Contacts of the helix formed by residues 2190 - 2209 (chain L) in PDB entry 6LTJ
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 GLY2190 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152L VAL* 3.3 4.9 - - - +
2188L GLN 3.0 2.2 + - - -
2189L LYS* 1.3 76.5 - - - +
2191L SER* 1.3 60.8 + - - +
2192L ILE 3.7 0.4 - - - -
2193L GLY* 4.0 8.3 - - - -
2194L ASN* 2.8 35.0 + - - +
2254L TYR* 4.6 9.9 - - - -
163P ARG* 6.5 0.2 - - - -
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Residues in contact with SER2191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2152L VAL* 3.7 25.5 - - - +
2155L LEU* 4.8 1.4 - - - +
2171L LEU* 5.3 2.5 - - - -
2185L ILE* 2.8 37.3 + - - -
2186L ALA* 3.4 11.8 + - - -
2188L GLN 3.2 10.1 + - - -
2189L LYS 3.6 0.2 - - - -
2190L GLY* 1.3 74.1 - - - +
2192L ILE* 1.3 65.5 + - - +
2193L GLY 3.2 1.1 - - - -
2194L ASN* 3.1 3.9 + - - +
2195L LEU* 2.9 35.9 + - - +
2241L LEU* 5.3 1.6 - - - -
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Residues in contact with ILE2192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2186L ALA* 4.4 11.4 - - + +
2191L SER* 1.3 80.1 + - - +
2193L GLY* 1.3 61.9 + - - +
2195L LEU* 3.4 8.9 + - - +
2196L LEU* 2.9 27.1 + - + +
2238L LEU* 3.8 17.5 - - + -
2241L LEU* 4.0 18.8 - - + -
2250L GLU* 3.6 37.0 - - + +
2251L PHE* 3.8 33.4 - - + -
2254L TYR* 3.7 28.0 - - + -
2258L LEU* 6.0 0.2 - - + -
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Residues in contact with GLY2193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2190L GLY* 4.0 5.5 - - - -
2191L SER 3.2 0.8 - - - -
2192L ILE* 1.3 80.0 - - - +
2194L ASN* 1.3 60.1 + - - +
2196L LEU* 3.5 1.1 + - - -
2197L GLY* 2.9 23.4 + - - -
2254L TYR* 3.5 36.3 + - - -
2257L ARG* 3.6 11.0 + - - -
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Residues in contact with ASN2194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2152L VAL* 2.8 36.1 + - + +
2155L LEU* 3.8 22.7 - - + +
2156L SER* 3.2 25.4 - - - +
2164L ARG* 4.7 2.9 + - - -
2190L GLY* 2.8 23.5 + - - +
2191L SER 3.1 5.4 + - - +
2193L GLY* 1.3 76.9 - - - +
2195L LEU* 1.3 59.7 + - - +
2197L GLY* 3.2 2.3 + - - +
2198L PHE* 2.9 28.4 + - - +
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Residues in contact with LEU2195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2155L LEU* 3.9 20.9 - - + -
2168L VAL* 4.0 23.8 - - + -
2171L LEU* 4.9 10.1 - - + -
2185L ILE* 5.7 1.1 - - + -
2191L SER* 2.9 21.4 + - - +
2192L ILE* 3.8 3.8 - - - +
2194L ASN* 1.3 77.5 - - - +
2196L LEU* 1.3 62.9 + - - +
2198L PHE* 3.2 7.6 + - - +
2199L LEU* 3.0 27.0 + - - +
2234L ALA* 4.4 7.4 - - + +
2237L ALA* 4.2 20.9 - - + -
2238L LEU* 3.8 34.1 - - + -
2241L LEU* 3.9 21.1 - - + -
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Residues in contact with LEU2196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2192L ILE* 2.9 20.2 + - + +
2193L GLY 3.7 4.5 - - - +
2195L LEU* 1.3 75.8 - - - +
2197L GLY* 1.3 58.2 + - - +
2199L LEU* 3.3 4.5 + - + +
2200L GLU* 2.9 37.3 + - - +
2238L LEU* 3.8 13.0 - - + -
2254L TYR* 3.5 50.3 - - + +
2257L ARG* 3.7 24.0 - - + +
2258L LEU* 3.6 28.5 - - + +
2261L ILE* 3.6 21.5 - - + -
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Residues in contact with GLY2197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2158L ARG* 5.0 4.3 - - - -
2164L ARG* 3.9 2.9 - - - -
2193L GLY 2.9 17.0 + - - -
2194L ASN* 3.2 4.5 + - - -
2195L LEU 3.2 0.2 - - - -
2196L LEU* 1.3 73.6 - - - +
2198L PHE* 1.3 60.7 + - - +
2200L GLU* 3.7 11.1 - - - +
2201L ASP* 2.8 41.1 + - - +
2257L ARG* 3.9 2.7 - - - +
170P GLU* 5.6 1.8 - - - -
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Residues in contact with PHE2198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2155L LEU* 4.6 10.3 - - + -
2164L ARG* 3.6 48.5 - - + +
2165L GLU* 4.0 33.4 - - + -
2168L VAL* 4.3 11.2 - - + -
2194L ASN 2.9 13.7 + - - +
2195L LEU* 3.4 10.5 - - - +
2197L GLY* 1.3 76.0 - - - +
2199L LEU* 1.3 65.2 + - + +
2201L ASP* 3.4 1.9 + - - +
2202L SER* 3.0 41.9 + - - -
2226L THR* 4.9 2.5 - - - -
2230L MET* 3.9 33.9 - - + -
2231L MET* 4.4 2.7 - - + -
2234L ALA* 3.9 18.2 - - + -
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Residues in contact with LEU2199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2195L LEU 3.0 12.5 + - - +
