.5 - - + -
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Residues in contact with ALA 231 (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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37A LEU* 3.4 8.7 - - + +
83A ARG* 3.5 24.9 - - - +
137A ILE* 5.2 0.4 - - + -
138A VAL 2.7 16.8 + - - +
139A GLY* 3.3 1.7 - - - -
140A LYS* 2.9 37.0 + - - +
229A TYR* 3.5 22.9 + - + -
230A TRP* 1.3 71.1 - - - +
232A VAL* 1.3 65.3 + - - +
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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