Contacts of the helix formed by residues 1072 - 1082 (chain C) in PDB entry 5YS0
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 PRO1072 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070C PRO 4.9 0.2 - - - +
1071C VAL* 1.3 92.2 - - + +
1073C LEU* 1.3 69.0 + - - +
1074C GLY 3.2 2.9 - - - +
1075C THR* 2.9 34.6 + - + +
1076C VAL 3.4 6.9 + - - -
1176C ASN* 3.2 31.4 - - - +
1177C THR 4.6 0.2 - - - +
1178C THR* 3.6 0.3 + - - -
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Residues in contact with LEU1073 (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 PRO* 1.3 72.4 - - - +
1074C GLY* 1.3 63.1 + - - +
1075C THR 3.1 1.4 + - - -
1076C VAL* 3.4 4.5 + - - +
1077C PHE* 3.2 19.4 + - - +
1140C ASP 3.9 3.6 - - - +
1141C LEU* 3.3 32.3 - - + +
1142C ASN 3.9 7.0 - - - +
1143C SER 3.9 24.0 - - - +
1144C PHE* 3.9 4.3 - - - +
1145C PHE* 3.4 27.5 - - + -
1170C TYR* 3.6 26.2 - - + +
1171C SER 4.0 5.8 - - - +
1172C TRP* 4.1 10.0 - - + +
1176C ASN* 4.2 2.0 + - - -
1177C THR 3.9 10.2 + - - +
1178C THR* 3.1 18.8 + - + +
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Residues in contact with GLY1074 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072C PRO* 3.2 3.8 - - - +
1073C LEU* 1.3 78.3 - - - +
1075C THR* 1.3 59.3 - - - +
1077C PHE* 3.8 3.1 + - - +
1078C SER* 3.3 21.1 + - - -
1141C LEU* 3.6 38.2 + - - +
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Residues in contact with THR1075 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071C VAL* 3.4 22.0 - - + -
1072C PRO* 2.9 22.3 + - + +
1074C GLY* 1.3 74.5 - - - +
1076C VAL* 1.3 67.5 + - - +
1077C PHE 3.0 1.1 - - - -
1078C SER* 2.9 6.4 + - - -
1079C LEU* 2.9 39.5 + - + +
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Residues in contact with VAL1076 (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 ILE* 4.3 10.5 - - + -
1071C VAL* 3.6 25.7 - - + +
1072C PRO 3.9 0.2 - - - +
1073C LEU 3.7 6.7 - - - +
1075C THR* 1.3 76.0 - - - +
1077C PHE* 1.3 64.1 + - - +
1079C LEU* 3.4 7.1 + - - +
1080C LEU* 3.0 45.1 + - + +
1145C PHE* 4.8 1.8 - - + -
1170C TYR* 3.9 26.0 - - + -
1178C THR* 3.4 30.1 - - + +
1217C LEU* 4.4 11.4 - - + -
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Residues in contact with PHE1077 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073C LEU 3.2 5.9 + - - +
1074C GLY 3.8 9.6 - - - +
1075C THR 3.0 0.4 - - - -
1076C VAL* 1.3 81.1 - - - +
1078C SER* 1.3 68.5 + - - +
1081C TYR* 2.8 46.0 + + + +
1082C GLY* 3.5 10.3 + - - -
1136C ILE* 3.8 29.8 - - + -
1139C MET* 4.0 24.2 - - + -
1141C LEU* 3.9 17.5 - - + -
1145C PHE* 3.5 47.8 - + + -
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Residues in contact with SER1078 (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 GLY 3.3 13.9 + - - -
1075C THR* 2.9 8.0 + - - -
1077C PHE* 1.3 85.8 - - - +
1079C LEU* 1.3 67.1 + - - +
1082C GLY* 3.2 26.8 + - - +
1084C ASP 4.7 5.0 + - - +
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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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1071C VAL* 5.2 2.5 - - + -
1075C THR* 2.9 37.6 + - + +
1076C VAL* 3.7 8.1 - - - +
1078C SER* 1.3 78.4 - - - +
1080C LEU* 1.3 61.2 + - + +
1082C GLY 4.9 0.2 + - - -
1084C ASP 4.6 5.5 - - - +
1085C THR* 5.9 0.2 - - - -
1087C TYR* 3.3 58.5 + - + +
1088C ILE* 4.0 4.9 + - - +
1217C LEU* 5.3 2.0 - - + -
1220C ILE* 3.4 32.3 - - + -
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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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1076C VAL* 3.0 35.7 + - + +
1079C LEU* 1.3 80.5 - - + +
1081C TYR* 1.3 81.6 + - + +
1082C GLY 3.8 0.2 - - - -
1087C TYR* 4.2 18.8 - - + -
1088C ILE* 3.2 36.8 - - + +
1091C ILE* 4.4 14.8 - - + -
1111C ARG* 2.9 17.5 + - - -
1170C TYR* 3.9 18.4 - - - +
1213C LEU* 5.0 9.6 - - + -
1217C LEU* 3.9 22.4 - - + -
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Residues in contact with TYR1081 (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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1077C PHE* 2.8 37.6 + + + +
1080C LEU* 1.3 97.3 - - + +
1082C GLY* 1.3 70.1 + - - +
1088C ILE* 5.1 4.5 - - + -
1106C PHE* 3.3 34.8 - + + -
1111C ARG* 3.5 6.2 + - - +
1134C GLU* 3.5 35.4 - - - -
1136C ILE* 4.9 0.7 - - + -
1145C PHE* 4.0 16.2 - + - -
1147C VAL* 3.4 31.8 - - + +
1168C PHE* 4.2 10.7 - - - +
1170C TYR* 2.7 36.6 + + - -
1213C LEU* 6.2 0.3 - - - +
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Residues in contact with GLY1082 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077C PHE* 3.5 9.4 + - - -
1078C SER* 3.2 30.6 + - - -
1079C LEU 4.8 0.2 - - - -
1080C LEU 3.8 0.6 - - - -
1081C TYR* 1.3 82.5 - - - +
1083C ASP* 1.3 64.4 + - - +
1084C ASP 3.5 4.9 + - - -
1085C THR* 3.9 13.9 - - - +
1105C LYS* 5.3 3.5 - - - -
1106C PHE* 5.2 0.2 - - - -
1111C ARG* 4.0 3.3 + - - -
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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