Contacts of the helix formed by residues 1038 - 1056 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033C LEU 3.8 10.1 - - - +
1034C LEU* 3.4 21.5 - - - +
1035C PHE 3.8 1.0 + - - -
1036C THR 3.1 1.8 + - - -
1037C ASN* 1.3 92.0 - - + +
1039C LEU* 1.3 69.6 + - + +
1040C LEU 3.5 1.3 - - - -
1041C LEU* 3.3 9.9 + - - +
1042C ASN* 2.9 44.8 + - - +
934D VAL* 3.7 24.5 - - + -
937D PHE* 5.4 4.3 - - + -
938D LEU* 5.6 5.4 - - + -
941D LEU* 5.1 15.7 - - + -
1044D LEU* 5.0 14.4 - - + -
1048D PHE* 4.2 9.9 - - + -
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Residues in contact with LEU1039 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034C LEU* 3.3 32.5 - - + +
1035C PHE* 3.5 33.1 + - + +
1038C ILE* 1.3 81.0 - - + +
1040C LEU* 1.3 66.5 + - + +
1042C ASN* 3.0 13.0 + - - +
1043C LEU* 2.9 25.3 + - - +
927D VAL* 5.1 14.1 - - + +
931D MET* 5.0 21.1 - - + -
934D VAL* 4.4 20.4 - - + -
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Residues in contact with LEU1040 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937C PHE* 3.6 29.6 - - + -
940C LEU* 4.1 16.4 - - + -
941C LEU* 4.1 22.0 - - + -
944C TRP* 4.6 20.4 - - + +
1035C PHE 4.5 5.6 + - - +
1036C THR* 4.8 9.3 + - - +
1038C ILE 3.5 0.4 - - - -
1039C LEU* 1.3 88.2 - - + +
1041C LEU* 1.3 57.2 + - + +
1043C LEU* 3.2 14.9 + - + +
1044C LEU* 2.9 31.6 + - - +
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Residues in contact with LEU1041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036C THR 3.3 25.8 - - - +
1037C ASN* 3.4 23.6 - - - +
1038C ILE 3.3 5.3 + - - +
1039C LEU 3.2 0.6 - - - -
1040C LEU* 1.3 77.6 - - + +
1042C ASN* 1.3 62.1 + - - +
1044C LEU* 3.3 9.8 + - + +
1045C ILE* 2.9 37.6 + - + +
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Residues in contact with ASN1042 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038C ILE* 2.9 30.1 + - - +
1039C LEU* 3.0 9.7 + - - +
1041C LEU* 1.3 76.4 - - - +
1043C LEU* 1.3 59.2 + - - +
1045C ILE* 3.3 13.9 + - - +
1046C ALA* 2.9 29.5 + - - +
927D VAL* 6.0 0.4 - - + -
930D MET* 3.7 27.7 - - + +
934D VAL* 3.5 12.1 - - - +
1048D PHE* 3.2 46.2 - - + -
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Residues in contact with LEU1043 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937C PHE* 3.6 33.7 - - + -
940C LEU* 5.1 11.2 - - + -
1039C LEU 2.9 12.0 + - - +
1040C LEU* 3.2 19.3 + - + +
1042C ASN* 1.3 75.7 - - - +
1044C LEU* 1.3 60.9 + - + +
1046C ALA* 3.4 5.0 + - - +
1047C MET* 2.9 40.3 + - + +
923D LYS* 4.8 17.9 - - + +
924D ILE* 5.3 8.1 - - + -
927D VAL* 3.7 35.6 - - + +
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Residues in contact with LEU1044 (chain C).
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* 4.9 13.2 - - + -
937C PHE* 3.5 50.3 - - + -
1040C LEU 2.9 19.8 + - - +
1041C LEU* 3.7 10.3 - - + +
1043C LEU* 1.3 77.8 - - + +
1045C ILE* 1.3 60.4 + - + +
1047C MET* 4.6 2.9 - - + -
1048C PHE* 2.8 74.9 + - + +
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Residues in contact with ILE1045 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B ILE* 6.4 3.4 - - + -
1041C LEU* 2.9 27.7 + - + +
1042C ASN* 3.3 15.5 + - - +
1044C LEU* 1.3 75.0 - - - +
1046C ALA* 1.3 58.5 + - + +
1048C PHE* 5.1 1.1 - - - -
1049C ASN* 3.0 42.7 + - + +
930D MET* 5.7 0.9 - - + -
1045D ILE* 6.4 2.9 - - + -
1048D PHE* 5.0 28.5 - - + +
1049D ASN* 5.5 4.7 - - + +
1052D PHE* 5.5 5.4 - - + -
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Residues in contact with ALA1046 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042C ASN 2.9 16.8 + - - +
1043C LEU* 3.7 6.3 - - - +
1045C ILE* 1.3 77.5 - - - +
1047C MET* 1.3 56.7 + - - +
1050C TYR* 2.9 31.3 + - - +
923D LYS* 5.2 4.5 - - + -
926D ILE* 4.0 25.1 - - + -
930D MET* 4.6 4.5 - - + -
1052D PHE* 3.2 33.9 - - + -
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Residues in contact with MET1047 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933C ASP* 4.4 13.2 - - + +
1043C LEU* 2.9 30.0 + - + +
1044C LEU* 4.3 4.9 - - + +
1046C ALA* 1.3 73.3 - - - +
1048C PHE* 1.3 66.3 + - + +
1050C TYR* 3.3 2.1 + - - +
1051C THR* 2.9 31.4 + - - +
923D LYS* 4.1 32.3 + - + +
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Residues in contact with PHE1048 (chain C).
