Contacts of the helix formed by residues 158 - 172 (chain C) in PDB entry 5LPN
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 ASN 158 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C GLU 3.3 27.3 + - - +
151C THR* 3.1 12.9 - - + +
156C ASN 4.4 0.2 + - - -
157C ILE* 1.3 71.0 - - + +
159C ILE* 1.3 58.3 + - - +
160C GLU 3.6 1.3 - - - +
161C LYS* 4.2 16.7 - - - +
162C ALA* 3.1 21.7 + - - +
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Residues in contact with ILE 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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25C VAL* 3.4 33.7 - - + +
28C ARG* 4.3 6.3 - - + +
29C PHE* 3.5 41.1 - - + +
122C ASN* 5.2 0.4 - - - +
151C THR* 3.5 22.2 - - + +
152C SER 3.8 20.2 - - - +
153C ALA* 4.4 5.8 - - - +
156C ASN* 4.9 5.4 - - - +
157C ILE 2.7 19.7 + - - +
158C ASN* 1.3 72.1 - - - +
160C GLU* 1.3 72.0 + - + +
162C ALA* 3.0 18.3 + - + +
163C PHE* 3.2 11.6 + - + -
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Residues in contact with GLU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 3.8 18.2 - - + -
49C LYS* 4.1 17.9 + - - -
158C ASN* 4.6 0.2 - - - +
159C ILE* 1.3 81.8 - - - +
161C LYS* 1.3 64.6 + - - +
163C PHE* 3.1 2.3 + - - +
164C LEU* 3.1 48.0 + - + +
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Residues in contact with LYS 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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158C ASN* 4.0 20.7 + - - +
159C ILE 3.3 0.4 - - - -
160C GLU* 1.3 79.8 - - - +
162C ALA* 1.3 62.1 + - - +
164C LEU* 4.1 19.5 - - + -
165C THR* 2.4 52.2 + - - +
168C GLU* 6.0 0.4 - - - +
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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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86C MET* 5.4 1.8 - - - -
118C MET* 3.1 33.8 - - + +
120C LEU* 6.2 3.4 - - + -
151C THR* 4.1 13.9 - - + -
158C ASN 3.1 21.5 + - - +
159C ILE* 3.0 10.8 + - + +
161C LYS* 1.3 75.9 - - - +
163C PHE* 1.3 64.9 + - + +
165C THR* 3.2 15.7 + - - -
166C LEU 3.4 0.7 + - - -
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Residues in contact with PHE 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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12C LEU* 4.3 16.8 - - + +
14C LEU* 4.8 3.4 - - + -
25C VAL* 4.2 21.8 - - + -
26C LEU* 4.4 14.4 - - + -
29C PHE* 3.1 65.7 - + + -
60C LEU* 5.7 5.1 - - + +
62C ILE* 4.4 14.8 - - + -
86C MET* 3.1 38.1 - - + -
118C MET* 5.0 0.4 - - - -
159C ILE* 3.2 15.7 + - + -
160C GLU 3.1 6.3 + - - +
162C ALA* 1.3 77.1 - - + +
164C LEU* 1.3 68.2 + - + +
166C LEU* 2.9 17.8 + - - +
167C ALA* 3.1 11.0 + - - +
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Residues in contact with LEU 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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29C PHE* 4.1 15.3 - - + -
49C LYS* 6.1 0.2 - - - +
51C VAL* 5.1 16.2 - - + -
53C LEU* 4.3 18.5 - - + +
160C GLU* 3.1 53.7 + - + +
161C LYS* 4.1 24.5 - - + +
163C PHE* 1.3 77.0 - - - +
165C THR* 1.3 61.2 - - - +
167C ALA* 3.3 12.6 - - + +
168C GLU* 2.9 19.8 + - - +
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Residues in contact with THR 165 (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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118C MET* 3.6 21.5 - - - -
161C LYS* 2.4 40.9 + - - +
162C ALA* 3.2 11.4 - - - -
163C PHE 3.0 0.2 - - - -
164C LEU* 1.3 76.1 - - - +
