Contacts of the strand formed by residues 153 - 158 (chain B) in PDB entry 5F3K
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 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B THR* 3.6 1.9 - - - -
148B ASN* 3.0 45.8 + - - +
151B LYS* 3.7 18.7 + - + +
152B GLY* 1.3 81.6 - - - +
154B ILE* 1.3 62.5 + - - +
155B THR* 4.6 4.9 + - - -
254B ILE* 4.4 11.7 - - + -
255B ILE 3.1 7.2 - - - +
256B HIS* 3.4 43.1 - - + +
257B LEU* 4.2 1.8 - - - -
265B SER* 3.5 11.1 - - - -
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.9 20.6 - - + -
113B ILE* 4.1 24.7 - - + -
116B LEU* 5.5 4.0 - - + -
145B LEU* 4.6 10.3 - - + -
146B GLN 3.4 12.3 - - - +
147B THR* 4.3 2.9 - - + +
153B THR* 1.3 73.4 - - - +
155B THR* 1.3 70.3 + - - +
253B ILE 3.9 0.5 - - - +
254B ILE* 3.7 0.3 - - - +
255B ILE* 2.9 49.4 + - + +
257B LEU* 4.2 9.6 - - + -
264B PHE 3.5 21.5 - - - +
270B VAL* 3.8 23.8 - - + -
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 6.2 0.4 - - - -
144B HIS 5.5 0.4 - - - +
145B LEU* 3.1 8.3 - - - +
146B GLN* 2.8 56.0 + - - +
153B THR* 4.6 6.1 + - - -
154B ILE* 1.3 80.3 + - - +
156B ILE* 1.3 68.2 + - - +
157B GLN* 4.9 1.8 - - + +
252B LYS* 3.6 36.1 - - + -
253B ILE 3.2 11.2 - - - +
254B ILE* 3.9 16.7 - - + +
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.6 49.3 - - + +
117B ILE* 3.8 23.3 - - + +
120B ALA* 4.0 5.2 - - + -
143B ILE* 3.9 15.7 - - + -
144B HIS 3.3 8.7 - - - +
145B LEU* 3.9 14.1 - - + -
155B THR* 1.3 76.4 - - - +
157B GLN* 1.3 64.9 + - - +
251B THR 3.9 1.0 - - - +
252B LYS* 3.2 2.1 - - - +
253B ILE* 2.7 68.8 + - + +
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Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLU 4.0 0.5 - - - +
143B ILE* 3.7 4.7 - - - +
144B HIS* 2.7 49.7 + - + +
146B GLN* 4.8 7.1 - - - +
155B THR* 5.2 2.7 - - + -
156B ILE* 1.3 78.5 - - - +
158B ASP* 1.3 70.9 + - - +
159B THR* 5.5 1.3 - - + -
247B VAL* 6.4 0.2 - - - +
248B ARG* 3.4 39.4 + - - +
251B THR 3.4 8.8 + - - +
252B LYS* 3.9 36.2 + - + +
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 3.6 33.9 - - + +
123B ALA* 3.9 5.4 - - - +
124B LEU* 4.1 10.5 - - + -
142B GLU 3.9 5.8 - - - +
143B ILE* 5.0 0.7 - - + -
157B GLN* 1.3 82.6 + - - +
159B THR* 1.3 61.2 + - - +
160B GLY* 2.8 28.9 + - - -
162B GLY 5.1 0.2 + - - -
200B GLN* 2.9 29.6 + - - -
249B THR 3.8 1.7 - - - +
250B GLY* 3.3 2.4 - - - -
251B THR* 2.9 39.9 + - - +
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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