Contacts of the helix formed by residues 1038 - 1056 (chain B) in PDB entry 6PUO
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 ILE1038 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033B LEU 3.8 10.3 - - - +
1034B LEU* 3.4 21.1 - - - +
1035B PHE 3.8 1.0 + - - -
1036B THR 3.1 1.6 + - - -
1037B ASN* 1.3 90.8 - - + +
1039B LEU* 1.3 68.4 + - + +
1040B LEU 3.5 1.1 - - - -
1041B LEU* 3.3 9.4 + - - +
1042B ASN* 2.9 45.2 + - - +
934C VAL* 3.7 23.8 - - + -
937C PHE* 5.4 4.5 - - + -
938C LEU* 5.6 5.4 - - + -
941C LEU* 5.1 15.5 - - + -
1044C LEU* 4.9 14.6 - - + -
1048C PHE* 4.2 9.6 - - + -
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Residues in contact with LEU1039 (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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1034B LEU* 3.3 32.1 - - + +
1035B PHE* 3.5 32.9 + - + +
1038B ILE* 1.3 82.5 - - + +
1040B LEU* 1.3 66.8 + - + +
1042B ASN* 3.0 13.5 + - - +
1043B LEU* 2.9 25.0 + - - +
927C VAL* 5.1 14.1 - - + +
931C MET* 5.0 20.2 - - + +
934C VAL* 4.4 22.0 - - + -
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Residues in contact with LEU1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937B PHE* 3.6 30.2 - - + -
940B LEU* 4.1 15.9 - - + -
941B LEU* 4.1 22.2 - - + -
944B TRP* 4.6 20.0 - - + +
1035B PHE 4.5 6.0 + - - +
1036B THR* 4.8 9.1 + - - +
1038B ILE 3.5 0.4 - - - -
1039B LEU* 1.3 86.7 - - + +
1041B LEU* 1.3 57.8 + - + +
1043B LEU* 3.2 14.9 + - + +
1044B LEU* 2.9 32.2 + - - +
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Residues in contact with LEU1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036B THR 3.3 26.5 - - - +
1037B ASN* 3.4 23.3 - - - +
1038B ILE 3.3 5.1 + - - +
1039B LEU 3.2 0.6 - - - -
1040B LEU* 1.3 76.0 - - + +
1042B ASN* 1.3 62.1 + - - +
1044B LEU* 3.3 10.6 + - + +
1045B ILE* 2.9 38.0 + - + +
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Residues in contact with ASN1042 (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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1038B ILE* 2.9 30.3 + - - +
1039B LEU* 3.0 9.5 + - - +
1041B LEU* 1.3 77.0 - - - +
1043B LEU* 1.3 60.6 + - - +
1045B ILE* 3.3 12.3 + - - +
1046B ALA* 2.9 29.3 + - - +
927C VAL* 6.0 0.4 - - + -
930C MET* 3.7 27.8 - - + +
934C VAL* 3.5 11.9 - - - +
1048C PHE* 3.2 47.3 - - + -
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Residues in contact with LEU1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937B PHE* 3.6 33.2 - - + -
940B LEU* 5.1 12.6 - - + -
1039B LEU 2.9 11.6 + - - +
1040B LEU* 3.2 18.6 + - + +
1042B ASN* 1.3 76.2 - - - +
1044B LEU* 1.3 61.3 + - + +
1046B ALA* 3.4 5.1 + - - +
1047B MET* 2.9 40.5 + - + +
923C LYS* 4.8 17.4 - - + +
924C ILE* 5.3 8.1 - - + -
927C VAL* 3.7 36.5 - - + +
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Residues in contact with LEU1044 (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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1038A ILE* 4.9 13.7 - - + -
937B PHE* 3.5 50.9 - - + -
1040B LEU 2.9 19.0 + - - +
1041B LEU* 3.7 9.9 - - + +
1042B ASN 3.2 0.2 - - - -
1043B LEU* 1.3 78.8 - - + +
1045B ILE* 1.3 59.6 + - - +
1047B MET* 4.6 2.9 - - + -
1048B PHE* 2.8 73.8 + - + +
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Residues in contact with ILE1045 (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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1045A ILE* 6.4 3.1 - - + -
1041B LEU* 2.9 28.1 + - + +
1042B ASN* 3.3 15.9 + - - +
1044B LEU* 1.3 75.2 - - + +
1046B ALA* 1.3 58.8 + - - +
1048B PHE* 5.1 0.4 - - - -
1049B ASN* 3.0 43.4 + - + +
930C MET* 5.7 1.1 - - + -
1045C ILE* 6.4 2.9 - - + -
1048C PHE* 5.0 27.6 - - + +
1049C ASN* 5.5 4.5 - - + +
1052C PHE* 5.5 5.2 - - + -
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Residues in contact with ALA1046 (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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1042B ASN 2.9 18.3 + - - +
1043B LEU* 3.7 5.8 - - - +
1045B ILE* 1.3 77.0 - - - +
1047B MET* 1.3 57.3 + - - +
1050B TYR* 2.9 30.9 + - - +
923C LYS* 5.2 4.5 - - + -
926C ILE* 4.0 25.4 - - + -
930C MET* 4.6 3.1 - - + -
1052C PHE* 3.2 34.6 - - + -
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Residues in contact with MET1047 (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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933B ASP* 4.4 12.9 - - - +
1043B LEU* 2.9 30.0 + - + +
1044B LEU* 4.3 4.5 - - + +
1046B ALA* 1.3 73.9 - - - +
1048B PHE* 1.3 65.6 + - + +
1050B TYR* 3.3 2.3 + - - +
