Contacts of the helix formed by residues 1044 - 1061 (chain C) in PDB entry 3EI4
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 SER1044 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C TYR* 4.1 0.7 - - - -
1022C THR 4.9 6.5 + - - -
1023C PRO 4.5 2.2 + - - -
1042C SER 4.4 0.2 + - - -
1043C LEU* 1.3 75.0 - - - +
1045C GLU* 1.3 58.5 + - - +
1046C SER* 3.3 18.9 + - - -
1047C TRP* 3.2 32.9 - - - +
1048C TYR* 2.7 36.6 + - - +
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Residues in contact with GLU1045 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 5.0 6.1 - - - +
3C TYR* 3.3 43.1 + - + +
1043C LEU 3.9 1.4 + - - -
1044C SER* 1.3 74.3 + - - +
1046C SER* 1.3 58.5 + - - +
1048C TYR* 3.5 2.6 + - - +
1049C ASN* 2.6 51.7 + - - +
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Residues in contact with SER1046 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044C SER* 3.3 10.9 + - - -
1045C GLU* 1.3 82.5 + - - +
1047C TRP* 1.3 65.7 + - - -
1049C ASN* 3.5 8.8 + - - +
1050C LEU* 3.5 18.0 + - - +
1115C ASP* 5.4 7.1 - - - +
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Residues in contact with TRP1047 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021C SER* 5.3 4.0 - - - -
1022C THR 4.4 3.0 - - - -
1023C PRO* 3.7 49.8 - - + +
1043C LEU* 4.0 9.4 - - + -
1044C SER* 3.2 37.5 + - - +
1046C SER* 1.3 79.2 - - - +
1048C TYR* 1.3 67.3 + - - +
1050C LEU* 3.2 31.0 + - + +
1051C LEU* 3.0 36.8 + - + +
1114C TYR* 5.0 5.2 - + - -
1132C VAL* 3.5 45.3 - - + -
1136C LEU* 5.2 3.1 - - + -
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Residues in contact with TYR1048 (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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3C TYR* 3.6 46.0 - + + -
1043C LEU* 4.5 5.6 - - + +
1044C SER 2.7 20.4 + - - +
1045C GLU* 3.6 4.0 - - - +
1046C SER 3.4 0.2 - - - -
1047C TRP* 1.3 74.1 - - - +
1049C ASN* 1.3 65.3 + - - +
1051C LEU 3.1 0.3 + - - -
1052C LEU* 2.7 69.7 + - + +
1086C THR* 4.0 5.7 - - - +
1087C GLY* 2.8 47.0 + - - -
1088C PHE 3.9 2.3 + - - -
1089C ILE* 3.5 27.8 - - + +
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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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1045C GLU* 2.6 45.4 + - - +
1046C SER* 3.7 8.0 + - - +
1047C TRP 3.2 0.8 - - - -
1048C TYR* 1.3 85.4 - - - +
1050C LEU* 1.3 64.0 + - - +
1052C LEU* 3.2 8.8 + - - +
1053C ASP* 2.9 25.7 + - - +
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Residues in contact with LEU1050 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046C SER 3.5 8.4 + - - +
1047C TRP* 3.2 40.7 + - + +
1049C ASN* 1.3 77.6 - - - +
1051C LEU* 1.3 55.5 + - + +
1053C ASP* 3.2 8.9 - - - +
1054C MET* 2.8 46.3 + - + +
1112C LEU* 3.9 35.2 - - + -
1113C GLN 5.5 2.9 - - - +
1114C TYR* 4.3 26.7 - - + -
1129C LEU* 4.6 12.3 - - + -
1132C VAL* 5.0 0.7 - - + -
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Residues in contact with LEU1051 (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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5C TYR* 4.1 20.4 - - + -
1043C LEU* 4.1 21.8 - - + -
1047C TRP* 3.0 23.7 + - + +
1048C TYR 3.7 1.3 - - - +
1050C LEU* 1.3 80.9 - - + +
1052C LEU* 1.3 67.9 + - - +
1054C MET* 3.0 15.6 + - + +
1055C GLN* 2.9 30.5 + - - +
1089C ILE* 3.4 31.6 - - + -
1094C ILE* 3.6 23.8 - - + -
1129C LEU* 5.8 0.9 - - + -
1132C VAL* 5.3 4.9 - - + -
1133C VAL* 5.8 2.9 - - + -
1136C LEU* 4.3 14.8 - - + -
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Residues in contact with LEU1052 (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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1048C TYR* 2.7 60.2 + - + +
1049C ASN* 3.4 10.1 - - - +
1051C LEU* 1.3 72.9 - - - +
1053C ASP* 1.3 61.4 + - - +
1055C GLN* 3.5 20.6 + - + +
1056C ASN* 3.2 38.6 + - - +
1088C PHE 4.3 5.6 - - - +
1089C ILE* 4.1 1.4 - - + +
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Residues in contact with ASP1053 (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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1049C ASN 2.9 11.8 + - - +
1050C LEU* 3.2 12.3 - - - +
