Contacts of the helix formed by residues 152 - 159 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150T THR* 3.1 17.3 + - - +
151T GLY* 1.3 78.0 - - - +
153T LYS* 1.3 72.9 + - - +
154T ALA* 3.5 14.1 - - + +
155T VAL* 3.3 20.1 + - + +
156T ASP* 3.1 23.2 + - - +
180T VAL* 4.7 17.5 - - + +
183T ASP* 5.2 14.6 - - + +
365T PRO* 3.4 44.0 - - + -
432T GLN* 3.5 20.0 - - + +
443T GLN* 4.1 3.1 - - - +
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Residues in contact with LYS 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151T GLY 4.2 0.4 - - - -
152T LEU* 1.3 72.1 - - - +
154T ALA* 1.3 64.3 + - - +
155T VAL 3.3 0.2 + - - -
156T ASP* 4.3 1.0 - - - +
157T ALA* 3.4 23.0 + - - +
429T LEU* 2.9 25.6 + - + +
430T LEU* 3.6 21.7 - - + +
431T LYS 3.6 16.2 + - - -
432T GLN* 2.7 43.3 + - - +
438T LEU* 3.6 12.8 - - + -
443T GLN* 4.6 20.7 - - + +
446T LEU* 4.4 12.8 - - + -
447T ILE* 5.2 3.5 - - + +
467T GLU* 2.7 41.7 + - - +
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Residues in contact with ALA 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152T LEU* 3.5 12.2 - - + +
153T LYS* 1.3 80.2 - - - +
155T VAL* 1.3 60.9 + - - +
157T ALA* 4.1 0.6 - - - +
158T LEU* 3.2 32.3 + - + +
159T VAL* 4.2 1.0 + - - +
365T PRO* 4.9 4.5 - - + +
367T ILE* 4.2 24.1 - - + +
430T LEU* 4.0 37.7 + - + +
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Residues in contact with VAL 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150T THR* 3.6 31.2 - - + +
152T LEU* 3.3 32.3 + - + +
153T LYS 3.2 1.0 - - - -
154T ALA* 1.3 73.0 - - - +
156T ASP* 1.3 62.1 + - - +
157T ALA 2.9 10.8 + - - -
159T VAL* 2.8 51.7 + - + +
161T ILE* 4.5 8.7 - - + -
180T VAL* 4.7 14.1 - - + -
352T ILE* 4.7 8.1 - - + -
367T ILE* 4.8 15.5 - - + -
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Residues in contact with ASP 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148T VAL 3.6 6.6 - - - +
149T GLN* 3.6 16.3 - - - +
150T THR* 3.2 22.4 + - - +
151T GLY* 3.1 28.9 + - - -
152T LEU 3.1 13.4 + - - +
153T LYS 4.7 0.2 - - - +
155T VAL* 1.3 78.2 - - - +
157T ALA* 1.3 56.3 + - - +
160T PRO* 4.1 11.7 - - - +
161T ILE 4.9 5.0 + - - -
381T GLN* 3.0 23.0 + - - +
385T LEU* 3.9 15.2 - - + +
443T GLN* 3.7 19.8 + - - +
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Residues in contact with ALA 157 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153T LYS 3.4 17.6 + - - +
154T ALA* 4.1 2.7 - - - +
155T VAL 2.9 2.4 + - - -
156T ASP* 1.3 79.3 - - - +
158T LEU* 1.3 68.2 + - + +
160T PRO* 4.5 1.3 - - - +
381T GLN* 3.3 22.3 + - - +
385T LEU* 5.5 5.4 - - + -
389T ALA* 4.9 12.1 - - + +
392T LEU* 4.8 9.7 - - + +
430T LEU* 5.4 1.1 - - + -
443T GLN* 5.8 0.7 - - - +
447T ILE* 4.3 24.2 - - + -
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Residues in contact with LEU 158 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154T ALA* 3.2 21.6 + - + +
157T ALA* 1.3 79.6 - - + +
159T VAL* 1.3 71.0 + - + +
160T PRO* 3.5 7.5 - - - +
367T ILE* 5.4 10.1 - - + -
369T VAL* 4.5 17.3 - - + -
372T SER* 6.4 0.7 - - - -
374T SER* 4.9 1.2 + - - -
392T LEU* 3.7 28.3 - - + +
393T LYS* 3.6 56.0 - - + +
396T LEU* 4.0 17.7 - - + -
430T LEU* 4.3 13.2 - - + -
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Residues in contact with VAL 159 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154T ALA 4.8 0.4 - - - +
155T VAL* 2.8 36.9 + - - +
158T LEU* 1.3 85.3 - - + +
160T PRO* 1.3 65.9 - - - +
161T ILE* 3.8 3.8 - - - +
167T GLU* 4.3 8.7 - - - +
351T GLN 4.7 0.7 - - - +
352T ILE* 4.0 29.8 - - + -
367T ILE* 4.8 7.9 - - + -
372T SER* 3.9 10.5 - - - +
373T VAL* 3.6 19.1 - - - +
374T SER* 3.4 29.6 - - - +
393T LYS* 5.0 1.3 - - + -
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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