Contacts of the helix formed by residues 154 - 164 (chain C) in PDB entry 1L9X
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 PRO 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ASN 3.7 1.6 - - - +
153C PHE* 1.3 86.1 - - + +
155C THR* 1.3 65.3 + - - +
156C GLU* 4.4 4.7 - - + +
157C LEU* 3.0 33.4 + - + +
158C LEU* 3.3 10.6 + - - +
242C LYS* 4.2 12.1 - - - +
246C TYR* 3.6 35.0 - - + +
154D PRO* 5.1 7.9 - - + -
246D TYR* 4.1 7.2 - - - +
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Residues in contact with THR 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C PHE 3.4 3.4 + - - -
154C PRO* 1.3 71.8 - - - +
156C GLU* 1.3 65.7 + - + +
158C LEU* 3.2 13.5 + - + +
159C LEU* 3.1 37.1 + - + +
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Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PRO* 3.2 5.6 - - + +
155C THR* 1.3 79.1 - - + +
157C LEU* 1.3 56.6 + - - +
159C LEU* 3.5 14.0 + - + +
160C SER* 3.0 32.2 + - - -
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C PHE* 3.6 29.8 - - + -
154C PRO* 3.0 31.0 + - + +
156C GLU* 1.3 77.2 - - - +
158C LEU* 1.3 61.5 + - - +
160C SER* 3.2 3.1 + - - -
161C LEU* 2.9 29.9 + - + +
239C ASN* 3.7 38.8 - - + +
242C LYS* 3.9 28.7 - - + +
243C THR* 3.7 22.2 - - - +
246C TYR* 4.1 5.8 - - + -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C PHE* 3.5 29.7 - - + -
144C GLN* 4.9 14.4 - - + +
145C LEU* 6.3 2.7 - - + -
150C PHE* 3.7 39.5 - - + +
153C PHE* 3.8 32.5 - - + +
154C PRO 3.3 5.6 + - - +
155C THR* 3.2 12.7 + - + +
157C LEU* 1.3 76.8 - - - +
159C LEU* 1.3 65.8 + - + +
161C LEU* 3.2 4.7 + - + -
162C ALA* 3.1 19.4 + - - +
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Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C THR* 3.1 27.4 + - + +
156C GLU* 3.7 15.9 - - + +
157C LEU 3.2 0.2 - - - -
158C LEU* 1.3 80.7 - - + +
160C SER* 1.3 61.2 + - - +
162C ALA* 3.3 19.8 + - + +
163C VAL* 3.5 13.6 + - - +
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Residues in contact with SER 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLU* 3.0 18.3 + - - +
157C LEU 3.6 5.6 - - - -
158C LEU 3.2 0.4 - - - -
159C LEU* 1.3 77.7 - - - +
161C LEU* 1.3 58.1 + - - +
163C VAL* 3.1 3.3 + - - -
164C GLU* 2.8 59.4 + - - +
166C LEU* 4.1 3.8 - - - -
239C ASN* 3.3 26.6 + - - -
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C PRO* 3.2 8.8 - - - +
138C LEU* 2.8 50.6 + - + -
140C PHE* 3.9 21.8 - - + -
150C PHE* 4.6 2.7 - - + -
153C PHE* 3.9 24.0 - - + -
157C LEU* 2.9 18.8 + - + +
158C LEU* 3.2 8.5 + - - +
160C SER* 1.3 76.0 - - - +
162C ALA* 1.3 56.3 + - - +
164C GLU 4.7 0.2 - - - -
166C LEU* 3.9 27.8 - - + +
167C THR* 4.1 11.0 - - + -
243C THR* 3.5 34.3 - - + +
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C PRO* 3.6 11.9 - - - +
138C LEU 3.4 17.1 - - - +
139C ASN* 4.7 5.0 - - - +
140C PHE* 4.0 11.9 - - + +
158C LEU 3.1 12.1 + - - +
159C LEU* 3.5 15.0 - - + +
160C SER 3.1 0.4 - - - -
161C LEU* 1.3 78.5 - - - +
163C VAL* 1.3 66.2 + - + +
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Residues in contact with VAL 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C PRO* 4.0 7.0 - - - +
159C LEU 3.6 16.8 - - - +
160C SER* 3.7 5.2 - - - +
162C ALA* 1.3 88.6 - - + +
164C GLU* 1.3 74.9 + - + +
165C PRO* 4.2 3.6 - - - +
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Residues in contact with GLU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C PRO* 3.0 19.6 - - - +
160C SER* 2.8 41.9 + - - +
161C LEU 3.7 2.4 - - - +
163C VAL* 1.3 82.8 - - + +
165C PRO* 1.3 69.1 - - + +
166C LEU* 2.8 34.8 + - + +
237C ALA* 5.5 1.2 - - - +
239C ASN* 3.3 21.1 + - - +
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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