Contacts of the helix formed by residues 152 - 157 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150S THR* 3.2 11.3 + - - +
151S GLY* 1.3 79.2 - - - +
153S LYS* 1.3 61.9 + - - +
154S ALA 4.6 1.3 - - - +
155S VAL* 3.0 23.9 + - + +
156S ASP* 2.9 31.7 + - - +
180S VAL* 3.6 48.0 - - + +
183S ASP* 4.6 21.5 - - + +
184S THR* 5.0 0.2 - - - +
365S PRO* 4.6 13.7 - - + -
432S GLN* 3.4 33.9 - - + +
433S ASN 5.4 1.1 - - - +
437S PRO* 5.7 1.1 - - + -
443S GLN* 4.4 1.1 - - - -
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Residues in contact with LYS 153 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151S GLY 3.7 1.0 + - - -
152S LEU* 1.3 72.6 - - - +
154S ALA* 1.3 59.7 + - - +
155S VAL 3.0 4.5 + - - -
157S ALA* 3.3 27.9 + - - +
429S LEU* 3.1 30.2 + - + +
430S LEU* 4.0 17.1 - - + +
431S LYS 3.1 15.7 + - - -
432S GLN* 2.9 28.5 + - - +
438S LEU* 3.6 25.4 - - + -
443S GLN* 3.9 24.0 - - + +
446S LEU* 3.7 14.1 - - + +
447S ILE* 4.5 10.1 - - + -
467S GLU* 2.8 32.7 + - - -
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Residues in contact with ALA 154 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152S LEU* 3.4 1.0 - - - +
153S LYS* 1.3 77.7 - - - +
155S VAL* 1.3 58.3 + - - +
158S LEU* 3.2 32.4 - - + +
159S VAL* 4.3 1.7 + - - +
365S PRO* 4.5 12.3 - - + +
367S ILE* 4.0 24.7 - - + +
430S LEU* 3.8 42.4 + - + +
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Residues in contact with VAL 155 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150S THR* 3.3 23.3 - - + +
152S LEU* 3.0 30.3 + - + +
153S LYS 3.0 0.6 - - - -
154S ALA* 1.3 81.3 - - - +
156S ASP* 1.3 64.3 + - - +
157S ALA 3.0 1.6 - - - -
159S VAL* 2.8 48.9 + - - +
161S ILE* 3.6 17.0 - - + -
180S VAL* 4.8 9.2 - - + -
352S ILE* 4.6 12.8 - - + -
365S PRO* 4.8 1.1 - - + -
367S ILE* 3.9 20.2 - - + -
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Residues in contact with ASP 156 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148S VAL 4.1 1.4 - - - +
149S GLN* 3.5 18.4 - - - +
150S THR* 2.8 34.0 + - - +
151S GLY* 2.8 22.3 + - - -
152S LEU 2.9 14.4 + - - +
155S VAL* 1.3 75.2 - - - +
157S ALA* 1.3 57.8 + - - +
160S PRO* 3.7 22.3 - - - +
161S ILE* 5.4 1.6 + - - +
381S GLN* 3.9 6.8 + - - +
385S LEU* 3.5 18.3 - - + +
440S THR* 4.8 2.5 + - - +
443S GLN* 3.4 25.7 + - - +
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Residues in contact with ALA 157 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153S LYS 3.3 16.8 + - - +
155S VAL 3.0 0.4 - - - -
156S ASP* 1.3 82.3 - - - +
158S LEU* 1.3 65.0 + - + +
160S PRO* 4.5 2.6 - - - +
381S GLN* 4.1 12.5 + - - +
385S LEU* 4.1 19.7 - - + -
389S ALA* 4.3 19.5 - - + +
392S LEU* 4.2 20.2 - - + -
393S LYS* 5.6 1.9 - - - +
430S LEU* 5.6 0.2 - - + -
443S GLN* 5.1 0.4 - - - +
447S ILE* 4.7 7.4 - - + -
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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