Contacts of the strand formed by residues 1144 - 1152 (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 PHE1144 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1073C LEU* 4.0 3.1 - - - -
1138C HIS* 3.4 40.6 - + + -
1139C MET 3.8 0.6 - - - -
1140C ASP* 2.8 34.3 + - + +
1143C SER* 1.3 97.1 + - - +
1145C PHE* 1.3 72.1 + - - +
1146C MET* 4.5 1.1 - - + -
1169C PHE* 4.4 27.4 - + - -
1170C TYR 3.1 15.0 - - - +
1171C SER* 3.9 9.9 - - - -
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Residues in contact with PHE1145 (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 LEU* 3.4 35.0 - - + -
1076C VAL* 4.8 1.6 - - + -
1077C PHE* 3.5 52.5 - + + -
1081C TYR* 4.0 11.2 - + - -
1136C ILE* 5.1 1.3 - - + -
1138C HIS 3.0 19.5 - - - +
1139C MET* 3.7 14.6 - - + -
1140C ASP 4.0 1.6 - - - +
1141C LEU* 4.2 10.5 - - + -
1144C PHE* 1.3 82.8 - - - +
1146C MET* 1.3 62.1 + - - +
1147C VAL* 4.3 8.3 - - + -
1169C PHE* 4.0 0.5 - - - -
1170C TYR* 3.0 67.6 + + + +
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Residues in contact with MET1146 (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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1136C ILE* 3.4 6.3 - - - +
1137C GLU* 2.9 47.7 + - + -
1138C HIS* 2.7 36.6 + - + +
1144C PHE* 4.5 2.7 - - + -
1145C PHE* 1.3 74.6 - - - +
1147C VAL* 1.3 63.9 + - - +
1148C LYS 3.4 27.8 - - - -
1167C ARG* 3.8 31.0 - - - +
1168C PHE 3.0 23.3 - - - +
1169C PHE* 3.8 35.0 - - + -
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Residues in contact with VAL1147 (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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1081C TYR* 3.4 48.7 - - + +
1134C GLU* 3.7 25.8 - - + -
1135C THR 3.2 25.4 - - - +
1136C ILE* 3.8 10.3 - - + +
1145C PHE* 4.3 11.2 - - + -
1146C MET* 1.3 80.2 - - - +
1148C LYS* 1.3 61.1 + - - +
1166C THR 3.6 1.9 - - - +
1168C PHE* 3.0 33.3 + - + +
1170C TYR* 4.3 4.7 - - + -
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Residues in contact with LYS1148 (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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1133C THR 3.8 1.1 - - - +
1134C GLU* 3.2 3.6 - - - +
1135C THR* 2.9 37.8 + - - +
1137C GLU* 3.2 37.4 + - + +
1146C MET* 3.4 9.1 - - - -
1147C VAL* 1.3 72.7 - - - +
1149C GLN* 1.3 68.0 + - - +
1150C ILE* 3.6 32.2 - - + +
1165C HIS* 4.7 9.2 - - + -
1166C THR 3.4 7.4 - - - +
1167C ARG* 3.3 39.8 - - - +
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Residues in contact with GLN1149 (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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1081C TYR* 6.1 0.2 - - - -
1092C ILE* 6.2 2.4 - - - +
1115C TYR* 5.8 0.2 + - - -
1132C VAL* 3.9 24.9 - - + +
1133C THR 3.8 1.6 - - - -
1134C GLU* 3.7 29.2 + - + +
1147C VAL* 6.3 0.2 - - + -
1148C LYS* 1.3 74.9 - - - +
1150C ILE* 1.3 64.7 + - - +
1151C VAL* 3.8 6.1 - - + +
1164C VAL 3.4 6.2 - - - +
1165C HIS* 3.4 1.0 - - - -
1166C THR* 2.6 44.5 + - - +
1168C PHE* 3.3 31.8 - - + -
1206C GLN* 3.6 16.5 - - - +
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Residues in contact with ILE1150 (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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1131C ILE 3.5 2.7 - - - +
1132C VAL* 3.3 5.7 - - - -
1133C THR* 2.8 57.6 + - + +
1135C THR* 6.4 0.9 - - + -
1148C LYS* 3.6 37.2 - - + +
1149C GLN* 1.3 71.2 - - - +
1151C VAL* 1.3 60.9 + - - +
1152C ARG* 4.9 14.6 - - + +
1163C SER* 4.4 10.3 - - - +
1164C VAL 4.0 2.2 - - - -
1165C HIS* 3.9 35.2 - - + +
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Residues in contact with VAL1151 (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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1115C TYR* 5.4 1.3 - - - +
1130C CYS* 5.3 9.6 - - + -
1132C VAL* 3.8 21.8 - - + -
1149C GLN* 4.5 15.3 - - + +
1150C ILE* 1.3 72.0 - - - +
1152C ARG* 1.3 60.6 + - - +
1153C SER* 4.0 16.8 - - - +
1162C PHE 4.5 0.5 - - - +
1163C SER* 3.2 5.4 - - - -
1164C VAL* 2.7 56.9 + - + +
1166C THR* 4.9 0.2 - - - +
1206C GLN* 4.6 18.2 - - - +
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Residues in contact with ARG1152 (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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1112C GLU* 5.2 2.2 + - - -
1130C CYS* 3.6 2.6 - - - +
1131C ILE* 2.9 78.4 + - - +
1133C THR* 4.8 6.1 + - - -
1150C ILE* 4.9 12.2 - - + +
1151C VAL* 1.3 76.4 - - - +
1153C SER* 1.3 60.1 + - - +
1154C PRO* 3.1 16.8 - - + +
1162C PHE 5.8 0.2 - - - -
1163C SER* 4.2 23.5 + - - +
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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
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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