Contacts of the helix formed by residues 2128 - 2137 (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 GLN2128 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461I LYS* 3.5 19.5 - - + +
2068L SER 5.0 0.8 + - - -
2069L GLY 3.9 18.8 + - - -
2070L GLN* 4.2 5.9 + - - +
2071L LEU 3.4 25.9 + - - -
2072L ASP* 3.6 23.7 - - - +
2124L LYS 4.8 1.8 - - - +
2125L LEU 3.0 12.2 + - - +
2126L SER 3.0 2.3 - - - +
2127L ILE* 1.3 89.6 - - + +
2129L ASP* 1.3 65.8 + - - +
2130L ASN* 3.4 7.3 + - - +
2131L ASN* 3.4 10.3 + - - +
2132L VAL* 3.1 23.4 + - - +
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Residues in contact with ASP2129 (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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461I LYS* 3.2 27.4 + - - +
465I GLU* 4.0 7.4 - - - +
2126L SER 5.2 0.7 - - - +
2127L ILE 4.7 3.5 - - - +
2128L GLN* 1.3 72.5 - - - +
2130L ASN* 1.3 63.1 + - - +
2132L VAL* 3.2 11.4 + - - +
2133L ASP* 2.9 34.4 + - - +
2173L ASN* 5.6 1.6 - - - +
2177L GLY* 5.9 1.0 - - - -
40M ARG* 4.1 25.8 + - - +
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Residues in contact with ASN2130 (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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461I LYS* 5.2 4.0 - - - -
2072L ASP* 3.7 19.9 - - - +
2074L SER* 3.0 28.4 + - - +
2128L GLN* 3.3 6.2 - - + +
2129L ASP* 1.3 79.3 + - - +
2131L ASN* 1.3 62.0 + - - +
2133L ASP* 3.2 12.5 + - - +
2134L LEU* 3.0 32.7 + - - +
39M PHE* 5.0 2.2 - - - -
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Residues in contact with ASN2131 (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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2071L LEU 2.7 28.7 + - - -
2072L ASP* 3.0 23.2 - - - +
2073L LEU* 3.3 17.6 + - + -
2085L LEU* 5.0 0.2 - - - +
2125L LEU* 3.1 50.8 + - + +
2128L GLN* 3.4 11.5 + - - +
2129L ASP 3.4 0.2 - - - -
2130L ASN* 1.3 75.8 - - - +
2132L VAL* 1.3 55.9 + - - +
2134L LEU* 3.8 8.2 - - - +
2135L ILE* 2.8 37.2 + - + +
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Residues in contact with VAL2132 (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* 3.1 40.6 - - - +
2128L GLN 3.1 12.2 + - - +
2129L ASP* 3.3 13.9 - - - +
2130L ASN 3.1 0.2 - - - -
2131L ASN* 1.3 77.4 - - - +
2133L ASP* 1.3 63.4 + - - +
2135L ILE* 3.3 6.5 + - - +
2136L LEU* 2.9 45.2 + - + +
2173L ASN* 4.1 15.0 - - + +
2174L LEU* 4.4 5.2 - - + -
2177L GLY* 3.7 11.7 - - - -
40M ARG* 3.7 16.4 - - - +
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Residues in contact with ASP2133 (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* 2.9 20.4 + - - +
2130L ASN* 3.2 11.2 + - - +
2132L VAL* 1.3 75.6 - - - +
2134L LEU* 1.3 62.2 + - - +
2136L LEU* 3.3 7.7 + - - +
2137L ALA* 2.9 24.8 + - - +
2177L GLY 4.8 1.2 - - - +
39M PHE* 3.4 45.8 - - + +
40M ARG* 2.6 45.5 + - - +
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Residues in contact with LEU2134 (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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2073L LEU* 3.3 46.7 - - + +
2074L SER* 4.3 2.9 - - - +
2081L CYS* 4.3 8.7 - - + -
2085L LEU* 3.6 18.1 - - + +
2130L ASN 3.0 19.8 + - - +
2131L ASN* 3.8 5.2 - - - +
2133L ASP* 1.3 76.5 - - - +
2135L ILE* 1.3 63.5 + - - +
2137L ALA* 3.2 10.9 + - - +
2138L THR* 3.3 11.4 + - - -
10M PHE* 3.7 31.8 - - + -
37M ARG* 4.1 12.8 - - - +
39M PHE* 3.4 28.5 - - + -
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Residues in contact with ILE2135 (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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2085L LEU* 3.7 22.9 - - + -
2089L LEU* 4.3 18.8 - - + +
2122L LEU* 4.0 28.7 - - + +
2125L LEU* 4.4 17.3 - - + -
2126L SER* 4.4 11.7 - - - +
2131L ASN* 2.8 26.6 + - + +
2132L VAL* 3.6 4.7 - - - +
2134L LEU* 1.3 76.1 - - - +
2136L LEU* 1.3 62.3 + - + +
2137L ALA 3.1 0.2 - - - -
2138L THR* 2.7 26.2 + - - -
2144L LEU* 4.3 15.2 - - + +
2147L LEU* 5.5 1.3 - - + -
2170L LEU* 5.7 1.3 - - + -
2174L LEU* 4.3 20.2 - - + -
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Residues in contact with LEU2136 (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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2132L VAL* 2.9 40.6 + - + +
2133L ASP* 3.6 7.6 - - - +
2135L ILE* 1.3 75.5 - - + +
2137L ALA* 1.3 57.4 + - - +
2138L THR 3.4 2.1 - - - +
2141L PHE* 5.3 6.1 - - + -
2144L LEU* 4.0 23.1 - - + +
2148L TYR* 3.3 26.2 - - - +
2174L LEU* 4.2 22.7 - - + +
2177L GLY* 4.6 0.4 - - - -
2178L ASP* 4.0 30.5 - - + +
2181L ALA* 3.8 15.0 - - + -
34M ASN* 4.6 4.7 + - - -
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Residues in contact with ALA2137 (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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2133L ASP 2.9 16.1 + - - +
2134L LEU 3.2 0.9 + - - +
2135L ILE 3.1 0.8 - - - -
2136L LEU* 1.3 76.1 - - - +
2138L THR* 1.3 66.5 + - - +
2139L PRO* 3.5 5.0 - - - +
10M PHE* 3.4 30.4 - - + +
34M ASN* 3.9 23.9 + - + +
39M PHE* 3.7 20.4 - - + -
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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