Contacts of the strand formed by residues 737 - 742 (chain A) in PDB entry 5E3H
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 LYS 737 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A PRO* 4.8 2.2 - - - -
457A GLN* 3.6 7.0 - - + +
459A PHE* 4.2 19.5 - - + -
621A GLU* 3.2 34.5 + - - +
624A LEU* 4.9 9.5 - - - +
710A ASN 2.9 12.1 + - - +
711A LEU* 3.5 7.8 - - + -
712A VAL* 2.9 26.7 + - - +
735A GLY* 3.5 19.1 - - - +
736A SER* 1.3 75.1 - - - +
738A CYS* 1.3 61.4 + - - +
739A PHE* 4.1 16.4 - - + -
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Residues in contact with CYS 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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456A PRO* 5.0 12.3 - - + +
457A GLN 2.9 14.1 + - - +
458A LYS* 3.3 21.4 - - + +
459A PHE* 2.7 34.8 + - - +
712A VAL* 3.2 24.7 - - + +
714A LEU* 3.8 29.8 - - - -
727A THR* 6.1 1.8 - - - -
737A LYS* 1.3 76.1 - - - +
739A PHE* 1.3 61.5 + - - +
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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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458A LYS* 5.9 0.2 - - - -
459A PHE* 3.4 40.6 - + + -
461A ARG* 3.9 31.9 - - + -
617A ILE* 4.1 28.5 - - + -
621A GLU* 4.2 17.3 - - - -
711A LEU* 3.7 30.7 - - + -
712A VAL 2.9 9.6 + - - +
713A ILE* 4.6 12.3 - - + -
714A LEU* 2.7 37.6 + - - +
737A LYS* 4.1 15.9 - - + -
738A CYS* 1.3 79.1 - - - +
740A LEU* 1.3 57.7 + - - +
741A LEU* 4.1 1.3 - - + +
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Residues in contact with LEU 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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458A LYS* 5.6 4.3 - - + -
459A PHE 2.8 14.8 + - - +
460A PHE* 3.7 23.5 - - + -
461A ARG* 2.7 35.8 + - - +
714A LEU* 3.5 31.6 - - + +
717A TYR 3.8 22.0 - - - +
739A PHE* 1.3 74.1 - - - +
741A LEU* 1.3 60.5 + - - +
742A THR* 4.0 1.5 + - + -
747A VAL* 4.2 20.9 - - + +
748A ILE* 4.2 9.9 - - + +
751A GLU* 3.7 34.8 - - + +
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Residues in contact with LEU 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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461A ARG* 3.5 15.5 - - + +
463A VAL* 3.6 35.4 - - + -
610A LYS* 3.6 21.3 - - + +
613A ASP* 4.2 2.5 - - - +
614A LEU* 3.7 43.7 - - + +
617A ILE* 4.1 13.0 - - + -
713A ILE* 5.1 4.9 - - + -
714A LEU 2.8 14.1 + - - +
715A TYR* 3.8 12.3 - - + -
716A GLU* 2.8 31.5 + - - +
739A PHE* 4.1 1.3 - - + -
740A LEU* 1.3 72.8 - - - +
742A THR* 1.3 64.1 + - - +
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Residues in contact with THR 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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461A ARG 3.1 6.5 + - - +
462A LYS* 3.5 5.2 - - - +
463A VAL* 3.2 23.0 + - - -
716A GLU* 2.9 26.0 + - - -
740A LEU* 4.7 2.0 - - + -
741A LEU* 1.3 78.7 - - - +
743A SER* 1.3 59.6 + - - +
744A ASN* 3.0 11.6 + - - +
745A ALA 4.5 2.9 - - - +
747A VAL* 3.4 30.9 - - + +
748A ILE* 3.3 39.7 - - + +
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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