Contacts of the helix formed by residues 2077 - 2094 (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 PRO2077 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1845L ARG* 4.0 14.6 - - + +
1846L ILE* 4.4 15.0 - - + +
2075L PRO 3.7 3.6 - - - +
2076L TYR* 1.3 90.3 - - + +
2078L GLU* 1.3 67.1 + - - +
2079L SER* 4.0 13.9 - - - +
2080L ILE* 2.9 35.9 + - + -
2081L CYS* 3.0 10.7 + - - -
7M SER* 4.4 25.4 - - - +
37M ARG* 4.2 2.7 - - - +
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Residues in contact with GLU2078 (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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2077L PRO* 1.3 72.1 - - - +
2079L SER* 1.3 60.1 + - - +
2080L ILE 3.1 0.2 - - - -
2081L CYS* 3.5 10.5 - - - -
2082L LEU* 2.9 57.1 + - + +
7M SER* 4.5 16.9 + - - +
9M THR* 3.4 21.2 + - - +
10M PHE* 3.8 18.4 - - + -
11M GLY* 2.4 36.8 + - - +
37M ARG* 3.8 6.0 - - - +
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Residues in contact with SER2079 (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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1734L TYR* 4.8 9.5 + - - -
1846L ILE* 3.7 24.9 - - - +
2009L LEU* 4.2 10.4 - - - +
2013L LYS* 6.0 0.9 - - - -
2077L PRO* 3.0 7.6 + - - +
2078L GLU* 1.3 80.1 + - - +
2080L ILE* 1.3 60.7 + - - +
2083L PRO* 3.2 21.0 - - - +
7M SER* 5.8 2.5 - - - -
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Residues in contact with ILE2080 (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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1845L ARG 3.9 3.8 - - - +
1846L ILE* 3.8 12.1 - - - -
1847L GLY 3.3 26.5 - - - +
2005L PRO* 3.9 14.6 - - + +
2008L LEU* 3.7 34.9 - - + +
2009L LEU* 3.9 20.9 - - + +
2012L GLY* 5.4 0.2 - - - -
2073L LEU* 5.7 1.3 - - + -
2076L TYR* 4.0 16.8 - - + -
2077L PRO* 2.9 19.9 + - + +
2079L SER* 1.3 85.3 + - - +
2081L CYS* 1.3 67.8 + - - +
2082L LEU 3.3 0.7 - - - -
2083L PRO* 3.3 9.7 - - - +
2084L VAL* 3.6 16.0 - - + +
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Residues in contact with CYS2081 (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* 3.9 40.3 - - + +
2076L TYR* 4.0 4.7 - - + +
2077L PRO 3.0 19.5 + - - +
2078L GLU* 3.5 9.0 - - - -
2080L ILE* 1.3 78.6 - - - +
2082L LEU* 1.3 67.4 + - - +
2084L VAL* 3.4 3.5 + - - +
2085L LEU* 3.1 28.8 + - + +
2134L LEU* 4.3 7.6 - - + -
10M PHE* 3.5 26.7 - - + -
37M ARG* 3.9 11.9 - - - -
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Residues in contact with LEU2082 (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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2078L GLU* 2.9 52.0 + - + +
2081L CYS* 1.3 77.8 - - - +
2083L PRO* 1.3 62.3 - - + +
2085L LEU* 4.6 2.2 - - + +
2086L ASP* 2.9 37.1 + - + +
2138L THR* 4.2 21.3 - - + -
2139L PRO* 4.3 10.1 - - + -
10M PHE* 3.5 27.1 - - + -
11M GLY* 4.3 11.4 - - - +
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Residues in contact with PRO2083 (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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2009L LEU* 6.3 0.2 - - + -
