Contacts of the helix formed by residues 1059 - 1080 (chain C) in PDB entry 4DAJ
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 THR1059 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015C LEU* 5.0 0.4 - - - -
1052C ARG* 5.3 7.0 - - - +
1057C VAL* 6.3 1.1 - - + -
1058C ILE* 1.3 77.6 - - - +
1060C LYS* 1.3 67.0 + - - +
1061C ASP* 3.2 11.1 + - - +
1062C GLU* 3.2 36.3 + - - +
1063C ALA* 3.1 20.0 + - - +
216D PRO* 5.7 8.1 - - + -
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Residues in contact with LYS1060 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 3.9 37.2 + - + +
174C THR* 4.5 6.6 - - + +
178C LYS* 4.4 13.9 - - - +
1013C LEU* 6.1 0.4 - - - -
1015C LEU* 3.8 29.8 - - + +
1058C ILE 4.0 0.2 + - - -
1059C THR* 1.3 73.1 - - - +
1061C ASP* 1.3 62.9 + - - +
1063C ALA* 3.2 10.6 - - - +
1064C GLU* 2.9 32.5 + - - +
2001C PO4 2.7 35.3 + - - +
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Residues in contact with ASP1061 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ARG* 6.1 2.9 - - - -
174C THR* 2.7 39.0 + - - +
1059C THR* 3.1 9.9 + - - +
1060C LYS* 1.3 75.7 - - - +
1062C GLU* 1.3 67.2 + - + +
1064C GLU* 3.1 12.8 + - - +
1065C LYS* 2.9 39.2 + - - +
214D THR* 3.9 23.2 - - - +
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Residues in contact with GLU1062 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050C ILE* 3.1 42.3 - - + +
1052C ARG* 3.3 31.3 + - - -
1058C ILE* 3.4 14.5 - - + +
1059C THR* 3.2 28.3 + - - +
1061C ASP* 1.3 76.5 - - + +
1063C ALA* 1.3 57.4 + - - +
1065C LYS* 3.3 20.0 + - + +
1066C LEU* 2.9 34.9 + - - +
216D PRO* 5.9 1.0 - - - +
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Residues in contact with ALA1063 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 5.0 6.7 - - + -
1013C LEU* 6.0 3.1 - - + -
1015C LEU* 5.4 6.7 - - + -
1028C GLY* 4.8 13.2 - - - -
1029C ILE* 5.5 9.0 + - + +
1058C ILE* 3.9 20.5 - - + +
1059C THR 3.1 12.8 + - - +
1060C LYS* 3.2 14.1 - - - +
1062C GLU* 1.3 73.5 - - - +
1064C GLU* 1.3 66.2 + - - +
1066C LEU* 3.2 7.4 + - - +
1067C PHE* 2.9 22.8 + - - +
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Residues in contact with GLU1064 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C THR 4.7 2.7 - - - +
171C ARG* 2.8 14.0 - - + +
172C PRO* 2.8 26.4 - - + +
173C LEU* 2.7 49.0 + - + +
174C THR* 2.4 27.3 + - - -
1004C PHE* 6.2 0.4 - - + -
1029C ILE* 6.5 0.7 - - - -
1060C LYS 2.9 15.7 + - - +
1061C ASP* 3.1 14.4 + - - +
1063C ALA* 1.3 74.8 - - - +
1065C LYS* 1.3 65.0 + - + +
1067C PHE* 2.9 10.9 + - - +
1068C ASN* 2.9 29.8 + - - +
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Residues in contact with LYS1065 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ARG* 5.9 5.4 - - - +
1061C ASP* 2.9 31.8 + - - +
1062C GLU* 3.5 17.1 - - + +
1064C GLU* 1.3 75.6 - - + +
1066C LEU* 1.3 65.1 + - + +
1068C ASN* 3.2 9.5 + - - +
1069C GLN* 2.9 25.4 + - - +
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Residues in contact with LEU1066 (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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1027C ILE* 5.1 2.9 - - + +
1031C HIS* 4.1 35.7 - - + +
1046C LEU* 4.8 7.2 - - + -
1049C ALA* 4.6 18.6 - - + +
