Contacts of the strand formed by residues 222 - 226 (chain F) in PDB entry 4GDF
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 ILE 222 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135F PRO 3.1 28.3 - - - +
136F LYS* 3.4 7.2 - - - +
137F ASP* 3.3 33.9 - - - +
138F PHE* 3.5 29.3 - - + +
160F ALA 3.6 1.2 - - - +
161F ILE* 3.2 5.0 - - - +
162F TYR* 2.6 51.6 + - + +
220F PHE* 4.4 4.3 - - + -
221F LEU* 1.3 82.0 - - - +
223F CYS* 1.3 64.9 + - - +
224F LYS* 4.3 10.3 - - + -
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Residues in contact with CYS 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F VAL* 3.2 23.6 - - - +
160F ALA 3.4 3.4 - - - +
161F ILE* 3.5 36.1 - - + -
205F VAL* 3.6 12.1 - - + +
208F ILE* 4.7 3.6 - - + -
209F ASN* 3.8 48.4 + - + +
212F ALA* 5.2 0.4 - - - -
221F LEU* 4.3 8.0 - - - -
222F ILE* 1.3 74.4 - - - +
224F LYS* 1.3 66.4 + - - +
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Residues in contact with LYS 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ASP* 3.0 25.1 + - - -
138F PHE* 3.6 27.0 - - + -
143F LEU* 5.3 0.2 - - - +
146F LEU* 4.2 12.3 - - + +
147F SER 3.7 12.3 - - - +
148F HIS* 2.9 41.3 + - - +
150F VAL* 3.2 34.5 - - + -
159F PHE* 3.6 5.2 - - - +
160F ALA* 3.0 32.4 + - - +
205F VAL* 4.0 8.5 - - - +
222F ILE* 4.3 6.3 - - + -
223F CYS* 1.3 75.4 - - - +
225F GLY* 1.3 68.6 + - - +
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Residues in contact with GLY 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F LEU* 3.2 11.6 - - - +
147F SER* 3.1 34.9 + - - -
150F VAL* 5.5 0.2 - - - +
156F LEU* 3.6 19.7 - - - -
158F CYS 3.8 2.7 - - - -
159F PHE* 4.3 0.9 - - - -
205F VAL* 3.7 19.0 - - - +
224F LYS* 1.3 74.7 - - - +
226F VAL* 1.3 62.0 + - - -
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Residues in contact with VAL 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F PHE 3.6 12.3 - - - +
146F LEU* 4.0 2.2 - - + -
156F LEU* 3.6 9.3 - - - +
158F CYS* 2.9 51.8 + - - +
159F PHE 3.5 24.2 - - - +
160F ALA* 3.8 13.2 - - + +
196F PHE* 4.5 3.1 - - + -
225F GLY* 1.3 74.6 - - - +
227F ASN* 1.3 64.4 + - - +
228F LYS 3.7 8.5 - - - +
229F GLU* 4.6 0.5 - - - +
232F MET* 3.5 35.9 - - + -
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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
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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