Contacts of the helix formed by residues 1055 - 1069 (chain C) in PDB entry 5Y3R
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 ASN1055 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996C THR* 5.2 5.4 - - - +
1000C LYS* 3.9 10.7 + - - -
1035C GLU* 3.9 17.8 + - - +
1036C PHE* 4.4 3.0 - - - -
1039C TRP* 2.9 51.6 - - + +
1052C SER* 2.7 41.9 + - - +
1053C PRO 2.7 14.9 - - - +
1054C VAL* 1.3 84.8 + - - +
1056C THR* 1.3 79.8 + - + +
1057C LYS 3.0 1.7 + - - -
1058C SER 3.4 0.2 + - - -
1059C LEU* 3.4 6.7 - - - -
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Residues in contact with THR1056 (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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1039C TRP* 3.4 39.2 - - + +
1049C GLN* 2.2 50.4 + - + +
1050C GLU* 3.6 2.7 - - - -
1052C SER 2.8 1.4 + - - -
1055C ASN* 1.3 76.6 + - - +
1057C LYS* 1.3 76.5 + - - +
1059C LEU* 3.1 22.5 - - - +
1060C PHE* 3.2 13.2 - - - -
1096C VAL* 3.9 27.6 - - + -
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Residues in contact with LYS1057 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050C GLU* 2.3 58.1 + - + +
1055C ASN 3.0 0.4 + - - -
1056C THR* 1.3 86.1 + - - +
1058C SER* 1.3 59.2 + - - +
1059C LEU 2.7 12.8 + - - -
1060C PHE* 2.8 13.8 + - - +
1061C LYS* 2.9 14.0 + - + -
1095C LEU* 3.6 21.7 - - - +
1096C VAL* 3.7 17.3 - - + -
1099C PHE* 3.3 42.4 - - + -
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Residues in contact with SER1058 (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 GLU 4.9 1.0 + - - -
1053C PRO* 3.0 32.7 - - - +
1055C ASN 3.4 3.2 + - - -
1057C LYS* 1.3 80.0 - - - +
1059C LEU* 1.3 66.8 + - - +
1061C LYS* 2.7 40.2 + - - +
1062C ARG* 2.9 42.3 + - - +
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Residues in contact with LEU1059 (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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1010C LEU* 6.3 4.7 - - + -
1032C CYS* 6.4 0.9 - - - -
1035C GLU* 3.6 8.1 - - - +
1036C PHE* 3.4 31.6 - - + -
1053C PRO 3.0 2.6 + - - -
1054C VAL* 3.0 26.0 - - + +
1055C ASN* 3.4 9.2 - - - -
1056C THR* 3.1 26.9 - - - +
1057C LYS 2.7 4.2 + - - -
1058C SER* 1.3 79.8 - - - +
1060C PHE* 1.3 61.6 + - + +
1062C ARG* 3.1 15.3 - - - +
1063C LEU* 2.7 53.0 + - + +
1086C TYR* 4.8 3.6 - - - +
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Residues in contact with PHE1060 (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 THR* 3.2 22.2 - - - -
1057C LYS* 2.8 6.1 + - - +
1059C LEU* 1.3 83.9 - - + +
1061C LYS* 1.3 64.9 + - - +
1063C LEU* 4.1 6.3 - - - -
1064C TYR* 2.8 65.8 + + + +
1082C PHE* 3.3 11.9 - + - -
1086C TYR* 3.2 50.3 - + - -
1090C ARG* 3.9 5.6 - - - -
1096C VAL* 4.5 6.5 - - + -
1100C VAL* 3.4 37.7 - - + -
1103C ALA* 6.1 0.7 - - + -
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Residues in contact with LYS1061 (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 PRO* 5.0 1.4 - - - +
1057C LYS* 2.9 9.3 + - + +
1058C SER* 2.7 47.4 + - - +
1059C LEU 2.9 0.6 + - - -
1060C PHE* 1.3 76.3 - - - +
1062C ARG* 1.3 58.9 - - - +
1064C TYR* 4.6 0.2 - - - +
1065C SER* 2.2 33.5 + - - -
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Residues in contact with ARG1062 (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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1007C VAL* 5.3 10.7 - - - +
1010C LEU* 5.7 4.3 - - - +
1011C GLU* 4.6 18.2 + - - -
1053C PRO* 3.2 16.8 + - - +
1054C VAL* 4.0 5.4 - - - +
1058C SER* 2.9 47.9 + - - +
1059C LEU* 2.9 52.5 - - - +
1061C LYS* 1.3 78.6 - - - +
1063C LEU* 1.3 69.8 + - + +
