Contacts of the strand formed by residues 910 - 918 (chain B) in PDB entry 3U44
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 VAL 910 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908B GLY 3.7 6.9 + - - +
909B PHE* 1.3 76.8 - - - +
911B PRO* 1.3 83.2 - - + +
912B ILE* 4.0 0.5 - - - +
947B ASP* 4.3 0.9 - - - -
948B LYS* 2.8 51.7 + - + +
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Residues in contact with PRO 911 (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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848B TRP* 6.4 2.0 - - + -
909B PHE 3.9 6.5 - - - +
910B VAL* 1.3 101.4 - - + +
912B ILE* 1.3 63.7 + - - +
913B GLY 5.1 2.0 - - - +
914B LEU* 5.5 6.5 - - + -
945B ARG* 4.3 22.9 - - + +
946B VAL 3.6 0.9 - - - +
947B ASP* 3.1 23.7 - - - +
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Residues in contact with ILE 912 (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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910B VAL 3.4 0.4 + - - +
911B PRO* 1.3 76.7 - - - +
913B GLY* 1.3 68.2 + - - +
914B LEU* 4.4 0.3 + - - +
946B VAL* 2.8 41.4 + - + +
947B ASP 4.2 0.2 - - - +
948B LYS* 3.3 42.6 - - + +
957B LEU* 3.7 28.3 - - + -
996B TRP* 3.8 28.0 - - + -
997B LEU* 4.9 9.0 - - + -
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Residues in contact with GLY 913 (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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911B PRO* 5.0 1.4 - - - +
912B ILE* 1.3 86.5 + - - +
914B LEU* 1.3 65.3 + - - +
916B LEU* 5.0 8.1 - - - -
945B ARG* 4.3 1.0 - - - +
946B VAL* 3.1 36.2 + - - +
996B TRP* 4.7 9.5 - - - -
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Residues in contact with LEU 914 (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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835B LYS* 4.6 20.9 - - + -
838B SER* 3.9 26.0 - - - +
842B ARG* 5.8 5.2 - - - +
911B PRO* 5.5 6.7 - - + -
913B GLY* 1.3 72.8 - - - +
915B GLU* 1.3 81.5 + - + +
916B LEU* 3.1 3.4 + - - +
944B ASP 3.2 18.8 - - - +
945B ARG* 3.5 31.4 - - + -
962B TYR* 5.0 8.7 - - + +
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Residues in contact with GLU 915 (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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831B HIS* 3.6 30.7 - - - +
835B LYS* 4.2 30.5 - - + +
914B LEU* 1.3 78.4 - - + +
916B LEU* 1.3 64.5 + - - +
917B GLY* 3.1 4.3 + - - -
942B ARG* 4.8 15.8 - - - +
943B ILE 3.2 6.7 + - - +
944B ASP* 2.9 34.7 + - - +
962B TYR* 5.1 4.3 - - - -
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Residues in contact with LEU 916 (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 GLY* 5.2 3.1 - - - -
914B LEU 4.0 9.6 - - - +
915B GLU* 1.3 72.6 - - - +
917B GLY* 1.3 82.2 + - - +
918B PHE* 3.1 9.3 + - + +
923B PRO* 4.2 11.4 - - + -
924B LEU* 3.3 36.6 - - + -
942B ARG* 3.8 2.6 - - - -
943B ILE* 2.9 50.3 + - + +
946B VAL* 4.3 14.8 - - + -
989B SER* 5.3 1.3 - - - +
996B TRP* 4.1 28.5 - - + -
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Residues in contact with GLY 917 (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 GLU 3.1 6.9 + - - -
916B LEU* 1.3 72.9 - - - +
918B PHE* 1.3 59.6 + - - -
919B GLY 4.1 0.9 - - - -
921B LYS 5.4 1.1 - - - -
922B GLY* 3.8 5.9 - - - -
923B PRO* 3.1 27.7 - - - +
924B LEU 3.0 25.8 + - - -
941B GLY 4.6 1.3 - - - -
942B ARG* 5.6 0.4 - - - -
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Residues in contact with PHE 918 (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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792B VAL* 4.7 4.7 - - + -
916B LEU* 3.1 15.1 + - + +
917B GLY* 1.3 72.8 - - - +
919B GLY* 1.3 63.6 + - - +
924B LEU* 4.2 6.3 - - + -
925B PRO 4.2 6.5 - - - -
927B LEU* 4.0 19.1 - - + -
939B LEU* 3.2 44.2 - - + -
940B VAL* 3.4 3.6 - - - +
941B GLY* 2.6 76.0 + - - +
942B ARG 4.0 6.1 - - - -
943B ILE* 4.3 9.2 - - + -
984B THR* 5.4 1.8 - - - -
985B TYR* 4.5 15.9 - + - -
988B LEU* 3.3 34.3 - - + -
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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