Contacts of the helix formed by residues 2036 - 2055 (chain B) in PDB entry 6D1U
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 VAL2036 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067B ARG* 5.0 3.1 - - - +
2034B LEU* 3.2 5.3 - - - +
2035B GLY* 1.3 76.4 - - - +
2037B THR* 1.3 67.2 + - - +
2038B ARG* 3.9 14.4 - - + +
2039B ASN* 3.1 23.2 + - - +
2040B LYS 2.9 18.9 + - - -
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Residues in contact with THR2037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2035B GLY 3.6 2.3 + - - -
2036B VAL* 1.3 73.9 - - - +
2038B ARG* 1.3 62.6 + - + +
2040B LYS* 3.1 10.9 + - - +
2041B ILE* 2.9 40.9 + - + +
2091B TYR* 2.7 30.4 + - + +
2092B PHE* 3.8 24.0 - - + -
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Residues in contact with ARG2038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B ARG* 3.1 44.4 - - - +
1071B ASP* 4.3 20.5 + - - -
2036B VAL* 3.3 7.5 - - + +
2037B THR* 1.3 82.4 - - + +
2039B ASN* 1.3 60.0 + - - +
2041B ILE* 3.3 10.2 + - + +
2042B MET* 2.9 37.5 + - + +
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Residues in contact with ASN2039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063B ILE* 3.7 27.9 - - + +
1064B ARG* 6.2 0.2 - - - -
1067B ARG* 2.8 38.8 + - - +
2034B LEU* 3.6 30.5 - - - +
2036B VAL* 3.1 18.6 + - - +
2038B ARG* 1.3 74.3 - - - +
2040B LYS* 1.3 58.8 + - - +
2042B MET* 3.8 3.0 - - - +
2043B THR* 2.9 34.7 + - - -
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Residues in contact with LYS2040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110B ALA 5.6 5.9 + - - -
2034B LEU 4.1 2.0 + - - +
2035B GLY* 3.3 36.6 - - - +
2036B VAL 2.9 8.1 + - - +
2037B THR* 3.4 10.3 - - - +
2039B ASN* 1.3 75.8 - - - +
2041B ILE* 1.3 62.0 + - - +
2043B THR* 3.7 6.4 - - - -
2044B ALA* 3.1 23.2 + - - +
2090B ASP* 3.0 45.1 + - - +
2091B TYR* 4.0 22.7 - - + +
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Residues in contact with ILE2041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2037B THR* 2.9 36.4 + - + +
2038B ARG* 3.7 10.8 - - + +
2040B LYS* 1.3 76.5 - - - +
2042B MET* 1.3 66.7 + - + +
2044B ALA* 3.3 3.3 + - - +
2045B GLN* 3.0 26.9 + - + +
2069B TRP* 3.9 6.1 - - + -
2071B GLY 3.7 22.0 - - - +
2072B TRP* 4.0 18.8 - - + +
2091B TYR* 3.6 33.4 - - + -
2092B PHE* 4.2 5.4 - - + -
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Residues in contact with MET2042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B TRP* 4.0 9.2 - - + -
1063B ILE* 4.7 4.5 - - + +
1066B TYR* 3.7 21.2 - - + -
1067B ARG* 3.8 37.9 - - + +
1070B ALA* 3.7 28.5 - - + -
1071B ASP* 4.6 7.9 - - - +
1084B TRP* 6.3 0.2 - - - -
2038B ARG* 2.9 27.4 + - + +
2039B ASN* 3.8 8.3 - - - +
2041B ILE* 1.3 82.4 - - + +
2043B THR* 1.3 60.2 + - - +
2045B GLN* 3.2 16.5 + - - +
2046B TYR* 2.9 30.5 + - - +
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Residues in contact with THR2043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059B TRP* 2.9 30.1 + - - +
1063B ILE* 4.2 1.6 - - - +
1109B ARG* 3.7 39.3 - - + +
1110B ALA 4.5 4.3 - - - +
2034B LEU* 4.5 6.2 + - - +
2039B ASN 2.9 27.5 + - - -
2040B LYS* 3.7 7.4 - - - -
2042B MET* 1.3 71.1 - - - +
2044B ALA* 1.3 59.1 + - - +
2046B TYR* 3.3 1.7 + - - +
2047B GLU* 3.0 39.0 + - - +
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Residues in contact with ALA2044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040B LYS 3.1 14.9 + - - +
2041B ILE 3.6 4.0 - - - +
2042B MET 3.2 0.2 - - - -
2043B THR* 1.3 74.0 - - - +
2045B GLN* 1.3 60.5 + - - +
2047B GLU* 3.9 6.5 - - - +
2048B CYS* 3.0 29.1 + - - +
2069B TRP* 3.6 11.7 - - + -
2072B TRP 4.4 0.2 - - - +
2073B LEU* 6.0 0.9 - - + -
2074B CYS* 5.4 0.3 - - - +
2091B TYR* 3.2 27.8 - - + +
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Residues in contact with GLN2045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066B TYR* 3.1 24.8 + - - +
1070B ALA* 4.0 12.8 - - - +
1084B TRP* 3.7 22.0 - - - -
1089B VAL* 6.4 0.2 - - - -
1093B PHE* 3.5 22.0 - - - -
2041B ILE* 3.0 11.5 + - - +
2042B MET* 3.2 15.4 + - - +
2044B ALA* 1.3 76.1 - - - +
2046B TYR* 1.3 63.9 + - - +
2048B CYS* 3.2 2.9 + - - +
2049B TYR* 3.0 40.1 + - + -
2069B TRP* 3.4 43.3 - - + +
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Residues in contact with TYR2046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056B TRP 4.6 1.6 + - - -
