Contacts of the helix formed by residues 152 - 159 (chain J) 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 LEU 152 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J THR* 3.1 21.0 + - - +
151J GLY* 1.3 76.2 - - - +
153J LYS* 1.3 67.8 + - - +
154J ALA 3.1 1.6 - - - +
155J VAL* 2.9 30.5 + - + +
156J ASP* 3.0 14.7 + - - +
180J VAL* 3.5 48.0 - - + +
183J ASP* 4.3 20.0 - - + +
184J THR* 4.9 0.2 - - - +
365J PRO* 4.1 22.4 - - + -
432J GLN* 3.5 21.8 - - + +
443J GLN* 4.3 1.3 - - - -
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Residues in contact with LYS 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J GLY 3.4 1.6 + - - -
152J LEU* 1.3 71.1 - - - +
154J ALA* 1.3 61.3 + - - +
157J ALA* 3.2 25.1 + - - +
429J LEU* 2.8 34.4 + - + +
430J LEU* 4.1 16.4 - - + +
431J LYS 3.0 22.2 + - - -
432J GLN* 2.9 23.2 + - - +
438J LEU* 3.5 27.6 - - + -
443J GLN* 4.3 20.4 - - + +
446J LEU* 4.2 12.8 - - + -
447J ILE* 5.4 6.3 - - + +
467J GLU* 3.3 33.0 + - - +
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Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152J LEU* 3.1 1.0 - - - +
153J LYS* 1.3 79.5 - - - +
155J VAL* 1.3 63.4 + - + +
158J LEU* 3.3 31.1 + - + +
159J VAL* 4.1 0.5 + - - +
365J PRO* 4.7 9.9 - - + +
367J ILE* 4.3 29.6 - - + +
369J VAL* 6.1 0.9 - - + -
430J LEU* 4.0 37.1 + - + +
432J GLN* 4.7 0.6 + - - -
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Residues in contact with VAL 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J THR* 3.5 28.9 - - + +
152J LEU* 2.9 32.2 + - + -
154J ALA* 1.3 76.5 - - + +
156J ASP* 1.3 59.9 + - - +
157J ALA 2.9 11.0 + - - -
159J VAL* 2.9 47.0 + - - +
161J ILE* 4.2 12.1 - - + -
180J VAL* 4.6 5.2 - - + -
352J ILE* 4.3 20.0 - - + -
365J PRO* 5.7 0.7 - - + -
367J ILE* 5.1 14.1 - - + -
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Residues in contact with ASP 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J VAL 3.4 11.4 - - - +
149J GLN* 3.8 9.6 - - - +
150J THR* 2.9 28.4 + - - +
151J GLY* 2.8 31.4 + - - -
152J LEU 3.0 9.9 + - - +
155J VAL* 1.3 79.2 - - - +
157J ALA* 1.3 57.3 + - - +
160J PRO* 4.1 10.4 - - - +
161J ILE* 5.1 3.6 + - - +
381J GLN* 2.8 22.5 + - - +
385J LEU* 3.1 19.7 - - + +
440J THR* 5.6 2.6 + - - +
443J GLN* 3.8 12.1 + - - +
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Residues in contact with ALA 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J LYS 3.2 21.8 + - - +
154J ALA* 4.3 0.9 - - - +
155J VAL 2.9 1.4 + - - -
156J ASP* 1.3 79.5 - - - +
158J LEU* 1.3 66.0 + - + +
160J PRO* 4.7 0.6 - - - +
381J GLN* 2.9 23.5 + - - +
385J LEU* 4.1 3.6 - - + -
389J ALA* 4.9 10.4 - - + +
392J LEU* 4.7 15.7 - - + -
430J LEU* 5.5 1.1 - - + -
443J GLN* 5.5 0.7 - - - +
447J ILE* 4.3 23.1 - - + -
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Residues in contact with LEU 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J ALA* 3.3 17.8 + - + +
157J ALA* 1.3 83.8 - - + +
159J VAL* 1.3 69.9 + - + +
160J PRO* 3.3 10.9 - - - +
367J ILE* 6.5 0.4 - - + -
369J VAL* 3.5 36.8 - - + -
374J SER 5.6 0.5 + - - -
392J LEU* 4.3 12.6 - - + -
393J LYS* 3.6 52.3 - - + +
396J LEU* 3.7 22.9 - - + -
430J LEU* 4.2 12.8 - - + -
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Residues in contact with VAL 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J ALA 4.1 0.8 + - - +
155J VAL* 2.9 23.3 + - - +
158J LEU* 1.3 89.4 - - + +
160J PRO* 1.3 62.0 - - - +
161J ILE* 3.3 10.6 - - - +
167J GLU* 3.3 27.1 - - - +
351J GLN 4.4 0.7 - - - +
352J ILE* 4.3 13.5 - - + -
367J ILE* 5.6 6.5 - - + -
369J VAL* 5.7 2.5 - - + -
372J SER* 3.4 32.1 - - - +
373J VAL* 3.9 5.2 - - + -
374J SER* 3.4 23.3 - - - +
393J LYS* 5.7 2.7 - - - -
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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