Contacts of the helix formed by residues 743 - 750 (chain B) in PDB entry 2XER
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 LEU 743 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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690B LEU* 3.7 44.0 - - + +
693B LEU* 4.2 4.3 - - + -
694B SER* 4.1 4.7 - - - +
739B ILE* 4.3 8.7 - - + -
740B PRO* 3.3 41.7 + - + +
741B THR 3.3 0.2 - - - -
742B ASN* 1.3 79.6 + - - +
744B VAL* 1.3 59.8 + - + +
746B LEU* 2.9 23.5 + - + +
747B PHE* 2.8 62.9 + - + -
763B LEU* 5.2 1.3 - - + -
765B LEU* 4.8 9.6 - - + -
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Residues in contact with VAL 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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741B THR 4.5 7.8 + - - +
742B ASN 3.4 0.4 - - - -
743B LEU* 1.3 76.0 - - + +
745B SER* 1.3 57.0 + - - +
747B PHE* 3.5 7.6 + - - -
748B SER* 3.1 27.5 + - - -
756B LEU* 3.9 16.0 - - + +
760B GLU* 3.2 27.8 - - + +
765B LEU* 3.3 40.6 - - + +
766B VAL* 6.5 0.2 - - + -
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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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697B GLU* 2.7 26.3 + - - -
741B THR 5.1 0.8 + - - -
742B ASN* 3.2 14.4 + - - +
743B LEU 3.1 0.8 - - - -
744B VAL* 1.3 76.2 - - - +
746B LEU* 1.3 61.4 + - - +
748B SER* 2.7 24.0 + - - -
749B ARG* 3.4 15.4 + - - +
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Residues in contact with LEU 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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693B LEU* 3.0 37.9 - - + +
694B SER* 4.2 3.1 - - - +
696B GLY* 3.8 7.2 - - - -
697B GLU* 3.4 39.0 + - + +
718B MET* 3.7 24.7 - - + -
742B ASN 2.9 13.4 + - - +
743B LEU* 2.9 17.9 + - + +
745B SER* 1.3 75.4 - - - +
747B PHE* 1.3 68.2 + - + +
749B ARG* 3.1 15.2 + - - +
750B TYR* 3.4 32.5 - - + -
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Residues in contact with PHE 747 (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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690B LEU* 5.1 0.9 - - + -
693B LEU* 4.3 11.4 - - + -
718B MET* 4.1 15.5 - - + -
722B THR* 3.7 28.5 - - + -
725B LEU* 3.9 27.4 - - + -
743B LEU* 2.8 60.6 + - + +
744B VAL* 4.0 3.4 - - - +
746B LEU* 1.3 75.4 - - + +
748B SER* 1.3 63.8 + - - +
749B ARG 3.0 1.8 + - - -
750B TYR* 3.1 13.2 + - - +
751B VAL* 3.2 16.6 + - - +
756B LEU* 3.7 19.3 - - + -
759B LEU* 4.0 19.5 - - + -
763B LEU* 4.4 14.6 - - + -
765B LEU* 4.8 7.4 - - + -
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Residues in contact with SER 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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744B VAL 3.1 15.7 + - - -
745B SER* 2.7 25.2 + - - -
747B PHE* 1.3 76.1 - - - +
749B ARG* 1.3 62.0 + - - +
751B VAL 3.3 16.4 - - - +
756B LEU* 3.8 24.4 - - - +
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Residues in contact with ARG 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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697B GLU* 3.2 52.6 + - - +
699B LEU* 5.5 10.9 + - - +
719B PHE* 5.8 0.2 - - - -
745B SER* 3.4 18.6 + - - +
746B LEU* 3.4 9.2 - - - +
747B PHE 3.0 0.8 + - - -
748B SER* 1.3 82.7 - - - +
750B TYR* 1.3 78.9 + - + +
751B VAL 3.6 0.2 - - - -
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Residues in contact with TYR 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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696B GLY 5.0 3.1 + - - -
699B LEU* 4.7 11.4 - - - +
714B TRP* 4.4 12.5 - - - +
715B THR* 3.5 33.6 + - + +
718B MET* 3.5 47.8 - - + +
719B PHE* 3.4 46.2 - + + -
722B THR* 4.8 0.7 - - + -
746B LEU* 3.4 29.2 - - + +
747B PHE 3.1 3.9 + - - +
749B ARG* 1.3 98.0 - - + +
751B VAL* 1.3 72.9 + - + +
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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