2196L LEU* 3.6 7.9 - - + +
2198L PHE* 1.3 76.9 - - + +
2200L GLU* 1.3 57.0 + - - +
2202L SER* 3.3 4.6 + - - -
2203L LEU* 2.9 31.5 + - - +
2231L MET* 3.3 45.3 - - + +
2234L ALA* 4.1 8.5 - - + -
2235L ALA* 4.5 7.6 - - + +
2238L LEU* 4.1 19.1 - - + -
2261L ILE* 3.8 20.9 - - + -
2267L MET* 4.6 4.6 - - + +
2271L VAL* 4.2 8.3 - - + -
2275L ILE* 3.9 29.6 - - + -
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Residues in contact with GLU2200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2196L LEU* 2.9 20.3 + - - +
2197L GLY* 3.7 7.1 - - - +
2199L LEU* 1.3 73.9 - - - +
2201L ASP* 1.3 61.8 + - - +
2203L LEU* 3.3 7.6 + - - +
2204L ALA* 2.9 28.3 + - - +
2257L ARG* 3.0 56.6 + - - +
2260L ASP* 5.9 1.2 - - - +
2261L ILE* 3.8 21.9 - - + +
170P GLU* 4.3 1.9 - - - +
173P LYS* 3.9 22.0 + - - +
174P ARG* 4.9 1.2 + - - -
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Residues in contact with ASP2201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2158L ARG* 2.3 50.4 + - - -
2164L ARG* 3.3 18.1 + - - +
2197L GLY* 2.8 20.2 + - - +
2198L PHE 3.8 3.6 - - - +
2200L GLU* 1.3 76.3 - - - +
2202L SER* 1.3 57.8 + - - +
2204L ALA* 3.2 10.3 + - - +
2205L ALA* 2.9 27.0 + - - +
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Residues in contact with SER2202 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2198L PHE* 3.0 32.7 + - - -
2199L LEU* 3.6 5.4 - - - -
2201L ASP* 1.3 78.0 - - - +
2203L LEU* 1.3 52.3 + - - +
2205L ALA* 3.3 3.9 + - - +
2206L THR* 2.7 36.4 + - - -
2226L THR* 3.3 26.5 + - - +
2231L MET* 3.5 31.1 - - - +
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Residues in contact with LEU2203 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2199L LEU 2.9 13.5 + - - +
2200L GLU* 3.7 7.0 - - - +
2201L ASP 3.3 0.2 - - - -
2202L SER* 1.3 74.5 - - - +
2204L ALA* 1.3 60.9 + - - +
2206L THR* 3.2 9.9 + - + +
2207L GLN* 2.9 32.3 + - - +
2231L MET* 4.9 2.0 - - - -
2261L ILE* 4.4 17.3 - - + +
2264L SER* 4.1 24.5 - - - +
2266L LEU* 3.6 35.7 - - + +
2267L MET* 3.6 44.0 - - + -
2268L ASN* 5.8 0.2 - - - +
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Residues in contact with ALA2204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2200L GLU 2.9 17.6 + - - +
2201L ASP* 3.2 12.5 + - - +
2203L LEU* 1.3 75.2 - - - +
2205L ALA* 1.3 58.3 + - - +
2207L GLN* 3.6 9.9 - - - +
2208L PHE* 2.8 34.0 + - - +
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Residues in contact with ALA2205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2201L ASP 2.9 15.0 + - - +
2202L SER 3.5 8.1 - - - +
2203L LEU 3.2 0.2 - - - -
2204L ALA* 1.3 71.8 - - - +
2206L THR* 1.3 63.2 + - - +
2207L GLN 2.9 6.3 + - - -
2208L PHE* 3.1 14.0 + - - -
2209L GLN* 3.7 21.0 + - - +
2225L PRO* 3.5 34.8 - - + -
2226L THR* 3.9 12.3 - - + -
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Residues in contact with THR2206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2202L SER 2.7 22.6 + - - -
2203L LEU* 3.2 10.7 + - + -
2205L ALA* 1.3 74.1 - - - +
2207L GLN* 1.3 56.6 + - - +
2209L GLN* 4.9 3.4 - - - -
2210L GLN* 3.0 24.5 - - - +
2226L THR* 4.4 3.2 - - - +
2231L MET* 3.3 19.9 - - + +
2266L LEU* 3.6 27.7 - - + +
2268L ASN* 5.2 7.4 - - - +
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Residues in contact with GLN2207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2203L LEU 2.9 15.9 + - - +
2204L ALA* 3.6 10.6 - - - +
2206L THR* 1.3 78.8 - - - +
2208L PHE* 1.3 69.3 + - - +
2209L GLN 3.3 2.5 - - - -
2210L GLN* 2.9 41.0 + - + +
2266L LEU* 3.7 30.7 - - + -
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Residues in contact with PHE2208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2204L ALA 2.8 20.3 + - - +
2205L ALA* 3.1 7.5 + - - +
2207L GLN* 1.3 85.4 + - - +
2209L GLN* 1.3 71.1 + - + +
2210L GLN 3.5 2.8 + - - -
2225L PRO* 6.3 2.9 - - + -
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Residues in contact with GLN2209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2205L ALA 3.7 16.1 + - - +
2206L THR* 4.9 2.6 - - - -
2207L GLN 3.3 0.4 - - - -
2208L PHE* 1.3 86.6 - - + +
2210L GLN* 1.3 77.5 + - - +
2225L PRO* 4.1 24.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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