Contacts of the helix formed by residues 1075 - 1090 (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 ARG1075 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014C LEU* 4.2 17.9 - - - +
1063C LEU* 4.6 1.7 + - - +
1066C LEU* 2.5 43.6 + - - +
1067C ALA* 2.9 36.2 - - + +
1070C PRO* 3.1 14.6 - - - +
1072C ALA* 3.1 23.1 + - + +
1074C LYS* 1.3 124.8 + - - +
1076C LEU* 1.3 54.3 + - + +
1078C ALA* 2.9 12.0 + - - -
1079C SER* 2.2 55.4 + - - +
1107C TYR* 4.8 0.2 - - - +
1111C LEU* 5.7 4.5 - - + -
3741C ARG* 4.5 0.4 - - - +
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Residues in contact with LEU1076 (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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1017C ILE* 5.0 12.3 - - + +
1072C ALA 4.5 5.8 - - - +
1073C PHE* 2.9 29.4 - - - +
1074C LYS 3.4 2.4 - - - -
1075C ARG* 1.3 82.6 - - + +
1077C GLY* 1.3 60.7 + - - +
1079C SER* 2.8 12.1 + - - -
1080C LEU 2.9 10.0 + - - -
1115C HIS* 6.0 5.8 - - + -
1120C SER* 4.4 7.4 - - - -
1123C THR* 3.1 30.7 - - - +
1124C ILE* 3.4 41.5 - - + +
1127C CYS* 3.0 26.4 - - + +
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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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597C ALA* 4.6 9.4 - - - -
1017C ILE* 6.2 0.6 - - - +
1025C LEU* 5.7 3.4 - - - -
1076C LEU* 1.3 79.3 - - - +
1078C ALA* 1.3 64.9 + - - +
1080C LEU* 2.9 20.7 + - - +
1081C ALA* 2.8 29.9 + - - +
1127C CYS* 3.3 2.6 - - - -
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Residues in contact with ALA1078 (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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1013C ILE 5.8 0.7 - - - +
1014C LEU* 5.2 2.9 - - - +
1025C LEU* 5.1 23.2 - - + +
1028C PHE* 5.3 10.3 - - + -
1029C CYS* 3.6 13.4 - - - -
1074C LYS 3.9 8.3 + - - +
1075C ARG* 3.0 28.0 - - + +
1077C GLY* 1.3 74.4 - - - +
1079C SER* 1.3 47.9 + - - +
1081C ALA* 5.3 0.2 - - - -
1082C PHE* 2.3 38.7 + - - +
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Residues in contact with SER1079 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067C ALA* 5.1 0.2 - - - +
1075C ARG* 2.2 52.2 + - - +
1076C LEU* 2.8 7.2 + - - -
1078C ALA* 1.3 67.0 - - - +
1080C LEU* 1.3 67.3 + - - +
1082C PHE* 2.9 26.2 - - - +
1083C ASN 2.9 8.5 + - - -
1107C TYR* 3.3 19.6 + - - -
1111C LEU* 5.0 4.6 - - - +
1127C CYS* 4.6 6.1 - - - -
1131C ILE* 3.6 16.8 - - - +
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Residues in contact with LEU1080 (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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593C ASN* 4.8 3.4 - - + +
594C GLY* 4.7 4.3 - - - +
597C ALA* 3.6 31.6 - - + -
1076C LEU 2.9 6.7 + - - -
1077C GLY* 2.9 16.1 + - - +
1079C SER* 1.3 77.2 - - - +
1081C ALA* 1.3 79.2 + - + +
1084C ASN* 2.7 46.0 + - - +
1126C GLN* 4.1 12.8 - - + +
1127C CYS* 3.3 34.1 - - - +
1130C ALA* 3.6 24.5 - - + -
1131C ILE* 3.8 11.1 - - - +
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Residues in contact with ALA1081 (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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590C GLU 5.6 0.7 - - - +
594C GLY* 3.6 31.6 - - - +
597C ALA* 6.1 0.2 - - + -
1025C LEU 5.9 1.6 - - - +
1026C ARG* 6.2 2.2 - - - -
1029C CYS* 3.8 17.0 - - + -
1077C GLY 2.8 16.3 + - - +
1080C LEU* 1.3 78.3 - - + +
1082C PHE* 1.3 56.0 + - - +
1084C ASN* 3.7 9.8 - - - +
1085C ILE* 2.9 34.2 + - - +
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Residues in contact with PHE1082 (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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1028C PHE* 6.2 2.2 - + + -
1029C CYS* 3.5 14.3 - - - -
1036C PHE* 6.1 0.4 - + - -
1060C PHE* 3.3 32.3 - + - -
1063C LEU* 4.5 26.7 - - + -
1064C TYR* 3.2 20.9 - + - -
1078C ALA 2.3 32.4 + - - +
1079C SER* 2.9 15.7 - - - +
1080C LEU 3.0 0.6 - - - -
1081C ALA* 1.3 75.5 - - - +
1083C ASN* 1.3 89.0 + - - -
1085C ILE* 2.9 28.6 - - + +
1086C TYR* 3.2 34.7 - + - -
1107C TYR* 5.0 3.4 - + - -