166C LEU* 1.3 57.8 + - - +
168C GLU* 2.8 25.2 + - - +
169C ASP* 2.8 29.9 - - - +
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Residues in contact with LEU 166 (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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12C LEU* 3.7 29.4 - - + -
84C GLY* 3.8 4.0 - - - -
85C ILE 3.4 33.9 - - - +
86C MET* 3.5 17.5 - - + -
116C GLU* 4.4 20.4 - - + -
117C ARG 5.1 0.4 - - - -
118C MET* 3.9 27.6 - - + +
162C ALA 3.4 5.2 + - - +
163C PHE* 2.9 11.4 + - - +
165C THR* 1.3 79.4 - - - +
167C ALA* 1.3 64.2 + - - +
169C ASP* 3.1 12.7 + - + +
170C ILE* 3.0 25.4 + - + +
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Residues in contact with ALA 167 (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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10C PHE* 4.2 22.7 - - + -
12C LEU* 5.7 1.4 - - - +
51C VAL* 5.8 3.6 - - + -
53C LEU* 3.5 22.0 - - + -
58C ILE* 5.6 1.6 - - + -
60C LEU* 5.4 14.2 - - + +
163C PHE 3.1 8.7 + - - +
164C LEU* 3.3 16.2 - - - +
166C LEU* 1.3 76.5 - - - +
168C GLU* 1.3 61.2 + - - +
170C ILE* 4.0 0.6 - - - +
171C LEU* 2.9 28.9 + - - +
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Residues in contact with GLU 168 (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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53C LEU* 4.4 6.4 - - + +
54C GLN* 5.8 7.6 - - - +
161C LYS* 6.0 0.2 - - - +
164C LEU 2.9 10.7 + - - +
165C THR* 2.8 22.5 + - - +
167C ALA* 1.3 71.7 - - - +
169C ASP* 1.3 84.6 + - - +
170C ILE 3.1 0.2 + - - -
171C LEU* 3.9 2.5 - - - +
172C ARG* 2.9 39.8 + - + +
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Residues in contact with ASP 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLU* 4.1 23.7 - - + +
118C MET* 6.4 0.2 - - - -
146C ILE* 5.2 7.1 - - - +
165C THR* 2.8 21.7 + - - +
166C LEU* 3.1 15.1 + - + +
168C GLU* 1.3 96.0 - - - +
170C ILE* 1.3 62.5 + - - +
172C ARG* 4.2 4.0 - - - +
173C LYS* 3.7 14.9 + - - +
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Residues in contact with ILE 170 (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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10C PHE* 3.7 27.8 - - + -
12C LEU* 3.9 15.3 - - + -
83C MET* 3.6 37.5 - - + +
84C GLY* 3.3 34.3 - - - +
116C GLU* 4.3 17.0 - - + -
166C LEU* 3.0 15.7 + - + +
167C ALA 4.0 1.3 - - - +
169C ASP* 1.3 77.8 - - - +
171C LEU* 1.3 62.1 + - - +
172C ARG 3.1 1.1 - - - -
173C LYS* 2.8 25.8 + - - +
174C THR* 3.1 11.4 + - - +
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Residues in contact with LEU 171 (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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8C LEU* 5.8 3.8 - - + -
10C PHE* 3.9 13.9 - - + -
53C LEU* 5.0 5.2 - - + -
54C GLN* 3.3 38.8 - - + +
56C LYS* 4.6 11.7 - - + -
58C ILE* 4.0 26.7 - - + -
167C ALA 2.9 21.3 + - - +
168C GLU* 4.3 2.7 - - - +
170C ILE* 1.3 77.3 - - - +
172C ARG* 1.3 58.4 + - + +
174C THR* 3.1 18.1 + - + -
175C PRO* 2.8 31.8 - - + +
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Residues in contact with ARG 172 (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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168C GLU* 2.9 30.9 + - + +
169C ASP* 4.5 4.0 - - - +
171C LEU* 1.3 78.9 - - + +
173C LYS* 1.3 63.0 + - - +
174C THR 3.1 0.2 - - - -
175C PRO* 3.2 20.3 - - - +
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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