Contacts of the helix formed by residues 2113 - 2127 (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 SER2113 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2100L GLN* 3.9 7.3 + - - -
2101L ASP 3.5 26.2 - - - -
2102L PRO* 5.1 0.2 - - - -
2103L PHE* 4.0 2.9 - - - -
2111L VAL 2.9 7.6 + - - -
2112L LEU* 1.3 74.6 - - - +
2114L PRO* 1.3 74.6 - - - +
2115L GLN* 3.5 7.5 + - - +
2116L ARG* 3.1 33.1 + - - +
2117L LEU* 3.2 22.9 + - - +
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Residues in contact with PRO2114 (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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2057L ARG* 6.4 0.4 - - + -
2061L LEU* 3.8 17.7 - - + -
2091L TRP* 3.9 26.5 - - + -
2098L GLU 3.4 22.0 - - - +
2099L ALA* 3.9 6.1 - - - +
2101L ASP 3.3 15.3 - - - +
2103L PHE* 3.5 30.7 - - + -
2113L SER* 1.3 86.5 - - - +
2115L GLN* 1.3 57.0 + - - +
2117L LEU* 3.3 2.1 + - + +
2118L VAL* 2.9 35.1 + - - +
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Residues in contact with GLN2115 (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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2091L TRP 4.0 8.9 + - - +
2092L ALA* 3.0 30.5 + - + +
2094L CYS 5.2 2.6 + - - -
2099L ALA* 4.7 1.1 - - + +
2100L GLN* 2.7 42.4 + - - +
2113L SER* 3.2 8.6 + - - +
2114L PRO* 1.3 80.8 - - - +
2116L ARG* 1.3 58.1 + - + +
2118L VAL* 3.1 9.7 - - - +
2119L LEU* 2.9 30.1 + - + +
2150L THR* 4.6 13.1 + - - +
2151L MET* 6.3 0.7 - - + -
2153L ARG* 5.6 2.8 - - - +
2154L PHE* 3.4 34.9 - - + -
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Residues in contact with ARG2116 (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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445I GLN* 2.9 35.1 + - - +
2111L VAL* 3.3 57.6 + - - +
2112L LEU* 4.6 2.2 - - + +
2113L SER* 3.1 21.2 + - - +
2115L GLN* 1.3 77.7 - - + +
2117L LEU* 1.3 58.4 + - - +
2119L LEU* 3.2 9.9 + - + +
2120L GLU 2.9 19.6 + - - -
2154L PHE* 5.8 4.0 - - + -
2160L ASN* 3.0 42.8 + - - +
2162L VAL* 5.1 7.5 - - - +
2163L CYS* 3.7 24.3 - - - -
2166L MET* 4.4 0.9 - - - +
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Residues in contact with LEU2117 (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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443I LYS* 4.0 16.6 - - + -
445I GLN* 3.8 4.9 - - - +
2061L LEU* 3.7 27.8 - - + +
2062L VAL* 3.7 18.4 - - + +
2065L ALA* 3.8 22.0 - - + +
2103L PHE* 3.5 33.9 - - + -
2112L LEU* 3.8 24.5 - - + -
2113L SER 3.2 12.2 + - - +
2114L PRO 3.7 7.0 - - - +
2116L ARG* 1.3 77.2 - - - +
2118L VAL* 1.3 58.1 + - - +
2120L GLU* 3.3 3.3 + - - +
2121L THR* 2.7 32.7 + - - -
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Residues in contact with VAL2118 (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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2061L LEU* 3.7 24.0 - - + -
2088L LEU* 3.7 24.0 - - + +
2091L TRP* 3.7 20.9 - - + -
2092L ALA* 3.6 31.6 - - + +
2114L PRO 2.9 16.2 + - - +
2115L GLN* 3.1 19.3 - - - +
2117L LEU* 1.3 76.5 - - - +
2119L LEU* 1.3 57.2 + - - +
2121L THR* 3.7 6.9 - - - -
2122L LEU* 2.8 34.3 + - - +
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Residues in contact with LEU2119 (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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2092L ALA* 5.9 1.8 - - + -
2115L GLN* 2.9 18.1 + - + +
2116L ARG* 3.5 4.9 - - - +
2117L LEU 3.2 0.2 - - - -
2118L VAL* 1.3 74.9 - - - +
2120L GLU* 1.3 66.0 + - - +
2122L LEU* 3.3 6.3 + - - +
2123L SER* 2.9 23.0 + - - -
2151L MET* 3.6 20.9 - - + -
2154L PHE* 3.7 28.7 - - + -
2163L CYS* 3.8 32.1 - - + +
2166L MET* 3.7 29.2 - - + -
2167L ALA 3.9 0.4 - - - +
2170L LEU* 3.5 23.8 - - + -
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Residues in contact with GLU2120 (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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443I LYS* 3.0 29.3 + - - -
445I GLN* 2.6 47.9 + - - +
449I GLU* 4.8 4.5 - - - +
450I ALA* 6.2 2.2 - - + -