1051B THR* 2.9 31.1 + - - +
923C LYS* 4.1 31.4 + - + +
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Residues in contact with PHE1048 (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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1038A ILE* 4.2 6.1 - - + -
1042A ASN* 3.2 41.7 - - + -
1045A ILE* 5.0 20.6 - - + +
930B MET* 3.5 15.6 - - + +
933B ASP* 4.4 13.9 - - - -
934B VAL* 3.7 27.4 - - + -
937B PHE* 5.7 0.7 - + - -
1044B LEU* 2.8 61.8 + - + +
1045B ILE* 4.5 0.7 - - - +
1047B MET* 1.3 79.9 - - + +
1049B ASN* 1.3 60.5 + - - +
1051B THR* 3.8 11.9 - - + -
1052B PHE* 2.9 32.4 + - - +
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Residues in contact with ASN1049 (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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1045A ILE* 5.5 6.4 - - + +
1049A ASN* 3.8 17.5 + - - +
1045B ILE* 3.0 25.6 + - + +
1048B PHE* 1.3 76.5 - - - +
1050B TYR* 1.3 57.2 + - - +
1052B PHE* 4.0 4.9 - - - -
1053B GLN* 2.9 53.1 + - - +
1049C ASN* 3.8 14.8 + - - +
1052C PHE* 3.2 32.2 - - + -
1053C GLN* 4.8 2.0 - - - +
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Residues in contact with TYR1050 (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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1046B ALA 2.9 19.5 + - - +
1047B MET 3.4 4.7 - - - +
1049B ASN* 1.3 77.4 - - - +
1051B THR* 1.3 63.5 + - - +
1053B GLN* 3.3 4.0 + - - +
1054B GLN* 3.1 34.7 + - + +
922C PRO* 6.5 0.7 - - + -
923C LYS* 3.3 26.7 - - - +
1052C PHE* 3.8 9.6 - + + -
1056C GLN* 3.8 36.8 + - + -
1060C ASP* 6.1 1.9 - - - +
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Residues in contact with THR1051 (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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926B ILE* 5.6 0.3 - - - +
929B ARG* 4.5 16.3 + - - +
930B MET* 3.7 30.9 - - + +
933B ASP* 4.3 16.7 + - - +
1047B MET 2.9 20.8 + - - +
1048B PHE* 3.6 11.9 - - + +
1050B TYR* 1.3 78.6 - - - +
1052B PHE* 1.3 65.0 + - - +
1054B GLN* 3.8 8.9 + - - +
1055B VAL* 3.3 22.7 + - - +
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Residues in contact with PHE1052 (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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1045A ILE* 5.2 5.2 - - + -
1046A ALA* 3.2 47.8 - - + -
1049A ASN* 3.2 33.2 - - + -
1050A TYR* 3.8 22.9 - + + -
1053A GLN* 5.1 7.4 - - - -
926B ILE* 4.5 9.2 - - + -
930B MET* 3.7 14.1 - - + -
1048B PHE 2.9 20.6 + - - +
1049B ASN* 3.8 6.3 - - - +
1051B THR* 1.3 80.1 - - - +
1053B GLN* 1.3 78.3 + - + +
1054B GLN 3.2 1.0 + - - -
1055B VAL* 4.3 2.4 - - - +
1056B GLN* 3.3 46.2 + - + +
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Residues in contact with GLN1053 (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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1049A ASN* 4.8 2.4 - - - +
1053A GLN* 4.4 19.0 + - - +
1049B ASN* 2.9 44.8 + - - +
1050B TYR* 3.8 4.2 - - - +
1052B PHE* 1.3 87.3 - - + +
1054B GLN* 1.3 61.2 + - - +
1056B GLN* 4.5 4.3 + - - +
1057B GLU* 5.2 6.2 + - - +
1052C PHE* 5.1 7.0 - - - -
1053C GLN* 4.5 14.4 + - - +
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Residues in contact with GLN1054 (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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1050B TYR* 3.1 23.8 + - + +
1051B THR* 4.1 10.5 - - - +
1052B PHE 3.1 0.6 - - - -
1053B GLN* 1.3 79.6 - - - +
1055B VAL* 1.3 67.4 + - + +
1056B GLN 3.7 0.2 - - - -
1057B GLU* 3.5 21.3 - - - +
1058B HIS* 5.1 2.4 + - - -
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Residues in contact with VAL1055 (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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926B ILE* 4.4 19.7 - - + -
929B ARG* 3.5 44.4 - - + +
1051B THR* 3.3 19.7 - - - +
1052B PHE* 3.6 2.0 + - - +
1054B GLN* 1.3 85.6 - - + +
1056B GLN* 1.3 58.9 + - - +
1057B GLU* 3.1 11.8 + - - -
1058B HIS* 3.8 16.1 + - + -
1059B THR* 3.7 25.0 + - - +
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Residues in contact with GLN1056 (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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1050A TYR* 3.8 27.9 + - + -
926B ILE* 4.3 15.9 - - + -
1052B PHE* 3.3 42.5 + - + +
1053B GLN* 4.5 3.3 - - - -
1054B GLN 3.7 1.0 - - - -
1055B VAL* 1.3 76.9 - - - +
1057B GLU* 1.3 60.4 + - - +
1058B HIS 3.6 0.4 - - - -
1059B THR* 4.4 8.6 - - - +
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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