Contacts of the strand formed by residues 220 - 224 (chain L) in PDB entry 5FHX
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 220 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124L GLN* 3.8 15.1 + - - +
125L SER 4.2 5.7 + - - -
126L PRO* 2.8 33.7 + - + +
127L ALA 3.3 6.3 - - - +
128L SER* 4.4 7.9 - - - +
129L LEU* 4.7 0.4 - - + -
139L LEU* 3.8 39.9 - - + +
140L THR 4.9 0.2 + - - -
202L ALA 3.7 0.9 - - - +
203L THR* 3.3 3.4 - - - -
204L TYR* 2.9 33.8 + - - +
219L GLY* 1.4 72.2 + - - -
221L LYS* 1.3 63.7 + - - +
222L LEU* 3.7 6.9 + - + +
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Residues in contact with LYS 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L ALA 3.1 13.0 + - - +
128L SER* 3.2 7.8 - - - -
129L LEU 3.0 24.3 + - - -
158L PRO* 6.4 1.6 - - - -
202L ALA 3.7 2.2 - - - +
203L THR* 3.4 23.1 - - + +
219L GLY 4.2 0.6 - - - -
220L THR* 1.3 71.0 - - - +
222L LEU* 1.3 67.6 + - - +
223L GLU* 3.4 33.1 + - + +
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Residues in contact with LEU 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L LEU* 3.5 25.6 - - + +
131L VAL* 4.4 8.5 - - + -
137L ILE* 4.5 3.4 - - + -
139L LEU* 4.2 24.7 - - + -
193L ILE* 4.0 11.0 - - + -
196L LEU* 3.8 22.9 - - + -
200L ASP 3.4 21.1 - - - +
201L ILE* 3.5 23.9 - - + +
202L ALA* 2.7 28.4 + - - +
204L TYR* 3.7 15.7 - - + -
220L THR* 4.5 3.8 - - + -
221L LYS* 1.3 80.5 - - - +
223L GLU* 1.3 61.9 + - - +
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Residues in contact with GLU 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L SER* 3.4 28.0 + - - -
129L LEU 2.9 12.5 + - - +
130L SER* 3.2 18.0 + - - +
131L VAL* 2.8 32.2 + - - +
201L ILE* 4.7 5.2 - - - -
221L LYS* 3.4 29.6 - - + +
222L LEU* 1.3 77.3 - - - +
224L ILE* 1.3 58.6 + - - +
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Residues in contact with ILE 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L SER* 4.7 2.8 + - - -
131L VAL 3.5 9.9 - - - +
132L SER* 5.2 1.6 - - - -
133L VAL* 4.4 23.8 - - + +
198L PRO* 5.4 4.3 - - + -
201L ILE* 3.8 38.5 - - + +
223L GLU* 1.3 75.0 - - - +
225L LYS* 1.3 69.5 + - - +
226L THR* 3.5 21.7 + - + +
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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