Contacts of the strand formed by residues 736 - 746 (chain A) in PDB entry 5TFM
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 THR 736 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645A PRO* 4.9 4.5 - - - +
646A PRO* 4.1 7.5 - - - +
724A ARG* 3.9 13.9 - - - +
725A ALA 3.2 11.0 + - - -
726A VAL* 3.7 15.1 - - - +
734A GLN* 5.2 2.0 - - - +
735A LYS* 1.3 81.7 - - - +
737A GLY* 1.3 67.3 + - - +
738A ILE* 4.2 8.9 - - + +
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Residues in contact with GLY 737 (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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646A PRO* 3.3 26.1 + - - +
647A THR* 5.0 0.7 - - - -
648A PHE* 3.7 12.3 - - - -
723A VAL 3.6 0.2 - - - +
724A ARG* 3.3 3.1 - - - -
725A ALA 2.8 31.4 + - - +
736A THR* 1.3 72.6 + - - +
738A ILE* 1.3 68.3 + - - +
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Residues in contact with ILE 738 (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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648A PHE* 3.7 10.3 - - - +
651A PRO* 4.5 7.3 - - - +
722A ILE* 3.9 24.2 - - + -
723A VAL 3.3 4.0 - - - +
724A ARG* 4.1 28.9 - - + +
736A THR* 4.2 10.3 - - + +
737A GLY* 1.3 80.4 - - - +
739A ALA* 1.3 71.5 + - - +
740A THR* 5.8 2.7 - - + -
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Residues in contact with ALA 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PHE* 3.8 15.7 - - + -
650A LYS 3.7 15.5 - - - +
651A PRO 3.3 13.5 - - - +
653A TYR* 3.9 16.6 - - + -
670A LEU* 5.8 0.4 - - + -
722A ILE* 3.7 1.8 - - - +
723A VAL* 2.9 36.5 + - + +
738A ILE* 1.3 82.9 - - - +
740A THR* 1.3 67.1 + - - +
741A VAL* 5.7 0.4 - - + -
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Residues in contact with THR 740 (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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651A PRO 2.9 8.9 + - - +
652A ALA* 3.1 25.8 - - - +
653A TYR* 2.9 25.1 + - - -
720A ILE* 4.5 14.1 - - + -
721A LEU 3.2 9.6 - - - +
722A ILE* 5.1 9.9 - - + -
738A ILE* 5.8 2.9 - - + -
739A ALA* 1.3 76.2 - - - +
741A VAL* 1.3 65.5 + - - +
742A ASN* 3.2 11.9 + - - -
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Residues in contact with VAL 741 (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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653A TYR* 3.5 12.3 - - + +
655A VAL* 4.3 9.9 - - + -
667A VAL* 5.8 1.1 - - + -
668A LEU* 4.3 21.1 - - + -
670A LEU* 4.2 14.6 - - + -
705A ILE* 4.3 11.4 - - + -
719A TYR 3.6 3.6 - - - +
721A LEU* 2.9 43.7 + - + +
723A VAL* 3.9 24.0 - - + -
739A ALA 5.2 0.2 - - - -
740A THR* 1.3 78.6 - - - +
742A ASN* 1.3 62.8 + - - +
743A ILE* 3.9 21.8 + - + +
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Residues in contact with ASN 742 (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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652A ALA* 4.1 1.2 - - - +
653A TYR 2.8 17.0 + - - -
654A PHE* 3.4 36.6 - - + +
655A VAL* 3.0 25.6 + - - +
719A TYR 3.4 6.3 - - - +
720A ILE* 3.6 29.0 - - + +
740A THR* 3.2 25.0 + - - -
741A VAL* 1.3 74.3 - - - +
743A ILE* 1.3 61.0 + - - +
744A THR* 5.4 0.8 + - - -
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Residues in contact with ILE 743 (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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655A VAL* 3.4 24.0 - - + +
657A VAL* 4.0 24.0 - - + -
667A VAL* 4.5 7.2 - - + -
696A PHE* 3.6 32.5 - - + -
705A ILE* 5.8 0.7 - - + -
718A GLU* 3.2 10.0 - - - +
719A TYR* 2.9 40.1 + - + +
721A LEU* 3.5 32.8 - - + -
741A VAL* 3.9 12.6 - - + +
742A ASN* 1.3 76.8 - - - +
744A THR* 1.3 64.2 + - - +
745A LEU* 4.0 10.3 - - + -
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Residues in contact with THR 744 (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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655A VAL 3.0 7.6 + - - -
656A SER* 3.4 19.2 - - - +
657A VAL* 3.0 28.6 + - - +
717A SER* 3.9 4.7 - - - +
718A GLU* 3.3 28.2 + - - +
742A ASN 4.2 1.1 + - - -
743A ILE* 1.3 72.9 - - - +
745A LEU* 1.3 75.8 + - - +
746A LEU* 4.8 7.6 - - + +
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Residues in contact with LEU 745 (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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657A VAL* 3.3 13.2 - - + +
659A GLU* 4.5 7.0 - - + -
696A PHE* 5.4 0.2 - - + -
711A LEU* 4.0 30.3 - - + -
712A ASP 4.2 1.1 - - - +
713A ARG* 3.6 40.1 - - + +
716A LYS 3.1 25.6 - - - +
717A SER* 3.0 18.0 + - - +
719A TYR* 4.1 21.8 - - + +
743A ILE* 4.0 18.2 - - + -
744A THR* 1.3 86.7 - - - +
746A LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 746 (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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656A SER* 3.9 33.4 - - - +
657A VAL* 2.9 21.7 + - - +
658A VAL* 3.6 18.8 - - + +
659A GLU* 3.0 27.7 + - - +
713A ARG* 4.3 0.9 - - - -
744A THR* 4.7 6.5 - - + +
745A LEU* 1.3 73.3 - - - +
747A ASP* 1.3 65.0 + - - +
748A ILE* 4.4 0.2 - - - +
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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