Contacts of the strand formed by residues 1131 - 1136 (chain A) in PDB entry 5J68
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 SER1131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789A THR 5.3 0.5 + - - -
1016A GLN* 4.1 14.6 - - - +
1017A PRO 3.0 23.8 - - - -
1018A VAL* 3.9 2.8 - - - +
1019A LEU* 3.2 27.7 + - - +
1117A THR* 3.1 4.3 - - - -
1118A LEU* 2.8 37.7 + - - +
1130A LEU* 1.3 76.9 - - - +
1132A THR* 1.3 66.8 + - - +
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Residues in contact with THR1132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789A THR 3.0 19.2 - - - +
790A GLY* 4.0 6.0 - - - -
791A ASP* 5.8 2.0 - - - +
1019A LEU* 4.7 0.7 - - - -
1115A LYS* 3.6 40.6 + - + +
1116A PHE 3.3 9.4 - - - +
1117A THR* 3.7 1.6 - - + +
1130A LEU* 3.2 23.0 - - - +
1131A SER* 1.3 75.7 + - - +
1133A VAL* 1.3 71.2 + - - +
1134A THR* 4.3 5.2 - - + -
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Residues in contact with VAL1133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788A LEU 4.7 2.0 - - - +
789A THR* 3.1 24.2 - - - +
790A GLY 3.4 4.3 - - - -
792A ILE* 3.6 22.2 - - + -
1019A LEU* 3.2 42.2 - - + +
1020A ARG* 4.5 2.0 - - - +
1021A LEU* 5.0 2.0 - - + -
1034A LEU* 4.7 6.3 - - + -
1115A LYS* 3.4 1.2 - - - -
1116A PHE* 2.7 45.0 + - + +
1132A THR* 1.3 74.1 - - - +
1134A THR* 1.3 63.4 + - - +
1135A LEU* 3.8 21.8 - - + -
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Residues in contact with THR1134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A GLY 3.2 4.4 + - - -
791A ASP* 3.1 21.6 + - - +
792A ILE* 2.6 34.3 + - - +
793A ARG* 2.7 29.5 + - - -
1057A VAL* 6.1 0.4 - - + -
1113A LEU* 4.5 6.1 - - + -
1114A TYR 3.2 5.8 - - - +
1115A LYS* 3.7 35.9 - - + +
1132A THR* 4.3 6.5 - - + +
1133A VAL* 1.3 77.0 - - - +
1135A LEU* 1.3 59.5 + - - +
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Residues in contact with LEU1135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A ILE* 3.8 23.1 - - + +
793A ARG* 4.5 0.7 - - - +
794A TYR* 6.1 2.2 - - + -
1021A LEU* 3.7 28.7 - - + -
1027A PRO* 4.2 13.2 - - + -
1032A VAL* 3.7 26.2 - - + -
1034A LEU* 4.5 0.4 - - + -
1112A GLY 3.9 0.2 - - - +
1113A LEU* 3.2 5.3 - - - +
1114A TYR* 2.8 34.9 + - + +
1116A PHE* 4.1 20.6 - - + -
1133A VAL* 3.8 21.5 - - + -
1134A THR* 1.3 75.3 - - - +
1136A ARG* 1.3 79.6 + - - +
1137A THR* 4.2 1.1 - - + +
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Residues in contact with ARG1136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A ILE 4.7 2.4 + - - +
793A ARG* 2.9 53.4 - - + +
794A TYR* 5.2 5.0 + - - -
1027A PRO* 5.1 5.0 - - - +
1111A ASP* 5.6 6.3 - - - +
1112A GLY 3.2 8.5 - - - +
1113A LEU* 3.2 37.2 - - + +
1135A LEU* 1.3 88.1 - - - +
1137A THR* 1.3 70.5 - - - +
1138A ALA 3.8 0.3 + - - -
1225A HIS* 5.7 15.8 + - - -
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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