1050C ILE* 3.8 26.0 - - + -
1058C ILE* 4.0 18.4 - - + -
1062C GLU 2.9 17.0 + - - +
1063C ALA* 3.4 7.6 - - - +
1065C LYS* 1.3 76.9 - - + +
1067C PHE* 1.3 62.8 + - - +
1069C GLN* 3.3 17.6 + - - +
1070C ASP* 2.9 34.9 + - - +
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Residues in contact with PHE1067 (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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172C PRO* 5.0 5.6 - - + -
259C LYS* 4.9 6.5 - - + -
1003C ILE* 4.6 2.2 - - + -
1004C PHE* 3.6 52.0 - + + -
1007C LEU* 3.6 35.2 - - + -
1029C ILE* 4.3 37.0 - - + +
1063C ALA 2.9 12.9 + - - +
1064C GLU* 3.2 13.2 - - - +
1066C LEU* 1.3 75.7 - - - +
1068C ASN* 1.3 72.8 + - - +
1070C ASP* 3.1 10.2 + - - +
1071C VAL* 2.9 48.4 + - + +
1104C PHE* 4.4 7.2 - + - -
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Residues in contact with ASN1068 (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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169C ILE 4.7 1.6 - - - +
170C THR* 3.3 33.6 + - - +
172C PRO* 4.8 3.3 - - - +
259C LYS* 3.2 36.2 + - - +
1064C GLU* 2.9 29.3 + - - +
1065C LYS* 3.6 8.7 - - - +
1067C PHE* 1.3 88.6 - - - +
1069C GLN* 1.3 64.4 + - - +
1071C VAL* 2.9 17.2 + - - +
1072C ASP* 2.9 17.0 + - - +
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Residues in contact with GLN1069 (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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1065C LYS 2.9 17.5 + - - +
1066C LEU* 3.7 16.8 - - + +
1068C ASN* 1.3 74.5 - - - +
1070C ASP* 1.3 61.6 + - - +
1072C ASP* 3.5 8.2 + - + +
1073C ALA* 2.9 26.9 + - + +
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Residues in contact with ASP1070 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029C ILE 4.6 2.9 - - - +
1030C GLY 5.8 0.2 - - - -
1031C HIS* 2.6 49.1 + - - +
1066C LEU* 2.9 21.7 + - - +
1067C PHE* 3.1 9.9 + - - +
1069C GLN* 1.3 78.2 - - - +
1071C VAL* 1.3 60.8 + - - +
1073C ALA* 3.5 9.3 - - - +
1074C ALA* 2.9 30.1 + - - +
1104C PHE* 3.6 22.2 - - + -
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Residues in contact with VAL1071 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C GLU* 4.2 2.9 - - - +
259C LYS* 3.7 23.6 - - + -
1003C ILE* 3.6 27.4 - - + -
1007C LEU* 4.8 2.5 - - + -
1067C PHE* 2.9 53.3 + - + +
1068C ASN* 2.9 7.8 + - - +
1070C ASP* 1.3 75.0 - - - +
1072C ASP* 1.3 59.9 + - - +
1074C ALA* 3.8 3.9 - - - +
1075C VAL* 2.9 45.9 + - + +
1100C ILE* 5.0 3.6 - - + -
1104C PHE* 4.7 7.2 - - + -
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Residues in contact with ASP1072 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C GLU* 5.3 0.5 - - - +
259C LYS* 2.7 36.2 + - - -
1068C ASN 2.9 9.8 + - - +
1069C GLN* 3.8 10.8 - - + +
1071C VAL* 1.3 76.6 - - - +
1073C ALA* 1.3 57.2 + - - +
1075C VAL* 4.7 3.9 - - - +
1076C ARG* 2.9 35.7 + - - +
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Residues in contact with ALA1073 (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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1069C GLN* 2.9 18.9 + - + +
1070C ASP* 3.5 13.2 - - - +
1071C VAL 3.2 0.4 - - - -
1072C ASP* 1.3 77.6 - - - +
1074C ALA* 1.3 55.9 + - - +
