Contacts of the helix formed by residues 2160 - 2178 (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 ASN2160 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2111L VAL* 5.9 0.3 - - - +
2116L ARG* 3.0 37.6 + - - +
2154L PHE* 5.9 4.0 - - - -
2157L ASP* 3.1 33.0 + - - +
2159L LYS* 1.3 83.9 - - - +
2161L PRO* 1.3 61.9 - - - +
2162L VAL* 3.4 4.3 - - + +
2163L CYS* 3.9 17.1 - - + +
2164L ARG* 3.0 19.8 + - - +
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Residues in contact with PRO2161 (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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447I LEU* 4.3 21.3 - - + -
2158L ARG 4.8 6.7 - - - +
2159L LYS* 3.2 15.0 - - - +
2160L ASN* 1.3 80.8 - - - +
2162L VAL* 1.3 66.5 + - + +
2164L ARG* 3.1 13.9 + - + +
2165L GLU* 2.9 32.9 + - + +
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Residues in contact with VAL2162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445I GLN* 3.6 22.4 - - + +
446I SER 3.3 27.8 - - - +
447I LEU* 3.7 22.6 - - + +
450I ALA* 4.4 5.6 - - + +
2116L ARG* 5.1 8.5 - - - +
2160L ASN* 5.0 2.0 - - - -
2161L PRO* 1.3 82.0 - - + +
2163L CYS* 1.3 72.9 + - - +
2165L GLU* 3.3 2.3 + - - +
2166L MET* 2.9 50.1 + - + +
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Residues in contact with CYS2163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445I GLN* 4.5 3.4 - - - -
2116L ARG* 3.7 51.1 - - - -
2119L LEU* 3.8 23.9 - - + +
2154L PHE* 4.1 12.9 - - + +
2157L ASP* 4.3 5.2 - - - +
2160L ASN* 3.5 19.0 + - + +
2161L PRO 3.4 0.2 - - - -
2162L VAL* 1.3 86.9 - - - +
2164L ARG* 1.3 57.2 + - - +
2166L MET* 3.4 4.9 + - - +
2167L ALA* 2.9 29.8 + - - +
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Residues in contact with ARG2164 (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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2154L PHE 3.5 17.5 + - - +
2155L LEU* 2.9 29.8 + - + +
2156L SER* 5.5 0.2 - - - +
2157L ASP* 3.8 5.8 - - - +
2158L ARG* 3.5 35.2 - - - +
2160L ASN 3.0 18.6 + - - +
2161L PRO* 3.1 10.7 + - - +
2163L CYS* 1.3 77.4 - - - +
2165L GLU* 1.3 56.8 + - - +
2167L ALA* 3.3 3.3 + - - +
2168L VAL* 3.0 26.5 + - - +
2194L ASN 4.7 1.4 + - - -
2197L GLY* 3.9 0.8 - - - -
2198L PHE* 3.6 50.6 - - + +
2201L ASP* 3.3 34.8 + - - +
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Residues in contact with GLU2165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447I LEU* 3.2 24.4 - - + +
450I ALA* 5.9 2.4 - - + +
451I ARG* 2.4 44.6 + - - +
454I GLU* 5.8 1.8 - - - +
2161L PRO* 2.9 17.1 + - + +
2162L VAL 3.9 3.4 - - - +
2164L ARG* 1.3 74.8 - - - +
2166L MET* 1.3 63.9 + - - +
2168L VAL* 3.0 9.4 - - - +
2169L VAL* 2.9 27.8 + - - +
2198L PHE* 4.0 23.0 - - + -
2226L THR* 4.3 6.8 + - - -
2230L MET* 3.7 24.5 - - + +
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Residues in contact with MET2166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445I GLN* 3.7 33.0 - - + +
446I SER 5.2 0.2 - - - +
450I ALA* 4.3 13.9 - - + -
454I GLU* 4.7 9.4 - - - +
2116L ARG 4.4 0.2 - - - +
2119L LEU* 3.7 22.7 - - + -
2120L GLU* 3.6 36.8 - - + +
2123L SER* 3.7 16.5 - - - +
2162L VAL* 2.9 42.0 + - + +
2163L CYS* 3.7 7.0 - - - +
