Contacts of the helix formed by residues 162 - 169 (chain S) in PDB entry 1L9J
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 PHE 162 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115S TRP* 5.9 0.4 - + - -
119S SER* 4.2 27.1 - - - -
120S PHE* 6.0 0.7 - - - -
122S MET* 4.7 4.3 - - + -
123S PHE* 4.1 28.0 - + + -
157S TRP* 3.6 31.9 - + - -
158S MET* 2.8 47.2 + - + +
161S GLY* 1.3 94.1 - - - +
163S ILE* 1.3 66.7 + - + +
165S PRO* 3.0 9.0 - - - +
166S ILE* 3.0 38.9 + - + +
171S TRP* 4.6 17.7 - + - -
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Residues in contact with ILE 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155S TRP* 3.9 16.6 - - + -
158S MET* 3.1 29.9 + - + +
159S VAL* 3.7 34.5 - - + +
162S PHE* 1.3 75.3 - - + +
164S ARG* 1.3 58.6 + - - +
166S ILE* 3.4 7.7 + - - +
167S LEU* 3.0 36.8 + - + +
285S LEU* 4.1 24.2 - - + -
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Residues in contact with ARG 164 (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 VAL* 3.2 13.2 + - + +
160S LEU 4.9 2.2 - - - +
163S ILE* 1.3 73.6 - - - +
165S PRO* 1.3 77.3 - - + +
166S ILE 3.0 1.6 - - - -
167S LEU* 3.2 3.3 + - - +
168S MET* 2.8 62.9 + - + +
173S GLU* 2.9 30.1 + - - +
185S TRP* 5.6 0.4 - - - -
189S PHE* 3.7 15.0 - - - -
193S HIS* 3.1 33.7 + - - -
284S ILE* 3.5 32.4 + - - +
285S LEU* 4.4 15.3 - - + -
287S SER 2.8 22.9 + - - -
288S GLY* 3.5 0.2 - - - -
289S THR* 4.2 8.5 - - + -
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Residues in contact with PRO 165 (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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103S LEU* 4.5 1.8 - - - -
159S VAL 3.4 7.6 - - - +
160S LEU 3.3 17.0 - - - +
161S GLY* 3.7 4.9 - - - -
162S PHE 3.0 24.0 - - - +
164S ARG* 1.3 95.5 - - + +
166S ILE* 1.3 60.5 + - - +
168S MET* 3.5 4.9 + - + +
169S GLY 3.2 14.6 + - - -
170S SER 3.2 25.9 + - - +
171S TRP* 4.4 14.6 - - + -
173S GLU* 4.5 7.6 - - + -
174S ALA* 4.0 24.7 - - + +
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Residues in contact with ILE 166 (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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103S LEU* 3.6 23.3 - - + +
162S PHE* 3.0 36.5 + - + +
163S ILE* 3.5 6.5 - - - +
165S PRO* 1.3 72.7 - - - +
167S LEU* 1.3 63.4 + - + +
168S MET 2.7 4.9 + - - -
169S GLY* 2.6 28.8 + - - -
171S TRP* 4.3 25.1 - - + -
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Residues in contact with LEU 167 (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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163S ILE* 3.0 29.1 + - + +
164S ARG* 4.0 4.3 - - - +
166S ILE* 1.3 79.2 - - + +
168S MET* 1.3 61.0 + - - +
285S LEU* 4.0 28.0 - - + -
289S THR* 4.7 15.2 - - + +
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Residues in contact with MET 168 (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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164S ARG* 2.8 67.8 + - + +
165S PRO 3.5 7.0 - - - +
166S ILE 2.7 0.2 + - - -
167S LEU* 1.3 79.3 - - - +
169S GLY* 1.3 60.1 + - - +
170S SER* 3.6 3.2 + - - +
173S GLU* 3.7 27.6 - - + +
193S HIS* 4.9 1.6 - - - +
288S GLY* 3.8 30.7 - - - +
289S THR* 4.1 9.2 - - + -
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Residues in contact with GLY 169 (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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102S GLY* 3.6 13.3 - - - -
103S LEU* 3.6 14.0 + - - +
165S PRO 3.2 0.6 + - - -
166S ILE 2.6 21.9 + - - -
167S LEU 3.3 0.8 - - - -
168S MET* 1.3 73.4 - - - +
170S SER* 1.3 64.0 + - - +
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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