Contacts of the helix formed by residues 154 - 163 (chain S) in PDB entry 5K0Y
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 154 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92S ILE* 3.6 46.4 - - + +
149S PRO* 3.7 13.6 - - + +
151S HIS* 3.3 15.2 + - + +
152S ASP 3.3 0.6 - - - -
153S ILE* 1.4 86.3 - - + +
155S MET* 1.4 61.5 + - - +
156S ALA 3.4 2.2 - - - -
157S THR* 3.2 28.7 + - + +
158S MET* 3.0 21.0 + - - +
463S HIS* 5.6 0.2 - - - -
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Residues in contact with MET 155 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151S HIS 4.8 1.1 - - - -
152S ASP* 3.1 18.9 + - - +
153S ILE 3.1 9.3 + - - +
154S LEU* 1.4 74.6 - - - +
156S ALA* 1.4 77.5 + - - +
158S MET* 3.1 13.8 + - + +
159S LEU* 2.9 46.2 + - + +
185S GLU* 4.0 13.7 - - - +
418S MET* 6.4 0.2 - - - -
457S SER* 3.6 19.5 - - - +
463S HIS* 4.2 1.8 - - + -
464S TRP* 3.6 32.1 - - - +
465S ARG* 3.6 12.6 - - - +
466S LEU* 3.4 38.8 - - + +
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Residues in contact with ALA 156 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S ILE 4.7 1.0 + - - -
154S LEU 3.4 0.8 - - - -
155S MET* 1.4 91.2 - - - +
157S THR* 1.4 58.5 + - - +
159S LEU* 3.6 6.1 - - - +
160S ASN* 3.0 34.8 + - - +
418S MET* 5.4 9.2 - - + -
420S ASN* 3.6 19.4 - - - +
425S SER* 4.2 10.8 - - - +
463S HIS* 4.6 11.4 - - + +
464S TRP* 6.2 0.2 - - + -
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Residues in contact with THR 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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94S LEU* 4.8 17.8 - - + +
149S PRO* 4.0 20.5 - - + +
154S LEU* 3.2 30.9 + - + +
156S ALA* 1.4 74.6 - - - +
158S MET* 1.4 59.1 + - - +
160S ASN* 3.2 12.6 + - + +
161S GLY* 3.0 26.5 + - - -
367S VAL* 5.4 9.4 - - + -
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Residues in contact with MET 158 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S ILE* 3.7 32.1 - - + -
148S CYS* 3.8 7.5 - - + -
149S PRO* 3.9 25.5 - - + +
151S HIS 5.6 1.3 - - - +
154S LEU 3.0 13.7 + - - +
155S MET* 3.1 21.1 + - + +
157S THR* 1.4 76.2 - - - +
159S LEU* 1.4 72.7 + - + +
162S ALA* 3.0 35.4 + - - +
185S GLU* 4.2 22.2 - - + +
186S HIS* 3.5 35.4 - - + +
189S ALA* 5.7 2.5 - - + -
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Residues in contact with LEU 159 (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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155S MET* 2.9 38.2 + - + +
156S ALA* 3.6 8.5 - - - +
158S MET* 1.4 89.9 - - + +
160S ASN* 1.4 62.8 + - - +
162S ALA* 3.4 4.6 + - + +
163S ALA* 3.0 24.5 + - - +
189S ALA* 3.9 28.7 - - + -
193S MET* 4.7 5.2 - - + +
420S ASN* 3.6 33.2 - - + +
455S ALA* 4.3 13.5 - - + -
457S SER* 4.7 0.2 - - - +
466S LEU* 4.0 19.7 - - + -
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Residues in contact with ASN 160 (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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94S LEU* 6.2 0.9 - - + -
156S ALA 3.0 15.2 + - - +
157S THR* 3.2 14.2 + - + +
159S LEU* 1.4 74.5 - - - +
161S GLY* 1.4 62.5 + - - +
163S ALA* 3.2 15.2 + - - +
164S VAL* 4.2 2.6 + - - +
272S ILE* 4.9 2.0 - - + -
367S VAL* 4.3 19.8 - - + +
420S ASN* 3.2 27.5 + - - +
422S GLY 4.9 1.1 + - - -
423S SER* 3.0 50.8 + - - +
424S LEU 3.4 8.7 + - - -
425S SER* 3.5 14.9 - - - -
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Residues in contact with GLY 161 (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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94S LEU* 3.9 29.1 - - - +
146S VAL* 3.7 11.5 - - - +
148S CYS* 4.0 6.3 - - - -
157S THR 3.0 14.8 + - - -
158S MET 4.1 0.7 - - - -
160S ASN* 1.4 74.6 - - - +
162S ALA* 1.4 60.6 - - - +
164S VAL* 3.3 21.0 - - - +
165S MET 4.3 1.9 + - - -
272S ILE* 4.8 6.5 - - - -
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Residues in contact with ALA 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S ILE* 4.1 15.3 - - + -
146S VAL* 5.4 0.2 - - - -
148S CYS* 3.6 5.1 - - - -
158S MET* 3.0 23.2 + - - +
159S LEU* 3.5 6.7 - - + +
161S GLY* 1.4 75.3 - - - +
163S ALA* 1.4 55.1 + - - +
164S VAL 3.0 6.7 + - - -
165S MET* 3.1 43.4 + - + +
189S ALA* 6.3 0.7 - - + -
190S ILE* 5.8 0.9 - - + -
193S MET* 3.4 21.4 - - + +
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Residues in contact with ALA 163 (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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159S LEU 3.0 13.1 + - - +
160S ASN 3.2 13.5 + - - +
162S ALA* 1.4 72.9 - - - +
164S VAL* 1.4 61.9 + - + +
165S MET 3.6 1.8 - - - +
193S MET* 4.0 17.7 - - + +
270S ILE* 5.8 0.3 - - - +
297S LEU* 5.9 2.3 - - - +
422S GLY 3.7 26.2 - - - +
423S SER* 4.6 1.6 - - - -
453S LYS* 4.5 22.2 + - - +
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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