Contacts of the strand formed by residues 152 - 156 (chain N) in PDB entry 3FKS
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 LYS 152 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211K LYS* 3.9 22.7 - - - +
150N GLY 4.8 1.6 - - - -
151N GLY* 1.3 76.5 - - - -
153N ILE* 1.3 63.9 + - - +
293N GLN* 2.8 55.2 + - - +
294N GLU* 4.6 3.2 + - - -
296N ILE* 3.1 34.5 - - + -
297N THR* 5.6 1.1 - - - -
306N SER* 3.6 4.9 - - - -
308N GLN* 5.0 4.3 - - - +
328N HIS* 3.6 27.6 + - + +
329N LEU* 4.0 12.1 - - + -
330N ASP* 2.8 38.9 + - - +
331N ALA 3.2 6.4 + - - -
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Residues in contact with ILE 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147N TYR* 3.8 55.4 - - + +
148N ALA* 4.2 6.1 - - + +
151N GLY 3.5 17.5 - - - +
152N LYS* 1.3 81.9 - - - +
154N GLY* 1.3 64.3 + - - +
305N THR* 3.7 16.8 - - + -
306N SER 2.7 17.3 + - - +
307N VAL* 3.4 14.1 - - + -
308N GLN* 2.7 34.9 + - - +
329N LEU* 3.8 4.2 - - - +
331N ALA* 3.2 20.4 - - + +
333N THR* 4.0 7.9 - - - +
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Residues in contact with GLY 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N ILE* 1.3 72.1 - - - +
155N LEU* 1.3 60.7 + - - -
156N PHE* 3.8 10.1 - - - -
308N GLN 3.4 6.5 - - - -
310N VAL* 3.9 9.0 - - - -
329N LEU* 3.5 21.7 - - - +
331N ALA 2.8 13.6 + - - -
332N THR* 3.3 5.3 - - - -
333N THR 2.9 26.4 + - - -
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Residues in contact with LEU 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N ILE 3.7 0.6 + - - -
154N GLY* 1.3 74.1 - - - -
156N PHE* 1.3 71.7 + - - +
163N LYS* 3.7 33.2 - - + -
166N PHE* 4.9 10.3 - - + -
167N ILE* 4.6 15.0 - - + -
254N PHE* 6.1 0.4 - - + -
307N VAL* 3.9 26.5 - - + +
308N GLN 2.8 14.0 + - - +
309N ALA* 3.2 14.3 - - + +
310N VAL 2.9 25.1 + - - +
333N THR* 3.3 38.1 - - + +
335N LEU* 4.5 10.3 - - + -
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Residues in contact with PHE 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N GLY* 3.8 18.4 - - - -
155N LEU* 1.3 82.2 - - - +
157N GLY* 1.3 68.1 + - - +
309N ALA* 5.9 0.2 - - - -
310N VAL* 3.6 37.5 - - + -
312N VAL* 4.6 9.9 - - + -
317N LEU* 6.5 0.2 - - + -
326N PHE* 3.3 31.0 - + - -
332N THR* 4.2 17.9 - - + -
333N THR 3.1 10.0 + - - +
334N VAL* 4.1 31.2 - - + -
335N LEU* 3.6 22.5 + - - +
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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