Contacts of the helix formed by residues 152 - 159 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150U THR* 3.3 9.1 + - - +
151U GLY* 1.3 76.0 - - - +
153U LYS* 1.3 67.1 + - - +
154U ALA 3.4 1.1 + - - +
155U VAL* 3.8 21.5 - - + +
156U ASP* 3.1 24.9 + - - +
180U VAL* 3.6 45.1 - - + +
183U ASP* 4.3 20.2 - - + +
184U THR* 4.5 6.5 - - - +
365U PRO* 4.6 22.0 - - + -
432U GLN* 3.7 27.1 - - + +
437U PRO* 5.8 0.4 - - + -
443U GLN* 4.0 0.9 - - - -
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Residues in contact with LYS 153 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151U GLY 3.5 2.2 + - - -
152U LEU* 1.3 70.5 - - - +
154U ALA* 1.3 65.1 + - - +
156U ASP* 4.5 0.5 - - - +
157U ALA* 3.1 28.9 + - - +
429U LEU* 3.4 20.9 + - + +
430U LEU* 4.0 19.1 - - + +
431U LYS 3.0 26.1 + - - -
432U GLN* 3.5 32.1 + - - +
438U LEU* 3.7 24.2 - - + -
443U GLN* 4.2 22.6 - - + +
446U LEU* 4.1 12.3 - - + -
447U ILE* 5.4 7.6 - - + -
467U GLU* 3.1 28.2 + - - +
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Residues in contact with ALA 154 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152U LEU* 3.4 1.0 - - + +
153U LYS* 1.3 79.9 - - - +
155U VAL* 1.3 64.0 + - - +
157U ALA* 5.0 0.9 - - - -
158U LEU* 3.0 35.3 + - + +
159U VAL* 4.9 0.7 - - - -
365U PRO* 4.9 10.2 - - + +
367U ILE* 4.3 23.1 - - + -
430U LEU* 4.0 37.3 + - + +
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Residues in contact with VAL 155 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U THR* 3.9 19.1 - - + +
152U LEU* 3.4 28.2 + - + +
153U LYS 3.4 0.6 - - - -
154U ALA* 1.3 74.6 - - - +
156U ASP* 1.3 61.0 + - - +
159U VAL* 2.6 62.0 + - + +
161U ILE* 3.9 19.3 - - + -
180U VAL* 4.5 7.4 - - + -
352U ILE* 4.9 6.5 - - + -
365U PRO* 5.3 0.2 - - + -
367U ILE* 3.6 25.1 - - + -
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Residues in contact with ASP 156 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U VAL 3.3 15.7 - - - +
149U GLN* 3.6 8.4 - - - +
150U THR* 3.0 24.8 + - - +
151U GLY* 3.0 27.0 + - - -
152U LEU 3.1 11.2 + - - +
155U VAL* 1.3 80.3 - - - +
157U ALA* 1.3 51.3 + - - +
158U LEU 3.8 0.2 + - - -
160U PRO* 3.9 8.5 - - - +
161U ILE* 4.7 5.4 + - - +
381U GLN* 2.7 33.8 + - + +
385U LEU* 3.2 19.3 - - + +
443U GLN* 3.9 11.0 + - - +
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Residues in contact with ALA 157 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153U LYS 3.1 21.0 + - - +
154U ALA* 4.2 1.8 - - - +
156U ASP* 1.3 77.0 - - - +
158U LEU* 1.3 72.6 + - + +
381U GLN* 4.0 10.8 + - - +
385U LEU* 4.0 19.7 - - + -
389U ALA* 4.1 19.9 - - + +
392U LEU* 5.1 4.0 - - + -
430U LEU* 5.6 1.3 - - + -
443U GLN* 5.5 0.9 - - - +
447U ILE* 4.7 17.0 - - + -
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Residues in contact with LEU 158 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154U ALA* 3.0 20.3 + - + +
157U ALA* 1.3 91.9 - - + +
159U VAL* 1.3 68.6 + - + +
160U PRO* 3.1 14.2 - - - +
367U ILE* 6.5 1.6 - - + -
369U VAL* 3.8 33.4 - - + -
374U SER* 5.1 0.3 - - - -
392U LEU* 3.6 20.2 - - + +
393U LYS* 3.2 51.3 + - + +
396U LEU* 4.0 15.0 - - + -
430U LEU* 4.7 8.7 - - + -
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Residues in contact with VAL 159 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154U ALA 4.4 2.5 - - - +
155U VAL* 2.6 41.6 + - + +
158U LEU* 1.3 79.2 - - + +
160U PRO* 1.3 66.0 - - - +
161U ILE* 3.4 13.7 - - - +
167U GLU* 4.7 0.2 - - - +
352U ILE* 3.4 27.1 - - + -
367U ILE* 5.3 6.3 - - + -
372U SER* 3.9 12.8 - - - +
373U VAL* 3.4 42.2 - - - +
374U SER* 3.7 8.5 - - - +
393U LYS* 4.5 2.9 - - - +
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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