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Residues in contact with ASN1083 (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* 3.3 14.2 + - - -
1079C SER 2.9 9.1 + - - -
1082C PHE* 1.3 102.8 - - - +
1084C ASN* 1.3 58.8 + - - +
1086C TYR* 2.7 42.9 + - + +
1087C ARG* 2.9 10.4 + - - +
1090C ARG* 3.4 7.4 - - - +
1104C LEU* 3.2 27.1 - - + +
1107C TYR* 4.7 0.2 - - - -
1131C ILE* 3.9 26.4 - - + +
1134C LEU* 4.1 13.4 - - + +
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Residues in contact with ASN1084 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590C GLU* 2.6 40.4 - - + +
593C ASN* 4.5 14.5 - - + +
1080C LEU* 2.7 45.6 + - - +
1081C ALA* 3.6 10.0 - - - +
1083C ASN* 1.3 76.8 - - - +
1085C ILE* 1.3 53.9 + - - +
1087C ARG* 2.6 41.8 + - - +
1130C ALA* 4.1 20.1 - - - +
1131C ILE* 5.2 1.7 - - - -
1133C HIS* 5.8 0.3 - - - +
1134C LEU* 5.1 4.4 - - - +
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Residues in contact with ILE1085 (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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590C GLU* 3.1 22.3 - - - +
1029C CYS* 3.0 46.9 - - + +
1032C CYS* 3.7 2.0 - - + -
1033C ILE* 3.4 28.2 - - + +
1036C PHE* 3.3 37.0 - - + -
1081C ALA 2.9 24.0 + - - +
1082C PHE* 2.9 13.0 - - + +
1084C ASN* 1.3 74.6 - - - +
1086C TYR* 1.3 70.0 + - + +
1088C GLU* 3.1 12.5 - - - +
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Residues in contact with TYR1086 (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 PHE* 3.6 30.4 - + - -
1059C LEU* 4.8 4.0 - - + +
1060C PHE* 3.2 28.4 - + - -
1063C LEU* 5.3 1.0 - - - +
1082C PHE* 3.2 48.3 - + - -
1083C ASN* 2.7 40.1 + - - +
1085C ILE* 1.3 82.6 - - + +
1087C ARG* 1.3 47.9 + - - +
1088C GLU* 2.5 17.2 + - - -
1089C PHE* 2.6 4.9 + - + +
1090C ARG* 2.2 65.7 + - + +
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Residues in contact with ARG1087 (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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584C GLU* 3.2 16.5 + - - -
586C GLN* 2.8 31.8 + - - +
590C GLU* 2.9 23.3 - - - +
593C ASN* 2.4 29.2 + - - -
1083C ASN 2.9 4.0 + - - -
1084C ASN* 2.6 68.4 + - - +
1086C TYR* 1.3 74.9 - - - +
1088C GLU* 1.3 60.3 + - - +
1090C ARG* 3.8 8.1 - - - -
1091C GLU* 4.8 1.7 - - - +
1133C HIS* 6.2 1.3 - - - -
1134C LEU* 3.8 32.1 - - + -
1136C ARG* 5.0 7.9 - - - +
1137C ILE* 3.3 16.3 - - + +
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Residues in contact with GLU1088 (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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586C GLN* 3.5 19.3 - - + +
587C THR* 4.0 21.4 - - + +
590C GLU* 2.2 35.2 + - - +
1033C ILE* 3.1 33.5 - - + +
1085C ILE 3.1 12.7 - - - +
1086C TYR 2.5 7.4 + - - -
1087C ARG* 1.3 70.2 - - - +
1089C PHE* 1.3 97.4 + - + +
1090C ARG 3.3 0.6 + - - -
1091C GLU* 3.7 23.6 + - - +
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Residues in contact with PHE1089 (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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587C THR* 6.1 0.9 - - + -
1040C SER* 5.3 14.6 - - - +
1086C TYR* 2.6 9.9 + - + +
1088C GLU* 1.3 108.3 - - + +
1090C ARG* 1.3 54.0 + - - -
1091C GLU 3.0 1.3 - - - +
1092C GLU 3.1 29.1 + - - +
1093C GLU* 3.2 10.6 + - + +
1097C GLU* 2.6 29.3 - - - +
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Residues in contact with ARG1090 (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* 3.7 4.2 - - - -
1083C ASN* 3.4 7.8 - - - +
1086C TYR* 2.2 80.4 + - + +
1087C ARG* 3.8 1.6 - - - -
1089C PHE* 1.3 66.6 - - - +
1091C GLU* 1.3 65.2 + - - +
1097C GLU* 3.4 22.0 - - - +
1100C VAL* 3.1 43.3 - - - +
1101C PHE* 3.7 30.5 - - - -
1104C LEU* 4.8 5.8 - - - +
1134C LEU* 4.3 7.8 - - + +
1137C ILE* 3.6 22.0 - - + -
1138C ILE* 3.9 24.7 - - + +
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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
------------------------------------------------------------
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