1076C ARG* 4.5 2.1 - - - +
1077C GLY* 2.9 23.8 + - - +
1080C ARG* 5.7 0.3 + - - -
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Residues in contact with ALA1074 (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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1070C ASP 2.9 16.9 + - - +
1071C VAL 3.9 3.1 - - - +
1073C ALA* 1.3 77.6 - - - +
1075C VAL* 1.3 60.8 + - - +
1077C GLY* 3.6 1.5 - - - -
1078C ILE* 2.9 34.0 + - - +
1100C ILE* 4.3 18.6 - - + +
1103C VAL* 3.8 20.3 - - + +
1104C PHE* 4.4 16.4 - - + -
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Residues in contact with VAL1075 (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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258C GLU* 4.3 11.4 - - - +
1071C VAL* 2.9 31.1 + - + +
1072C ASP* 4.4 3.4 - - - +
1074C ALA* 1.3 74.3 - - - +
1076C ARG* 1.3 60.1 + - - +
1078C ILE* 2.9 21.8 + - - +
1079C LEU* 2.9 26.5 + - + +
1088C TYR* 3.7 24.5 - - + +
1100C ILE* 3.9 33.7 - - + -
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Residues in contact with ARG1076 (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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1072C ASP* 2.9 20.5 + - + +
1073C ALA* 4.5 2.7 - - - +
1075C VAL* 1.3 74.3 - - - +
1077C GLY* 1.3 65.0 + - - +
1079C LEU* 3.9 7.8 - - - +
1080C ARG* 2.9 41.8 + - + +
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Residues in contact with GLY1077 (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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1073C ALA 2.9 23.2 + - - -
1074C ALA* 3.6 3.6 - - - -
1075C VAL 3.2 0.6 - - - -
1076C ARG* 1.3 76.3 - - - +
1078C ILE* 1.3 61.2 + - - +
1080C ARG* 3.8 12.0 + - - +
1081C ASN* 3.7 9.0 + - - +
1084C LEU* 5.3 0.2 - - - -
1103C VAL* 5.4 2.2 - - - -
1108C GLU* 3.5 37.8 - - - +
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Residues in contact with ILE1078 (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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1074C ALA 2.9 22.7 + - - +
1075C VAL* 2.9 10.7 + - - +
1077C GLY* 1.3 74.2 - - - +
1079C LEU* 1.3 67.6 + - + +
1080C ARG 3.2 1.3 - - - -
1081C ASN* 3.2 20.6 + - - +
1084C LEU* 3.8 23.4 - - + +
1085C LYS 3.9 2.0 + - - +
1088C TYR* 3.7 52.9 - - + -
1099C LEU* 4.2 10.8 - - + -
1100C ILE* 4.3 12.8 - - + -
1103C VAL* 3.5 34.5 - - + -
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Residues in contact with LEU1079 (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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1075C VAL* 2.9 29.0 + - + +
1076C ARG* 3.3 6.9 + - - +
1078C ILE* 1.3 77.8 - - + +
1080C ARG* 1.3 59.4 + - + +
1081C ASN 3.1 9.1 + - - +
1085C LYS* 4.3 34.5 - - + +
1088C TYR* 4.2 25.8 - - + -
1089C ASP* 6.4 0.7 - - + -
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Residues in contact with ARG1080 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073C ALA 5.7 0.2 + - - -
1076C ARG* 2.9 35.5 + - + +
1077C GLY* 4.1 9.1 - - - +
1078C ILE 3.2 0.2 - - - -
1079C LEU* 1.3 77.7 - - + +
1081C ASN* 1.3 58.4 + - - +
1082C ALA 4.0 1.0 + - - -
1108C GLU* 3.6 26.0 + - - +
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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