Contacts of the strand formed by residues 737 - 743 (chain A) in PDB entry 6EJ9
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 737 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725A PHE* 4.5 7.0 - - + -
727A ILE* 4.3 15.4 - - + +
735A GLY* 3.5 4.3 - - - +
736A ARG* 1.3 77.0 - - - +
738A GLN* 1.3 60.8 + - - +
739A PHE 3.4 27.6 - - - +
770A GLN* 4.2 10.1 - - + -
771A LYS 3.6 8.5 - - - +
772A TRP* 3.6 32.4 - - + -
825A ILE* 3.8 20.4 - - + -
832A VAL* 3.7 23.1 - - + -
833A ALA* 3.5 32.5 - - + -
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Residues in contact with GLN 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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725A PHE* 3.6 15.9 - - - -
727A ILE* 5.4 1.0 - - - +
736A ARG 3.6 11.9 - - - +
737A LEU* 1.3 75.3 - - - +
739A PHE* 1.3 65.2 + - - +
771A LYS* 2.9 49.9 + - + +
772A TRP 3.7 3.6 - - - +
773A GLY* 3.4 27.1 - - - +
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Residues in contact with PHE 739 (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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725A PHE* 3.6 40.5 - + + -
737A LEU* 3.4 10.6 - - - +
738A GLN* 1.3 81.0 - - - +
740A SER* 1.3 78.7 + - - +
741A GLU* 3.5 38.1 - - + -
769A MET* 4.4 11.2 - - + -
770A GLN* 3.5 0.5 - - - -
771A LYS* 2.9 43.0 + - + -
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Residues in contact with SER 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A PHE* 3.5 26.6 - - - +
737A LEU* 4.9 0.7 - - - -
739A PHE* 1.3 89.1 - - - +
741A GLU* 1.3 65.5 + - - +
742A VAL* 6.0 0.2 - - - +
769A MET* 3.3 14.1 + - - -
770A GLN* 4.3 3.3 + - - +
823A VAL* 5.1 5.4 + - - +
825A ILE* 4.1 24.5 - - - +
833A ALA* 5.8 0.2 - - - -
834A GLU* 5.6 1.1 - - - -
835A THR* 3.7 30.6 + - - +
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Residues in contact with GLU 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A PHE* 3.5 26.5 - - + -
740A SER* 1.3 76.6 + - - +
742A VAL* 1.3 76.5 + - - +
753A PHE* 3.8 24.1 - - + +
755A ASN 5.7 0.5 - - - +
756A PHE 5.1 6.8 - - - +
758A GLY* 6.2 0.5 - - - -
767A VAL 3.9 0.3 - - - +
768A GLY* 3.7 1.6 - - - -
769A MET* 2.8 54.2 + - + +
835A THR* 4.5 6.3 - - - -
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Residues in contact with VAL 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A GLU* 1.3 88.9 - - - +
743A GLY* 1.3 62.6 + - - +
753A PHE* 4.1 3.1 - - - -
758A GLY* 5.0 7.1 - - - -
760A LEU* 4.6 3.5 - - + +
766A PRO* 3.7 23.1 - - + -
767A VAL 3.2 11.7 - - - +
768A GLY* 4.4 3.8 - - - -
784A TRP* 4.2 8.5 - - + -
823A VAL* 3.7 23.8 - - + -
835A THR* 4.5 8.5 + - + +
836A LYS 5.7 1.0 + - - -
837A PHE* 3.6 50.1 - - + +
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Residues in contact with GLY 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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742A VAL* 1.3 78.4 - - - +
744A THR* 1.3 68.1 + - - +
753A PHE* 3.5 20.5 - - - -
755A ASN 5.7 0.4 - - - -
758A GLY* 5.2 9.0 - - - -
760A LEU* 5.0 8.1 - - - -
766A PRO* 3.7 1.0 - - - +
767A VAL* 2.8 34.6 + - - +
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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