1052C LEU* 1.3 73.6 - - - +
1054C MET* 1.3 66.9 + - - +
1056C ASN* 3.0 21.1 + - - +
1057C ARG* 2.9 53.0 + - - +
1112C LEU* 3.6 12.2 - - + +
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Residues in contact with MET1054 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050C LEU* 2.8 27.4 + - + +
1051C LEU* 3.0 29.4 + - + +
1053C ASP* 1.3 71.2 - - - +
1055C GLN* 1.3 65.5 + - + +
1057C ARG* 3.0 8.7 + - - +
1058C LEU* 2.8 38.3 + - + +
1094C ILE* 5.0 1.3 - - + -
1097C PHE* 5.8 3.8 - - - -
1108C VAL* 4.3 27.7 - - + +
1109C VAL* 5.5 0.4 - - - -
1112C LEU* 3.5 40.4 - - + -
1129C LEU* 3.7 28.0 - - + -
1133C VAL* 6.5 0.2 - - - -
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Residues in contact with GLN1055 (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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998C PHE* 6.3 0.4 - - - -
1051C LEU 2.9 21.3 + - - +
1052C LEU* 3.5 18.8 - - + +
1054C MET* 1.3 70.5 - - - +
1056C ASN* 1.3 54.4 + - - +
1058C LEU* 3.0 7.3 + - - +
1059C ASN* 2.7 44.2 + - - +
1070C HIS* 3.7 10.9 - - + -
1088C PHE 4.2 3.0 + - - +
1089C ILE* 3.3 35.9 - - - +
1090C ASP* 3.5 18.6 + - - +
1093C LEU* 3.5 29.6 - - + +
1094C ILE* 3.7 15.5 - - + -
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Residues in contact with ASN1056 (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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1052C LEU* 3.2 34.1 + - - +
1053C ASP* 3.0 12.7 + - - +
1055C GLN* 1.3 80.6 - - - +
1057C ARG* 1.3 61.9 + - + +
1059C ASN* 3.5 16.4 + - - +
1060C LYS* 3.3 28.6 + - - +
1071C SER* 6.1 1.2 - - - -
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Residues in contact with ARG1057 (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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1053C ASP* 2.9 43.3 + - - +
1054C MET* 3.0 5.7 + - - +
1056C ASN* 1.3 74.1 - - + +
1058C LEU* 1.3 65.3 + - - +
1059C ASN 3.1 1.3 - - - -
1060C LYS* 3.1 20.9 + - - +
1061C VAL* 3.3 16.1 + - - +
1107C GLU 5.0 1.8 - - - +
1108C VAL* 2.8 60.5 + - + +
1110C ALA 2.7 29.3 + - - -
1111C ASN* 4.2 5.8 + - - +
1112C LEU* 3.1 37.8 - - - +
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Residues in contact with LEU1058 (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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1054C MET* 2.8 37.0 + - + +
1055C GLN* 3.3 10.3 - - - +
1057C ARG* 1.3 76.8 - - - +
1059C ASN* 1.3 52.5 + - - +
1061C VAL* 2.6 32.4 - - + +
1062C ILE* 3.3 30.6 - - + +
1093C LEU* 3.8 31.4 - - + +
1094C ILE* 4.5 12.1 - - + -
1096C SER 4.8 0.2 - - - +
1097C PHE* 4.0 35.2 - - + -
1100C ILE* 5.1 7.6 - - + -
1108C VAL* 4.1 15.0 - - + +
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Residues in contact with ASN1059 (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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58C TYR* 5.2 0.7 + - - -
1055C GLN* 2.7 29.0 + - - +
1056C ASN* 3.5 18.4 + - - +
1057C ARG 3.1 0.2 - - - -
1058C LEU* 1.3 69.7 - - - +
1060C LYS* 1.3 59.6 + - + +
1061C VAL 2.8 14.6 - - - +
1062C ILE* 4.4 4.5 - - - +
1069C GLU* 6.2 2.4 - - + +
1070C HIS* 3.8 30.6 + - - +
1071C SER* 4.5 12.1 + - - +
1093C LEU* 3.3 24.2 - - - +
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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
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1056C ASN* 3.3 17.9 + - - +
1057C ARG* 3.1 11.4 + - - +
1059C ASN* 1.3 79.3 - - + +
1061C VAL* 1.3 60.0 + - + +
1107C GLU* 5.3 7.6 - - - +
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Residues in contact with VAL1061 (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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1057C ARG 3.3 13.8 + - - +
1058C LEU* 2.6 20.2 - - + +
1059C ASN 2.8 14.4 - - - +
1060C LYS* 1.3 76.5 - - + +
1062C ILE* 1.3 79.0 + - + +
1100C ILE* 5.0 10.3 - - + -
1104C LYS* 3.6 49.4 - - + +
1107C GLU* 4.5 19.3 - - - +
1108C VAL* 3.8 19.5 - - + -
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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
------------------------------------------------------------
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