Contacts of the strand formed by residues 118 - 122 (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 MET 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ILE 2.9 15.7 + - - +
86C MET* 3.0 36.4 - - + -
87C LEU* 2.9 29.9 + - - +
117C ARG* 1.3 73.8 - - - +
119C LEU* 1.3 70.0 + - - +
120C LEU* 5.7 4.9 - - + -
146C ILE* 4.3 13.2 - - + +
162C ALA* 3.1 37.0 - - + +
165C THR* 3.6 27.4 - - - -
166C LEU* 3.9 17.0 - - + -
169C ASP* 6.4 0.2 - - - -
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Residues in contact with LEU 119 (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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87C LEU* 3.1 36.6 - - + +
88C VAL 4.5 0.7 - - - -
89C TYR* 3.8 15.3 - - + -
97C PHE* 5.4 7.4 - - + -
100C ILE* 5.3 18.8 - - + -
104C LEU* 6.4 1.6 - - + -
118C MET* 1.3 83.9 - - - +
120C LEU* 1.3 74.2 + - - +
121C GLY 4.2 0.3 + - - -
137C GLY 5.9 2.7 - - - +
140C ILE* 6.0 8.3 - - + -
141C ALA* 5.6 3.8 - - + +
146C ILE* 3.6 25.8 - - + +
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Residues in contact with LEU 120 (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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14C LEU* 4.9 3.6 - - + -
25C VAL* 4.2 31.2 - - + -
86C MET* 4.2 29.4 - - + -
87C LEU 3.1 14.8 + - - +
88C VAL* 3.3 16.4 - - + -
89C TYR* 2.9 57.8 + - - +
118C MET* 5.7 5.8 - - + -
119C LEU* 1.3 76.2 - - - +
121C GLY* 1.3 58.0 + - - +
122C ASN* 4.3 11.4 - - + -
150C GLU 6.0 0.4 - - - +
151C THR* 4.6 13.0 - - + +
162C ALA* 6.2 2.7 - - + -
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Residues in contact with GLY 121 (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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89C TYR* 3.2 11.2 - - - -
91C ILE* 4.6 13.5 - - - -
119C LEU 4.2 0.4 + - - -
120C LEU* 1.3 72.1 - - - +
122C ASN* 1.3 56.2 + - - -
124C CYS 5.3 0.2 - - - -
150C GLU* 3.1 18.9 - - - +
151C THR* 2.4 39.7 + - - +
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Residues in contact with ASN 122 (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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20C VAL 3.8 4.9 + - - +
21C GLY* 3.6 24.2 + - - -
25C VAL* 4.5 12.1 - - + +
88C VAL* 5.5 0.2 - - + -
89C TYR 2.7 15.8 + - - +
90C ASP* 2.8 18.4 - - - +
91C ILE* 3.3 10.4 + - - +
120C LEU* 4.3 11.7 - - + -
121C GLY* 1.3 74.0 - - - -
123C LYS* 1.3 85.6 + - + +
124C CYS 3.1 1.7 + - - -
151C THR* 2.9 21.0 + - - +
152C SER* 3.5 0.2 - - - -
153C ALA* 3.2 11.4 + - - +
159C ILE* 5.2 0.3 - - - +
202C GNP 3.1 35.5 + - - +
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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