Contacts of the strand formed by residues 1025 - 1032 (chain B) in PDB entry 3I8E
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 GLN1025 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1024B THR* 1.3 84.4 + - - +
1026B GLY* 1.3 67.2 + - - +
1041B THR* 3.3 0.5 - - - +
1042B SER* 3.0 45.1 + - - +
1043B LEU* 5.8 3.3 - - - +
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Residues in contact with GLY1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024B THR* 5.0 0.2 + - - -
1025B GLN* 1.3 82.2 - - - +
1027B SER* 1.3 66.0 + - - -
1041B THR* 3.3 13.4 - - - +
1042B SER* 5.6 1.8 - - - -
1139B ILE* 5.7 1.7 - - - +
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Residues in contact with SER1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009B HIS* 3.5 14.5 + - - +
1010B GLY 3.1 38.0 + - - -
1011B SER* 4.1 13.0 + - - -
1026B GLY* 1.3 75.3 - - - -
1028B VAL* 1.3 64.7 + - - +
1039B LEU* 3.1 21.0 - - - +
1040B VAL 3.8 7.0 - - - -
1041B THR* 4.6 2.2 - - - -
1139B ILE* 5.0 4.7 + - - +
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Residues in contact with VAL1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958B GLU* 3.9 9.6 - - + -
960B LEU* 3.7 22.7 - - + -
966B LEU* 4.7 3.6 - - + -
1007B PHE* 3.8 37.0 - - + -
1008B CYS 3.5 11.0 - - - +
1009B HIS* 3.5 27.1 - - + +
1027B SER* 1.3 80.3 + - - +
1029B LEU* 1.3 61.5 + - - +
1030B PHE* 3.9 1.6 + - - -
1039B LEU* 3.4 4.8 - - - +
1040B VAL* 2.9 48.2 + - + +
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Residues in contact with LEU1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 5.7 2.5 - - + -
362B MET* 3.8 14.8 - - + +
364B VAL* 3.9 19.1 - - + -
375B LEU* 4.0 15.9 - - + -
1007B PHE* 3.3 3.1 - - - -
1008B CYS* 2.9 35.3 + - - +
1010B GLY* 3.2 29.4 - - - +
1011B SER* 4.0 10.1 - - - +
1012B LEU* 4.4 21.1 - - + +
1027B SER 4.2 0.2 - - - -
1028B VAL* 1.3 73.1 - - - +
1030B PHE* 1.3 60.4 + - - +
1037B ILE* 5.0 8.5 - - + -
1038B GLY 3.4 8.1 - - - +
1039B LEU* 3.6 28.0 - - + -
1140B HIS* 5.7 2.2 - - + -
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Residues in contact with PHE1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.7 6.3 - - + -
7B VAL 5.1 1.1 - - - -
362B MET* 4.0 4.7 - - - -
974B LEU* 4.7 4.3 - - + -
1000B LEU* 3.5 33.4 - - + -
1004B VAL* 3.6 17.9 - - + -
1006B VAL 3.2 5.2 - - - +
1007B PHE* 3.3 38.1 - + + -
1028B VAL 4.5 0.2 - - - -
1029B LEU* 1.3 73.4 - - - +
1031B GLY* 1.3 60.4 + - - +
1032B THR* 3.9 6.7 - - + -
1036B MET* 3.7 21.5 - - + -
1037B ILE* 3.5 5.2 - - - +
1038B GLY* 2.8 59.4 + - - +
1039B LEU* 3.4 23.3 - - - -
1040B VAL* 4.2 17.9 - - + -
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Residues in contact with GLY1031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ILE* 4.0 14.1 - - - -
362B MET* 3.9 19.5 - - - +
1004B VAL* 4.6 0.7 - - - -
1005B ASN* 3.1 26.9 + - - +
1006B VAL* 2.9 16.8 + - - +
1030B PHE* 1.3 73.3 - - - +
1032B THR* 1.3 64.4 + - - -
1036B MET 3.8 4.0 - - - -
1037B ILE* 4.9 1.1 - - - -
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Residues in contact with THR1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ILE* 3.3 24.9 + - - +
1002B GLU* 3.6 26.9 + - + -
1003B PHE 3.2 18.4 - - - +
1004B VAL* 4.4 2.9 - - + -
1005B ASN* 4.4 2.9 - - - -
1030B PHE* 3.9 15.3 - - + -
1031B GLY* 1.3 75.9 - - - -
1033B VAL* 1.3 64.2 + - - +
1034B ASN 3.8 3.2 + - - -
1035B GLY 3.4 6.8 + - - -
1036B MET* 2.7 58.2 + - - +
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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