2012L GLY* 4.0 28.9 - - - +
2013L LYS* 5.6 6.3 - - + -
2015L ILE* 4.4 1.0 - - - +
2016L LEU* 5.6 0.2 - - - +
2078L GLU 3.5 2.7 - - - +
2079L SER* 3.2 28.9 - - - +
2080L ILE* 3.3 8.5 - - - +
2082L LEU* 1.3 94.5 - - + +
2084L VAL* 1.3 57.1 + - - +
2086L ASP* 3.9 3.9 - - + +
2087L GLY* 2.9 27.4 + - - -
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Residues in contact with VAL2084 (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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2008L LEU* 3.9 19.1 - - + +
2011L LEU 4.9 0.7 - - - -
2012L GLY* 3.8 20.0 - - - +
2015L ILE* 3.8 10.6 - - + +
2064L LEU* 4.4 21.1 - - + -
2071L LEU* 5.2 2.7 - - + -
2073L LEU* 4.8 20.0 - - + -
2080L ILE 3.6 13.8 + - - +
2081L CYS* 3.4 9.1 + - - +
2082L LEU 3.3 0.6 - - - -
2083L PRO* 1.3 78.7 - - - +
2085L LEU* 1.3 63.7 + - + +
2088L LEU* 2.9 46.4 + - + +
2125L LEU* 5.2 2.5 - - + -
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Residues in contact with LEU2085 (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* 3.7 23.3 - - + -
2081L CYS 3.1 19.3 + - - +
2082L LEU* 4.1 3.1 - - + +
2084L VAL* 1.3 76.9 - - + +
2086L ASP* 1.3 57.2 + - - +
2088L LEU* 3.4 5.4 + - + +
2089L LEU* 2.9 38.1 + - + +
2122L LEU* 5.4 1.6 - - + -
2125L LEU* 4.5 11.9 - - + -
2131L ASN 5.0 0.2 - - - +
2134L LEU* 3.6 45.1 - - + +
2135L ILE* 3.7 25.6 - - + -
2138L THR* 4.3 11.9 - - + +
10M PHE* 4.1 13.5 - - + -
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Residues in contact with ASP2086 (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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2016L LEU* 4.1 12.7 - - + +
2082L LEU* 2.9 24.7 + - + +
2083L PRO* 3.9 4.9 - - + +
2085L LEU* 1.3 76.6 - - - +
2087L GLY* 1.3 58.7 + - - +
2090L HIS* 2.9 24.9 + - - +
2138L THR* 3.9 12.0 - - + +
2139L PRO* 5.1 1.7 - - - +
2140L PRO* 4.6 3.6 - - - +
2143L ARG* 2.3 47.1 + - - +
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Residues in contact with GLY2087 (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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2015L ILE* 3.5 26.9 - - - -
2016L LEU* 3.6 17.2 - - - +
2083L PRO 2.9 14.8 + - - -
2084L VAL 3.9 0.2 - - - -
2086L ASP* 1.3 74.6 + - - +
2088L LEU* 1.3 65.2 + - - +
2090L HIS* 3.8 0.3 - - - +
2091L TRP* 2.9 30.5 + - - -
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Residues in contact with LEU2088 (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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2015L ILE* 4.3 13.4 - - + +
2061L LEU* 4.6 4.9 - - + -
2064L LEU* 4.5 9.0 - - + -
2084L VAL* 2.9 32.5 + - + +
2085L LEU* 3.8 5.4 - - - +
2087L GLY* 1.3 77.5 - - - +
2089L LEU* 1.3 56.9 + - - +
2091L TRP 3.4 0.7 + - - -
2092L ALA* 2.9 28.8 + - - +
2118L VAL* 3.7 31.7 - - + +
2121L THR* 3.5 34.5 - - + +
2122L LEU* 4.3 20.9 - - + -
2125L LEU* 3.7 20.4 - - + -
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Residues in contact with LEU2089 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2085L LEU* 2.9 24.1 + - + +
2086L ASP 3.9 1.8 - - - +