2065L ALA* 3.8 12.8 - - + +
2116L ARG 2.9 7.1 + - - +
2117L LEU* 3.6 3.1 - - - +
2119L LEU* 1.3 77.7 - - - +
2121L THR* 1.3 61.9 + - - +
2123L SER* 2.6 22.6 + - - +
2124L LYS* 3.0 43.8 + - + +
2166L MET* 3.6 18.8 - - + -
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Residues in contact with THR2121 (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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2061L LEU* 4.4 2.1 + - - +
2064L LEU* 3.8 15.9 - - + +
2065L ALA* 3.2 19.5 + - - +
2068L SER* 3.6 27.2 + - - -
2071L LEU* 6.1 0.7 - - + -
2088L LEU* 3.5 29.6 - - + +
2117L LEU 2.7 23.5 + - - -
2118L VAL* 3.7 8.5 - - - -
2120L GLU* 1.3 77.0 - - - +
2122L LEU* 1.3 58.2 + - - +
2124L LYS 3.4 0.2 + - - -
2125L LEU* 2.9 37.0 + - + +
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Residues in contact with LEU2122 (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* 5.4 2.0 - - + -
2088L LEU* 4.2 31.6 - - + +
2089L LEU* 4.3 20.6 - - + -
2092L ALA* 4.1 26.0 - - + -
2118L VAL 2.8 24.3 + - - +
2119L LEU* 3.8 3.8 - - - +
2120L GLU 3.2 0.2 - - - -
2121L THR* 1.3 73.8 - - - +
2123L SER* 1.3 61.8 + - - +
2125L LEU* 3.7 4.0 - - + +
2126L SER* 2.9 31.0 + - - -
2135L ILE* 4.0 29.2 - - + +
2147L LEU* 4.7 12.1 - - + -
2170L LEU* 3.4 18.4 - - + +
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Residues in contact with SER2123 (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* 4.5 6.7 + - - -
2119L LEU 2.9 14.4 + - - -
2120L GLU* 2.6 26.7 + - - +
2122L LEU* 1.3 74.4 - - - +
2124L LYS* 1.3 62.8 + - - +
2126L SER* 2.7 23.5 + - - -
2127L ILE* 3.0 12.4 + - - +
2166L MET* 3.7 30.5 - - - +
2169L VAL* 4.0 16.2 - - - -
2170L LEU* 3.5 7.9 - - - +
2173L ASN* 4.2 1.4 + - - -
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Residues in contact with LYS2124 (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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443I LYS* 4.9 2.2 - - - +
450I ALA* 5.6 6.5 - - - +
453I THR* 3.6 28.4 + - + +
454I GLU* 5.0 7.6 - - - +
457I GLU* 4.2 13.9 - - - +
2065L ALA 3.3 13.4 + - - +
2066L ASN* 4.7 7.7 + - - +
2068L SER* 3.1 38.3 - - - +
2069L GLY* 4.2 9.2 - - - +
2120L GLU* 3.0 41.4 + - + +
2123L SER* 1.3 83.8 + - - +
2125L LEU* 1.3 61.5 + - - +
2127L ILE* 3.2 27.7 - - + +
2128L GLN* 4.4 3.5 + - - +
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Residues in contact with LEU2125 (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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2068L SER* 4.0 10.8 - - - +
2071L LEU* 3.6 34.3 - - + +
2073L LEU* 4.4 17.0 - - + -
2084L VAL* 5.2 3.1 - - + -
2085L LEU* 4.5 9.4 - - + -
2088L LEU* 3.7 29.8 - - + -
2121L THR* 2.9 23.4 + - + +
2122L LEU* 3.7 7.9 - - + +
2124L LYS* 1.3 77.8 - - - +
2126L SER* 1.3 58.9 + - - +
2127L ILE 3.0 5.1 + - - -
2128L GLN* 3.0 11.8 + - - +
2131L ASN* 3.1 45.6 + - + +
2135L ILE* 4.4 4.3 - - + -
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Residues in contact with SER2126 (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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2122L LEU 2.9 16.3 + - - -
2123L SER* 2.7 22.7 + - - -
2125L LEU* 1.3 71.3 - - - +
2127L ILE* 1.3 65.2 + - - +
2128L GLN 3.0 3.3 + - - -
2129L ASP* 5.2 0.9 - - - +
2132L VAL* 3.1 27.7 - - - +
2135L ILE* 4.4 7.1 - - - +
2170L LEU* 3.7 14.0 - - - +
2173L ASN* 3.1 36.5 + - - +
2174L LEU* 4.4 7.6 - - - -
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Residues in contact with ILE2127 (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* 3.6 39.9 - - + +
457I GLU* 3.2 43.1 - - + +
458I LYS* 4.0 27.8 + - + +
461I LYS* 3.5 15.2 - - + +
2069L GLY 5.8 1.8 - - - +
2123L SER 3.0 15.4 + - - +
2124L LYS* 3.2 19.5 - - - +
2125L LEU 3.0 0.8 - - - -
2126L SER* 1.3 78.3 - - - +
2128L GLN* 1.3 63.8 + - + +
2129L ASP* 4.1 3.6 + - - +
2169L VAL* 4.7 1.3 - - + -
2173L ASN* 3.8 15.2 - - - +
2233L ARG* 5.2 4.3 - - - +
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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