1057B CYS* 5.1 1.7 + - - -
1059B TRP* 3.3 38.4 - + + -
1062B THR* 5.3 0.4 + - - -
1066B TYR* 3.6 21.5 + + + -
1097B HIS* 3.3 12.7 - + - -
1101B PHE* 3.3 49.8 - + + +
1104B CYS* 3.6 19.9 - - - +
1109B ARG* 3.3 38.5 + - - -
2042B MET 2.9 17.2 + - - +
2043B THR 3.7 3.8 - - - +
2045B GLN* 1.3 76.2 - - - +
2047B GLU* 1.3 61.9 + - + +
2049B TYR 3.3 1.9 + - - -
2050B GLN* 3.0 44.3 + - + +
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Residues in contact with GLU2047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106B ILE* 3.4 19.8 - - - +
1107B SER* 3.3 19.4 - - - -
1108B GLY 4.2 1.1 + - - -
1109B ARG* 3.1 51.0 + - - +
1110B ALA* 4.5 5.2 + - - -
2043B THR* 3.0 30.9 + - - +
2044B ALA* 4.2 5.7 - - - +
2046B TYR* 1.3 75.5 - - + +
2048B CYS* 1.3 60.5 + - - +
2050B GLN* 3.4 3.7 + - - +
2051B LYS* 3.0 29.8 + - - +
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Residues in contact with CYS2048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2044B ALA 3.0 19.4 + - - +
2045B GLN 3.2 5.1 + - - +
2047B GLU* 1.3 76.2 - - - +
2049B TYR* 1.3 57.9 + - - +
2051B LYS* 3.2 5.1 + - - +
2052B ILE* 2.8 43.1 + - - +
2068B THR 3.9 0.2 - - - -
2069B TRP* 3.7 25.4 - - + -
2074B CYS* 2.1 59.9 - - + -
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Residues in contact with TYR2049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066B TYR* 3.7 6.3 - - - -
1085B PRO* 5.0 0.2 - - - +
1089B VAL* 3.7 11.3 - - - +
1090B ASP* 2.7 50.9 + - + -
1093B PHE* 3.5 32.8 - + + +
1094B LEU* 4.6 6.3 - - + +
1097B HIS* 3.4 28.0 + - + +
2045B GLN* 3.0 47.1 + - + +
2048B CYS* 1.3 73.4 - - - +
2050B GLN* 1.3 59.7 + - - +
2052B ILE* 3.9 22.3 - - + +
2053B MET* 2.9 30.7 + - - +
2069B TRP* 3.4 25.3 + + + +
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Residues in contact with GLN2050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097B HIS* 2.8 28.2 + - - +
1101B PHE* 3.0 34.2 + - - +
1104B CYS* 3.3 26.5 + - - +
1105B PRO 3.3 9.9 + - - +
1106B ILE* 3.8 20.1 - - + +
2046B TYR* 3.0 37.3 + - + +
2047B GLU 3.5 8.5 - - - +
2048B CYS 3.3 0.2 - - - -
2049B TYR* 1.3 76.8 - - - +
2051B LYS* 1.3 55.6 - - - +
2053B MET* 3.4 8.0 + - - +
2054B GLN* 3.0 35.5 + - + +
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Residues in contact with LYS2051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106B ILE* 4.2 19.0 - - + +
2047B GLU 3.0 18.7 + - - +
2048B CYS* 3.5 4.7 - - - +
2050B GLN* 1.3 71.7 - - - +
2052B ILE* 1.3 61.1 + - + +
2054B GLN* 4.4 1.8 - - - +
2055B ASP* 2.7 73.8 + - - +
2074B CYS* 4.8 18.4 - - + -
2076B ASN* 3.0 31.8 + - - +
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Residues in contact with ILE2052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090B ASP* 5.6 1.3 - - - +
1094B LEU* 4.5 18.9 - - + +
2048B CYS* 2.8 38.9 + - - +
2049B TYR* 3.9 24.0 - - + +
2051B LYS* 1.3 76.4 - - + +
2053B MET* 1.3 64.4 + - - +
2055B ASP* 4.0 1.7 + - - +
2067B ARG* 3.4 53.0 + - + +
2068B THR* 3.9 27.1 - - - +
2069B TRP 4.2 0.2 - - - +
2074B CYS* 4.1 6.7 - - - -
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Residues in contact with MET2053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094B LEU* 3.3 38.1 - - + +
1097B HIS* 3.6 14.8 - - + +
1098B GLY* 3.3 32.8 - - - +
1102B ARG* 3.3 43.0 + - - +
2049B TYR 2.9 19.4 + - - +
2050B GLN* 3.6 9.0 - - - +
2052B ILE* 1.3 78.7 - - - +
2054B GLN* 1.3 75.2 + - + +
2055B ASP 4.5 1.9 - - - +
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Residues in contact with GLN2054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102B ARG* 4.3 25.1 + - - +
1104B CYS 6.2 0.2 - - - +
1106B ILE* 3.7 34.2 - - + +
2050B GLN* 3.0 22.7 + - - +
2051B LYS* 3.2 2.4 + - - +
2053B MET* 1.3 94.0 + - + +
2055B ASP* 1.3 66.1 + - - +
2056B PRO* 3.5 5.7 - - - +
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Residues in contact with ASP2055 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106B ILE* 5.9 1.6 - - - +
2051B LYS* 2.7 61.6 + - - +
2052B ILE* 4.1 2.6 - - - +
2053B MET 3.7 2.1 - - - +
2054B GLN* 1.3 75.4 - - - +
2056B PRO* 1.3 71.3 - - + +
2057B ILE 3.8 0.2 + - - -
2067B ARG* 2.8 32.7 + - - +
2076B ASN* 4.1 4.9 - - - +
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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