2088L LEU* 1.3 77.0 - - - +
2090L HIS* 1.3 63.6 + - - +
2092L ALA* 3.1 6.3 + - - +
2093L VAL* 3.0 25.8 + - - +
2122L LEU* 4.3 18.4 - - + -
2135L ILE* 4.3 12.3 - - + +
2138L THR* 3.4 40.2 - - + +
2143L ARG* 3.6 26.7 - - + +
2144L LEU* 4.4 10.1 - - + -
2147L LEU* 3.7 32.3 - - + -
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Residues in contact with HIS2090 (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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2016L LEU* 3.7 25.7 - - + +
2019L HIS* 3.0 11.4 + + - -
2021L HIS* 3.3 17.9 - + - -
2086L ASP 2.9 14.2 + - - +
2087L GLY 3.8 3.4 - - - +
2088L LEU 3.3 0.2 - - - -
2089L LEU* 1.3 76.0 - - - +
2091L TRP* 1.3 55.3 + + - +
2093L VAL* 3.0 9.7 + - - +
2094L CYS* 2.6 44.4 + - + -
2095L PRO* 5.4 2.2 - - + -
2143L ARG* 3.3 21.8 + - - +
2301L ZN 2.0 37.2 - - - -
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Residues in contact with TRP2091 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2015L ILE* 3.2 34.3 + - + +
2016L LEU* 3.4 13.2 - - + +
2019L HIS* 3.5 38.6 - + - -
2057L ARG* 3.4 29.8 - - + +
2061L LEU* 4.8 8.5 - - + -
2087L GLY 2.9 25.7 + - - +
2090L HIS* 1.3 77.4 - + - +
2092L ALA* 1.3 62.9 + - - +
2094L CYS* 3.8 15.4 + - + +
2098L GLU* 4.2 11.7 - - + -
2099L ALA* 3.6 41.9 - - + +
2114L PRO* 3.9 20.2 - - + +
2115L GLN* 4.0 12.8 - - - +
2118L VAL* 3.7 25.1 - - + +
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Residues in contact with ALA2092 (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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2088L LEU 2.9 14.9 + - - +
2089L LEU* 3.4 10.5 - - - +
2090L HIS 3.1 0.4 - - - -
2091L TRP* 1.3 78.5 - - - +
2093L VAL* 1.3 60.3 + - - +
2094L CYS 3.7 0.3 + - - -
2115L GLN* 3.0 32.1 + - + +
2118L VAL* 3.6 15.7 - - + +
2119L LEU* 5.6 0.9 - - - +
2122L LEU* 4.1 11.0 - - + -
2147L LEU* 3.9 24.9 - - + -
2150L THR* 4.6 5.7 + - - +
2151L MET* 5.5 4.6 - - + +
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Residues in contact with VAL2093 (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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2089L LEU* 3.0 20.6 + - + +
2090L HIS* 3.7 10.8 - - - +
2092L ALA* 1.3 80.6 - - + +
2094L CYS* 1.3 64.3 + - - +
2095L PRO* 3.3 8.7 - - - +
2115L GLN* 5.7 0.2 - - - -
2143L ARG* 3.7 26.2 - - + +
2146L LYS* 4.1 23.9 - - + +
2147L LEU* 3.7 39.9 - - + +
2150L THR* 4.9 6.1 - - + -
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Residues in contact with CYS2094 (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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2019L HIS* 3.6 5.6 - - - -
2021L HIS* 3.6 3.8 - - - -
2090L HIS* 2.6 21.8 + - - +
2091L TRP* 3.8 18.7 + - + +
2092L ALA 3.4 4.0 - - - +
2093L VAL* 1.3 73.2 - - - +
2095L PRO* 1.3 64.3 - - - +
2096L SER* 3.2 30.0 + - - +
2099L ALA* 4.1 13.7 - - + +
2100L GLN* 4.6 10.7 - - - +
2115L GLN* 5.2 1.4 + - - -
2301L ZN 2.2 38.1 - - - -
155P ARG* 5.2 0.3 + - - -
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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