1064C TYR 2.6 1.6 + - - -
1065C SER* 2.4 43.5 + - - -
1066C LEU* 2.6 29.6 + - + -
3725C ARG* 5.7 7.2 - - - +
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Residues in contact with LEU1063 (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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1010C LEU* 5.9 3.6 - - + -
1028C PHE* 4.8 23.6 - - + -
1032C CYS* 6.2 2.0 - - - -
1036C PHE* 6.1 1.8 - - + -
1059C LEU* 2.7 53.5 + - + +
1060C PHE* 4.1 3.1 - - - +
1062C ARG* 1.3 84.4 - - + +
1064C TYR* 1.3 52.4 + - - +
1066C LEU* 3.7 17.5 - - + -
1067C ALA* 2.6 37.9 + - - +
1075C ARG* 4.6 2.1 + - - +
1082C PHE* 4.5 26.9 - - + -
1086C TYR* 5.3 1.3 - - - +
1107C TYR* 4.6 0.5 + - - -
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Residues in contact with TYR1064 (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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1060C PHE* 2.8 46.0 + + + +
1061C LYS 4.6 0.4 - - - +
1062C ARG 2.6 3.2 + - - -
1063C LEU* 1.3 69.8 - - - +
1065C SER* 1.3 68.9 + - - +
1067C ALA* 2.7 19.9 + - - +
1068C LEU* 2.9 13.6 + - + +
1082C PHE* 3.2 24.5 - + - -
1083C ASN* 3.3 7.4 + - - -
1100C VAL* 2.9 27.1 - - + +
1103C ALA* 4.0 19.3 - - + +
1104C LEU* 3.0 35.1 - - + +
1107C TYR* 3.3 46.0 - + + -
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Residues in contact with SER1065 (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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1061C LYS 2.2 28.2 + - - -
1062C ARG* 2.4 16.7 + - - -
1064C TYR* 1.3 73.1 - - - +
1066C LEU* 1.3 55.7 + - - -
1068C LEU* 2.1 46.9 + - - +
1069C HIS* 2.8 29.7 + - - -
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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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1011C GLU* 4.6 11.9 - - - +
1014C LEU* 5.3 15.5 - - + -
1062C ARG* 2.6 43.1 + - + -
1063C LEU* 3.7 21.1 - - + -
1065C SER* 1.3 78.0 + - - +
1067C ALA* 1.3 56.5 + - - +
1069C HIS* 3.1 13.7 - - + -
1070C PRO* 3.0 9.9 - - - +
1075C ARG* 2.5 40.7 + - - +
3723C ASP* 5.4 4.5 - - - +
3725C ARG* 6.0 4.9 - - - +
3741C ARG* 4.5 11.4 - - - +
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Residues in contact with ALA1067 (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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1063C LEU 2.6 24.9 + - - +
1064C TYR 2.7 13.5 + - - +
1066C LEU* 1.3 73.5 - - - +
1068C LEU* 1.3 62.5 + - + +
1070C PRO* 3.3 7.8 - - - +
1072C ALA* 3.3 17.7 + - - +
1075C ARG* 2.9 31.1 - - + +
1079C SER* 5.1 0.2 - - - +
1107C TYR* 3.6 23.3 - - + +
1111C LEU* 5.3 2.0 - - + -
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Residues in contact with LEU1068 (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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1064C TYR* 2.9 16.2 - - + +
1065C SER* 2.1 36.7 + - - +
1067C ALA* 1.3 70.5 - - - +
1069C HIS* 1.3 52.8 + - + +
1071C ASN* 2.7 36.2 + - - +
1107C TYR* 3.6 34.5 - - + -
1110C SER* 4.8 10.3 - - - +
1111C LEU* 3.8 28.9 - - + +
1114C ALA* 5.5 8.8 - - + +
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Residues in contact with HIS1069 (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 SER* 2.8 49.7 + - - -
1066C LEU* 3.1 9.6 - - + +
1068C LEU* 1.3 74.9 - - + +
1070C PRO* 1.3 62.4 - - + +
1071C ASN* 2.9 8.5 + - - -
3690C PHE* 5.0 9.6 - + - -
3721C GLY* 5.3 4.3 + - - -
3722C PHE 2.9 28.1 + - - -
3723C ASP* 2.7 22.7 + - - -
3741C ARG* 3.0 35.5 - - + +
3742C GLY 3.3 17.7 + - - +
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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