Contacts of the strand formed by residues 954 - 959 (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 MET 954 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912B LEU* 4.7 3.1 - - - +
913B TYR* 3.3 22.9 + - + -
925B ASP 3.0 29.2 - - - +
926B LEU* 3.1 9.7 + - - +
929B SER* 3.4 16.8 - - - +
930B VAL* 3.7 12.1 - - + -
952B ASN* 3.7 14.6 - - - +
953B TRP* 1.3 76.3 - - - +
955B SER* 1.3 61.0 + - - +
956B ALA 3.8 9.9 - - - +
957B VAL* 3.5 27.1 - - + -
967B GLY* 3.9 7.0 - - - -
968B ALA 3.5 3.8 - - - +
970B ASN* 3.6 5.9 + - - +
975B PHE* 3.5 37.7 - - + -
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Residues in contact with SER 955 (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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913B TYR* 3.3 27.8 + - - -
954B MET* 1.3 74.4 - - - +
956B ALA* 1.3 61.6 + - - +
968B ALA* 2.9 13.5 + - - +
969B GLU* 3.4 10.7 + - - -
970B ASN* 3.1 19.5 + - - -
1003B PHE* 3.7 19.1 - - - -
1004B VAL 3.4 17.1 + - - +
1005B ASN* 3.4 18.2 - - - +
162D GLU* 5.5 1.4 - - - +
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Residues in contact with ALA 956 (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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913B TYR* 5.1 3.6 - - - -
954B MET* 3.8 0.7 - - - +
955B SER* 1.3 81.0 - - - +
957B VAL* 1.3 68.8 + - - +
967B GLY* 3.6 1.9 - - - -
968B ALA* 3.2 35.0 + - + +
1004B VAL* 3.9 10.1 - - + +
1005B ASN 4.0 12.6 - - - +
1006B VAL* 4.2 3.6 - - - +
1007B PHE* 3.5 29.6 - - + +
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Residues in contact with VAL 957 (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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913B TYR* 3.9 31.6 - - + +
915B LYS* 2.6 41.2 + - + +
923B VAL* 3.6 44.4 - - + +
924B GLY* 4.6 2.9 - - - -
930B VAL* 3.8 10.8 - - + -
954B MET* 3.5 23.3 - - + -
956B ALA* 1.3 81.9 - - - +
958B GLU* 1.3 60.2 + - - +
965B PHE* 6.0 0.7 - - + -
966B LEU 3.5 7.4 - - - +
1007B PHE* 3.9 2.1 - - - -
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Residues in contact with GLU 958 (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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915B LYS* 2.7 39.3 + - - +
957B VAL* 1.3 76.6 - - - +
959B ILE* 1.3 75.2 + - - +
960B LEU* 3.6 1.7 + - + +
965B PHE* 3.7 2.8 - - - +
966B LEU* 2.8 42.2 + - + +
1007B PHE* 3.2 37.6 - - + +
1008B CYS* 3.8 6.2 - - - -
1009B HIS* 2.9 33.3 + - - +
1028B VAL* 3.9 17.9 - - + -
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Residues in contact with ILE 959 (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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915B LYS* 3.3 34.9 - - + +
916B THR 3.9 0.9 - - - -
917B LYS* 3.3 47.3 - - + +
921B ILE* 4.2 11.0 - - + -
923B VAL* 3.6 17.7 - - + -
958B GLU* 1.3 79.4 + - - +
960B LEU* 1.3 61.7 + - - +
961B ASP* 3.5 22.0 - - - +
965B PHE* 3.7 21.5 - - + -
1009B HIS* 3.1 24.6 + - - -
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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