2165L GLU* 1.3 75.8 - - - +
2167L ALA* 1.3 57.8 + - - +
2169L VAL* 3.3 8.1 + - - +
2170L LEU* 3.0 28.2 + - - +
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Residues in contact with ALA2167 (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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2119L LEU* 3.9 0.6 - - - +
2151L MET* 3.6 31.4 - - - +
2154L PHE* 3.6 24.0 - - + -
2155L LEU* 4.2 6.5 - - + +
2163L CYS 2.9 17.9 + - - +
2164L ARG 3.5 6.3 - - - +
2166L MET* 1.3 77.2 - - - +
2168L VAL* 1.3 57.5 + - - +
2170L LEU* 3.4 2.5 + - - +
2171L LEU* 2.9 33.1 + - - +
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Residues in contact with VAL2168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2155L LEU* 3.8 14.6 - - + +
2164L ARG 3.0 10.4 + - - +
2165L GLU* 3.0 30.3 - - - +
2167L ALA* 1.3 77.2 - - - +
2169L VAL* 1.3 57.5 + - - +
2171L LEU* 4.4 4.0 - - - +
2172L ALA* 2.9 29.0 + - + +
2195L LEU* 4.0 15.7 - - + -
2198L PHE* 4.3 14.4 - - + -
2230L MET* 3.6 17.5 - - + +
2233L ARG* 4.7 2.0 - - + -
2234L ALA* 3.7 39.0 - - + +
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Residues in contact with VAL2169 (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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454I GLU* 3.9 31.6 - - + -
2123L SER* 4.0 20.6 - - - +
2127L ILE* 4.7 1.3 - - + -
2165L GLU 2.9 21.9 + - - +
2166L MET 3.6 4.7 - - - +
2168L VAL* 1.3 74.8 - - - +
2170L LEU* 1.3 66.4 + - - +
2172L ALA* 3.8 3.8 - - - +
2173L ASN* 3.0 46.9 + - - +
2230L MET* 3.6 20.9 - - + -
2233L ARG* 3.9 20.2 - - - +
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Residues in contact with LEU2170 (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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2119L LEU* 3.5 28.5 - - + +
2122L LEU* 3.4 49.6 - - + +
2123L SER* 3.5 12.8 - - - +
2126L SER* 3.7 12.6 - - - +
2135L ILE* 5.7 1.1 - - + -
2147L LEU* 5.1 4.7 - - + -
2151L MET* 3.6 24.5 - - + -
2166L MET 3.0 8.3 + - - +
2167L ALA 3.6 7.6 - - - +
2169L VAL* 1.3 77.4 - - - +
2171L LEU* 1.3 58.1 + - - +
2173L ASN* 3.8 0.5 - - - +
2174L LEU* 2.9 50.9 + - + +
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Residues in contact with LEU2171 (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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2148L TYR* 4.5 11.4 - - + -
2151L MET* 3.9 30.3 - - + -
2152L VAL* 4.4 11.9 - - + -
2155L LEU* 3.5 28.3 - - + -
2167L ALA 2.9 22.5 + - - +
2168L VAL* 4.0 5.8 - - - +
2170L LEU* 1.3 75.2 - - - +
2172L ALA* 1.3 57.8 + - - +
2174L LEU* 5.2 1.8 - - + -
2175L ALA* 2.9 34.1 + - - +
2185L ILE* 3.7 41.1 - - + +
2191L SER* 5.3 1.8 - - - -
2195L LEU* 4.9 13.9 - - + -
2237L ALA* 4.5 2.7 - - + -
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Residues in contact with ALA2172 (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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2168L VAL 2.9 18.5 + - - +
2169L VAL* 3.8 3.8 - - - +
2171L LEU* 1.3 77.1 - - - +
2173L ASN* 1.3 59.3 + - - +
2175L ALA* 3.9 0.7 - - - +
2176L GLN* 2.9 48.7 + - - +
2233L ARG* 3.4 36.1 - - + +
2237L ALA* 3.6 13.8 - - + +