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* 4.2 5.6 - - + -
1042B ASN* 3.2 42.0 - - + -
1045B ILE* 5.0 20.6 - - + -
930C MET* 3.5 14.8 - - + +
933C ASP* 4.4 14.1 - - - -
934C VAL* 3.7 27.6 - - + -
937C PHE* 5.7 0.7 - + + -
1044C LEU* 2.8 61.3 + - + +
1045C ILE* 4.5 0.9 - - - +
1047C MET* 1.3 77.4 - - + +
1049C ASN* 1.3 60.2 + - - +
1051C THR* 3.8 11.9 - - + -
1052C PHE* 2.9 32.6 + - - +
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Residues in contact with ASN1049 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B ILE* 5.5 6.2 - - + +
1049B ASN* 3.8 17.2 + - - +
1045C ILE* 3.0 26.0 + - + +
1048C PHE* 1.3 77.1 - - - +
1050C TYR* 1.3 57.7 + - - +
1052C PHE* 4.0 4.9 - - - -
1053C GLN* 2.9 53.2 + - - +
1049D ASN* 3.8 13.7 + - - +
1052D PHE* 3.2 31.3 - - + -
1053D GLN* 4.8 2.4 - - - +
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Residues in contact with TYR1050 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046C ALA 2.9 20.1 + - - +
1047C MET 3.4 4.9 - - - +
1048C PHE 3.2 0.2 - - - -
1049C ASN* 1.3 77.6 - - - +
1051C THR* 1.3 63.0 + - - +
1053C GLN* 3.3 4.1 + - - +
1054C GLN* 3.1 34.2 + - + +
922D PRO* 6.5 0.9 - - + -
923D LYS* 3.3 26.0 - - - +
1052D PHE* 3.9 9.4 - + + -
1056D GLN* 3.8 35.3 + - + -
1060D ASP* 6.1 2.1 - - - +
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Residues in contact with THR1051 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926C ILE* 5.6 0.3 - - - +
929C ARG* 4.5 16.3 + - - +
930C MET* 3.7 32.6 - - + +
933C ASP* 4.3 16.7 + - - +
1047C MET 2.9 20.9 + - - +
1048C PHE* 3.6 11.0 - - + +
1050C TYR* 1.3 78.5 - - - +
1052C PHE* 1.3 65.7 + - - +
1054C GLN* 3.8 9.7 + - - +
1055C VAL* 3.3 22.2 + - - +
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Residues in contact with PHE1052 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B ILE* 5.2 4.7 - - + -
1046B ALA* 3.2 46.7 - - + -
1049B ASN* 3.2 33.0 - - + -
1050B TYR* 3.8 23.1 - + + -
1053B GLN* 5.1 7.4 - - - -
926C ILE* 4.5 10.1 - - + -
930C MET* 3.7 13.5 - - + -
1048C PHE 2.9 20.3 + - - +
1049C ASN* 3.8 7.0 - - - +
1051C THR* 1.3 78.1 - - - +
1053C GLN* 1.3 78.8 + - + +
1054C GLN 3.1 1.3 + - - -
1055C VAL* 4.3 2.3 - - - +
1056C GLN* 3.3 43.5 + - + +
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Residues in contact with GLN1053 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B ASN* 4.8 2.4 - - - +
1053B GLN* 4.5 19.0 + - - +
1049C ASN* 2.9 43.7 + - - +
1050C TYR* 4.1 3.9 - - - +
1052C PHE* 1.3 87.2 - - + +
1054C GLN* 1.3 62.6 + - - +
1055C VAL 3.6 0.2 - - - -
1056C GLN* 4.5 5.1 + - - +
1057C GLU* 5.2 5.7 + - - +
1052D PHE* 5.1 6.8 - - - -
1053D GLN* 4.5 15.7 + - - +
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Residues in contact with GLN1054 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050C TYR* 3.1 24.9 + - + +
1051C THR* 4.1 9.6 - - - +
1052C PHE 3.1 0.6 - - - -
1053C GLN* 1.3 80.4 - - - +
1055C VAL* 1.3 68.8 + - + +
1056C GLN 3.7 0.2 - - - -
1057C GLU* 3.5 21.2 - - - +
1058C HIS* 5.1 2.1 + - - -
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Residues in contact with VAL1055 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926C ILE* 4.4 19.7 - - + +
929C ARG* 3.5 45.1 - - + +
1051C THR* 3.3 19.5 - - - +
1052C PHE* 4.3 2.5 - - - +
1054C GLN* 1.3 84.3 - - + +
1056C GLN* 1.3 59.1 + - - +
1057C GLU* 3.1 11.2 + - - -
1058C HIS* 3.8 15.5 + - + -
1059C THR* 3.7 25.1 + - - +
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Residues in contact with GLN1056 (chain C).
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* 3.8 28.0 + - + -
926C ILE* 4.3 15.3 - - + -
1052C PHE* 3.3 42.7 + - + +
1053C GLN* 4.5 3.9 - - - +
1054C GLN 3.7 1.0 - - - -
1055C VAL* 1.3 77.1 - - - +
1057C GLU* 1.3 60.7 + - - +
1058C HIS 3.6 0.2 - - - -
1059C THR* 4.4 9.4 - - - +
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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