Contacts of the helix formed by residues 2149 - 2160 (chain C) in PDB entry 4ILG
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 LYS2149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2148C SER* 1.3 72.0 - - - +
2150C ASN* 1.3 69.1 + - - +
2152C TRP* 3.8 11.8 - - + +
2153C ARG* 3.2 48.6 + - - +
2388C ARG* 3.4 37.2 - - - +
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Residues in contact with ASN2150 (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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2148C SER* 3.0 20.9 + - - +
2149C LYS* 1.3 80.4 + - - +
2151C GLU* 1.3 69.4 + - - +
2153C ARG* 2.9 28.1 + - - +
2154C LYS* 3.5 10.3 + - - +
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Residues in contact with GLU2151 (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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2148C SER* 3.5 19.6 + - - +
2150C ASN* 1.3 83.3 - - + +
2152C TRP* 1.3 66.9 + - - +
2154C LYS* 3.1 39.7 + - - +
2155C SER* 3.3 23.7 + - - -
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Residues in contact with TRP2152 (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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2148C SER 3.8 10.0 + - - +
2149C LYS* 3.8 16.2 - - + +
2151C GLU* 1.3 78.5 - - - +
2153C ARG* 1.3 78.7 + - + +
2155C SER* 3.2 7.7 + - - -
2156C ALA* 3.1 23.3 + - + +
2361C PHE* 3.7 25.4 - + + -
2383C TYR* 2.9 62.7 + + - +
2384C ASN 3.5 11.7 - - - -
2385C GLU* 4.4 3.3 - - - +
2387C HIS* 3.8 3.4 - - + -
2388C ARG* 3.3 65.0 - - + +
2389C PRO* 5.7 0.2 - - + -
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Residues in contact with ARG2153 (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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2030B PRO* 3.9 33.4 - - + -
2149C LYS* 3.2 52.2 + - - +
2150C ASN* 2.9 17.2 + - - +
2152C TRP* 1.3 93.4 - - - +
2154C LYS* 1.3 60.7 + - + +
2156C ALA* 3.4 5.6 + - + +
2157C ILE* 3.1 32.8 + - + +
2388C ARG* 5.2 0.8 - - - +
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Residues in contact with LYS2154 (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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2024B MET* 4.4 8.1 - - + +
2028B SER 5.1 12.1 - - - +
2030B PRO* 6.1 2.5 - - + -
2150C ASN 3.9 11.9 - - - +
2151C GLU* 3.1 37.4 + - - +
2152C TRP 3.3 0.6 - - - -
2153C ARG* 1.3 74.2 - - + +
2155C SER* 1.3 65.5 + - - +
2157C ILE* 3.4 12.0 + - + +
2158C ALA* 3.2 20.6 + - - +
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Residues in contact with SER2155 (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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2151C GLU 3.3 11.4 + - - -
2152C TRP* 3.2 7.0 + - - -
2154C LYS* 1.3 75.7 - - - +
2156C ALA* 1.3 65.3 + - - +
2158C ALA* 3.4 7.3 + - - +
2159C ASN* 3.3 25.6 + - - +
2198C ASP* 4.7 0.6 - - - +
2199C VAL* 5.3 3.3 - - - +
2383C TYR* 3.4 34.1 + - - -
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Residues in contact with ALA2156 (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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2152C TRP* 3.1 16.9 + - + +
2153C ARG* 3.7 10.8 - - + +
2155C SER* 1.3 79.5 - - - +
2157C ILE* 1.3 61.9 + - + +
2159C ASN* 3.3 14.1 + - - +
2160C THR* 3.3 16.8 + - - +
2383C TYR* 3.7 30.5 - - + +
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Residues in contact with ILE2157 (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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2024B MET* 4.4 10.3 - - + -
2027B LEU* 3.7 48.0 - - + +
2028B SER* 4.4 4.9 - - - +
2030B PRO* 3.5 35.7 - - + -
2153C ARG* 3.1 22.6 + - + +
2154C LYS* 3.7 11.2 - - - +
2155C SER 3.2 0.4 - - - -
2156C ALA* 1.3 74.6 - - + +
2158C ALA* 1.3 65.9 + - - +
2160C THR* 2.6 32.6 + - + +
2161C LEU* 4.1 3.3 + - - +
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Residues in contact with ALA2158 (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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2020B GLU* 5.2 2.1 - - - +
2024B MET* 3.7 30.9 - - + -
2154C LYS 3.2 8.1 + - - +
2155C SER* 3.4 9.4 + - - +
2157C ILE* 1.3 78.6 - - - +
2159C ASN* 1.3 63.6 + - - +
2161C LEU* 3.2 19.6 + - - +
2162C LEU* 4.1 1.4 + - - +
2199C VAL* 4.0 27.9 - - + +
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Residues in contact with ASN2159 (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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2155C SER 3.3 5.5 + - - +
2156C ALA* 3.3 10.4 + - - +
2157C ILE 3.1 1.0 - - - -
2158C ALA* 1.3 78.8 - - - +
2160C THR* 1.3 59.3 + - - +
2161C LEU 3.1 1.9 + - - -
2162C LEU* 3.2 28.4 + - + +
2195C GLU* 4.6 7.5 - - - +
2197C SER 3.4 19.7 + - - +
2198C ASP* 2.7 24.5 + - - +
2199C VAL* 3.0 32.6 + - - +
2381C GLU* 6.5 1.8 - - + -
2382C PHE* 4.0 5.5 - - - +
2383C TYR* 3.4 19.8 - - - +
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Residues in contact with THR2160 (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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2027B LEU* 4.4 7.1 - - - +
2156C ALA 3.3 16.8 - - - +
2157C ILE* 2.6 22.8 + - + +
2159C ASN* 1.3 74.9 - - - +
2161C LEU* 1.3 68.2 + - - +
2162C LEU 3.4 0.4 - - - -
2163C TYR* 3.2 24.6 - - - -
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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