Contacts of the helix formed by residues 741 - 751 (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 ASP 741 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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974A ARG* 5.1 1.2 + - - -
988A PHE* 3.5 34.1 - - + +
989A ALA* 4.8 10.0 - - + +
990A PHE* 4.5 8.1 - - + -
709B ASP* 4.8 3.6 + - - +
739B ILE 4.7 4.1 - - - +
740B SER* 1.3 72.4 + - - +
742B VAL* 1.3 63.2 + - - +
743B TRP 3.1 2.7 - - - -
744B TRP* 3.1 30.7 + - + +
745B SER* 3.0 17.6 + - - -
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Residues in contact with VAL 742 (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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990A PHE* 4.0 28.3 - - + -
994A ALA* 4.6 1.3 - - + +
709B ASP 4.9 1.3 - - - +
712B GLN* 4.0 16.2 - - + +
713B LEU* 3.5 40.8 - - + -
716B VAL* 4.4 3.6 - - + -
740B SER* 3.3 19.6 + - - +
741B ASP* 1.3 78.4 - - - +
743B TRP* 1.3 78.6 + - + +
745B SER* 3.5 3.5 - - - -
746B THR* 2.7 40.2 + - - +
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Residues in contact with TRP 743 (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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704B PRO* 3.6 27.1 - - + +
712B GLN* 3.7 23.2 - - + +
715B TYR* 3.4 28.3 - + + -
716B VAL* 4.4 12.6 - - + -
722B ALA* 4.2 4.3 - - - -
725B PHE* 3.5 25.4 - + + -
726B THR* 3.4 32.5 - - + +
729B GLN* 3.4 43.0 + - + -
730B LEU* 5.4 5.9 - - + +
739B ILE* 4.7 7.4 - - + -
740B SER* 3.3 24.9 + - - +
741B ASP 3.1 0.6 - - - -
742B VAL* 1.3 90.1 - - + +
744B TRP* 1.3 60.7 + - - +
746B THR* 3.7 7.8 - - - -
747B TYR* 2.9 27.9 + - - +
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Residues in contact with TRP 744 (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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974A ARG* 3.5 30.4 - - + +
978A ILE* 4.6 9.6 - - + -
983A PRO* 4.6 15.7 - - + -
988A PHE* 3.7 25.1 - + + -
730B LEU* 4.2 19.3 - - + -
733B TRP* 3.4 56.3 - + - -
739B ILE* 3.6 32.2 + - + +
740B SER 3.8 2.4 - - - -
741B ASP* 3.1 45.4 + - - +
743B TRP* 1.3 76.6 - - - +
745B SER* 1.3 64.9 + - - +
747B TYR* 3.3 8.0 - + + +
748B ASN* 3.0 31.5 + - - +
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Residues in contact with SER 745 (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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988A PHE* 3.7 11.7 - - - +
990A PHE* 3.3 6.7 - - - +
991A ASP* 3.1 41.8 + - - +
994A ALA* 3.8 11.0 - - - -
741B ASP 3.0 13.2 + - - -
742B VAL 3.5 7.0 - - - -
744B TRP* 1.3 74.7 - - - +
746B THR* 1.3 66.2 + - - +
748B ASN* 3.1 9.5 + - - +
749B VAL* 3.0 28.2 + - - +
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Residues in contact with THR 746 (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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994A ALA* 3.9 11.3 - - + +
998A LEU* 4.4 8.5 - - + -
716B VAL* 3.5 23.0 - - + +
722B ALA* 3.8 24.2 - - + -
726B THR* 3.4 24.9 - - + -
742B VAL 2.7 22.0 + - - -
743B TRP* 3.7 7.7 - - + -
745B SER* 1.3 77.4 - - - +
747B TYR* 1.3 65.0 + - - +
749B VAL* 3.4 4.7 + - - +
750B LEU* 3.1 26.8 + - + +
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Residues in contact with TYR 747 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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978A ILE* 2.9 40.9 + - + +
981A GLY 2.7 19.8 + - - -
982A GLU* 3.5 2.9 - - - -
983A PRO* 3.0 39.9 - - + -
726B THR* 4.7 4.2 - - + +
730B LEU* 4.0 23.3 - - + -
743B TRP 2.9 16.7 + - - +
744B TRP* 3.3 15.7 - + + +
745B SER 3.1 0.4 - - - -
746B THR* 1.3 73.5 - - - +
748B ASN* 1.3 65.0 + - - +
750B LEU* 3.0 12.9 + - - +
751B MET* 2.9 48.1 + - + +
763B PHE* 3.9 30.0 - + - +
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Residues in contact with ASN 748 (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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982A GLU* 3.2 11.8 - - + +
983A PRO* 2.9 43.1 + - - +
984A VAL* 5.2 2.1 - - - +
988A PHE* 3.6 26.9 - - - -
991A ASP* 5.2 9.1 + - - +
744B TRP 3.0 20.0 + - - -
745B SER* 3.7 7.9 - - - +
747B TYR* 1.3 79.3 - - - +
749B VAL* 1.3 64.1 + - + +
751B MET* 3.2 15.4 + - - +
752B SER* 3.4 14.6 + - - -
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Residues in contact with VAL 749 (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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991A ASP* 4.7 9.2 - - - +
994A ALA* 4.2 5.2 - - + -
995A ARG* 4.1 55.6 - - + +
998A LEU* 3.6 24.9 - - + -
745B SER 3.0 19.0 + - - +
746B THR 3.5 6.1 - - - +
748B ASN* 1.3 76.9 - - - +
750B LEU* 1.3 64.0 + - + +
752B SER* 2.8 25.1 + - - +
753B GLU* 3.9 13.6 + - + +
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Residues in contact with LEU 750 (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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998A LEU* 4.1 18.8 - - + -
719B LYS* 3.9 30.5 - - + +
722B ALA* 5.1 0.2 - - + -
723B GLN* 3.8 28.3 - - + +
726B THR* 4.3 11.7 - - - +
746B THR* 3.3 29.2 - - + +
747B TYR* 3.0 7.6 + - - +
749B VAL* 1.3 77.9 - - - +
751B MET* 1.3 68.2 + - + +
752B SER 3.2 1.7 + - - -
753B GLU* 3.9 20.3 + - - +
755B ASP* 4.6 0.6 - - - +
756B ARG* 3.8 18.2 + - - +
759B SER* 4.1 11.9 + - - +
763B PHE* 4.4 9.9 - - + -
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Residues in contact with MET 751 (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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980A ARG 5.1 4.7 - - - +
981A GLY* 4.2 7.9 - - - +
982A GLU* 3.4 30.9 - - + +
747B TYR* 2.9 61.8 + - + +
748B ASN 3.4 9.2 - - - +
749B VAL 3.0 0.8 - - - -
750B LEU* 1.3 80.0 - - + +
752B SER* 1.3 56.3 + - - +
753B GLU 3.6 0.7 - - - -
756B ARG* 3.3 22.6 + - - +
759B SER* 3.6 30.7 - - - -
760B LYS* 4.4 9.0 - - + +
763B PHE* 3.7 22.4 - - + -
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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