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Residues in contact with ASN2173 (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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458I LYS* 3.8 21.1 + - - -
2126L SER* 3.1 50.4 + - - +
2127L ILE* 3.8 9.4 - - - +
2129L ASP* 5.6 1.7 - - - +
2132L VAL* 4.1 6.5 - - + +
2169L VAL* 3.0 37.9 + - - +
2170L LEU 3.9 0.2 - - - +
2172L ALA* 1.3 78.9 - - - +
2174L LEU* 1.3 59.8 + - - +
2176L GLN* 3.4 11.1 + - - +
2177L GLY* 2.9 24.9 + - - -
2233L ARG* 4.6 6.2 + - - +
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Residues in contact with LEU2174 (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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2126L SER* 4.4 16.2 - - - -
2132L VAL* 4.4 11.2 - - + -
2135L ILE* 4.3 22.9 - - + -
2136L LEU* 4.2 14.6 - - + +
2144L LEU* 5.7 0.4 - - + -
2147L LEU* 4.6 14.1 - - + -
2148L TYR* 3.7 27.6 - - + +
2151L MET* 6.2 1.1 - - + -
2170L LEU* 2.9 36.8 + - + +
2171L LEU* 4.1 4.3 - - + +
2173L ASN* 1.3 77.5 - - - +
2175L ALA* 1.3 58.5 + - - +
2177L GLY* 2.9 18.9 + - - -
2178L ASP 3.4 0.2 + - - -
2181L ALA* 3.4 22.2 - - + +
2185L ILE* 4.2 9.2 - - + -
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Residues in contact with ALA2175 (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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2171L LEU 2.9 20.4 + - - +
2172L ALA* 3.9 2.7 - - - +
2174L LEU* 1.3 75.3 - - - +
2176L GLN* 1.3 57.8 + - - +
2178L ASP 2.8 23.7 - - - +
2182L ALA* 3.8 11.4 - - - +
2185L ILE* 3.9 11.7 - - + +
2237L ALA* 4.4 5.6 - - + +
2240L ALA* 3.5 23.8 - - + +
2241L LEU* 3.9 22.9 - - + -
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Residues in contact with GLN2176 (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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458I LYS* 5.6 3.3 + - - +
2172L ALA* 2.9 37.9 + - - +
2173L ASN* 3.7 10.8 + - - +
2175L ALA* 1.3 73.8 - - - +
2177L GLY* 1.3 67.1 - - - +
2178L ASP 4.6 0.7 - - - +
2233L ARG* 5.8 0.6 - - - +
2236L ARG* 3.7 35.8 - - - +
2240L ALA* 3.9 17.3 - - + -
40M ARG* 4.5 5.6 + - - -
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Residues in contact with GLY2177 (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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2129L ASP* 5.9 1.3 - - - -
2132L VAL* 3.7 9.6 - - - -
2133L ASP* 4.8 0.6 - - - +
2136L LEU* 4.6 1.6 - - - -
2173L ASN 2.9 11.5 + - - -
2174L LEU 2.9 11.2 + - - -
2176L GLN* 1.3 80.7 - - - +
2178L ASP* 1.3 57.4 + - - -
40M ARG* 3.4 41.9 + - - +
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Residues in contact with ASP2178 (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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2136L LEU* 4.0 15.7 - - + +
2174L LEU 3.4 5.1 + - - -
2175L ALA 2.8 20.1 - - - +
2176L GLN 4.4 0.5 - - - +
2177L GLY* 1.3 76.9 - - - +
2179L SER* 1.3 85.4 + - - +
2180L LEU* 3.0 26.9 + - - +
2181L ALA* 3.8 17.0 - - + +
2182L ALA* 3.7 7.3 + - - +
30M SER* 5.8 0.2 + - - -
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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
------------------------------------------------------------
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