Contacts of the strand formed by residues 1161 - 1165 (chain J) in PDB entry 6PSU
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 GLY1161 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1159J ILE* 3.9 2.8 - - - +
1160J SER* 1.3 74.1 - - - +
1162J ILE* 1.3 64.5 + - - -
1163J VAL 3.6 0.5 + - - -
1177J ILE* 3.9 5.4 - - - +
1178J THR 3.2 13.2 + - - -
1179J PRO 4.5 5.8 - - - -
1180J VAL* 4.7 2.7 - - - -
1202J GLU 3.3 0.5 - - - +
1203J ARG* 3.3 18.8 - - - -
1204J VAL* 2.8 29.4 + - - +
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Residues in contact with ILE1162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090J ILE* 6.4 1.1 - - + -
1093J THR* 4.7 29.8 - - + +
1161J GLY* 1.3 70.8 - - - -
1163J VAL* 1.3 58.9 + - - +
1178J THR* 2.6 56.0 + - + +
1179J PRO 4.2 8.6 + - - +
1180J VAL* 5.9 0.2 - - - +
1201J GLY* 3.0 32.8 - - - +
1202J GLU* 3.0 22.4 - - - -
1203J ARG* 3.4 14.4 - - + +
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Residues in contact with VAL1163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161J GLY 4.7 0.2 - - - +
1162J ILE* 1.3 80.2 - - - +
1164J SER* 1.3 59.5 + - - +
1175J LEU* 3.2 24.5 - - + -
1176J VAL 2.9 21.8 - - - +
1177J ILE* 3.3 25.4 - - + -
1178J THR* 3.9 1.8 - - - +
1198J VAL* 4.5 7.6 - - + -
1199J PHE 3.1 27.6 - - - +
1200J GLU* 2.6 26.7 - - - +
1201J GLY* 3.5 4.7 + - - -
1202J GLU 2.6 24.1 + - - +
1204J VAL* 4.7 5.8 - - + -
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Residues in contact with SER1164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163J VAL* 1.3 79.2 - - - +
1165J PHE* 1.3 70.5 + - - +
1175J LEU* 3.0 5.5 - - - +
1176J VAL* 2.6 42.3 + - - +
1178J THR* 4.2 11.2 + - - -
1200J GLU* 3.1 20.6 + - - -
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Residues in contact with PHE1165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075J ARG* 3.1 50.0 - - + -
1100J PHE* 5.4 5.4 - + - -
1164J SER* 1.3 94.3 + - - +
1166J GLY* 1.3 86.2 + - - +
1168J GLU* 3.4 11.4 - - - +
1173J ARG* 5.9 3.1 - - - -
1174J ARG 4.0 4.0 - - - +
1175J LEU* 3.3 25.2 - - + -
1176J VAL* 4.1 4.3 + - - +
1200J GLU* 3.1 41.5 - - + +
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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