Contacts of the strand formed by residues 740 - 744 (chain B) in PDB entry 5M64
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 740 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B GLU* 3.7 14.6 - - + +
738B ASP* 3.4 14.8 - - - +
739B ASN* 1.3 108.8 + - + +
741B LEU* 1.3 63.1 + - - +
742B TYR* 4.9 15.5 - - + +
804B TYR* 3.2 14.6 - - - +
805B LYS* 3.5 42.2 - - + +
806B THR 5.4 3.4 + - - +
807B GLU* 6.2 2.6 - - - +
25T T 4.8 11.1 + - - -
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Residues in contact with LEU 741 (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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489B GLU 4.1 1.3 - - - +
490B LYS* 3.3 29.6 - - + +
729B PRO* 4.0 17.7 - - + -
733B LEU* 5.3 10.1 - - + +
736B ARG* 4.6 18.4 - - + +
738B ASP* 3.2 38.6 - - - +
740B LYS* 1.3 73.1 - - - +
742B TYR* 1.3 77.9 + - - +
803B MET* 3.2 4.4 - - - +
804B TYR* 2.8 60.6 + - + +
904B LYS* 5.1 4.9 - - - +
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Residues in contact with TYR 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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489B GLU* 6.1 2.9 - - + -
490B LYS 5.1 1.7 + - - +
491B ILE* 3.6 27.1 - - + +
726B MET* 3.5 28.0 - - + -
727B GLY 3.9 12.0 - - - +
729B PRO* 3.9 13.3 - - - +
740B LYS* 4.9 11.9 - - + +
741B LEU* 1.3 86.8 - - - +
743B ARG* 1.3 63.9 + - - +
802B THR 3.7 5.4 - - - -
803B MET* 3.5 22.5 - - + -
804B TYR* 5.8 1.1 - - - -
805B LYS* 5.4 4.9 + - - -
909B ARG* 3.3 40.6 + - - -
1037B ARG* 3.6 37.9 + - + +
1042B ASP* 5.4 3.3 + - - -
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Residues in contact with ARG 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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726B MET* 4.7 1.4 - - - +
727B GLY 4.9 4.0 - - - -
728B THR* 5.1 7.0 - - + +
729B PRO* 5.5 4.3 - - + -
733B LEU* 3.5 29.0 - - + +
742B TYR* 1.3 78.1 - - - +
744B LEU* 1.3 80.4 + - - +
745B GLN* 6.0 1.4 - - - +
801B GLY* 3.2 3.5 - - - -
802B THR* 2.9 47.8 + - - +
804B TYR* 3.1 20.6 + - + -
906B ARG* 3.2 34.8 - - - +
91C VAL 4.9 9.9 + - - -
93C GLN* 3.3 21.5 - - - +
1J MET* 5.4 9.7 - - - -
60J PHE* 4.4 21.4 - - + -
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Residues in contact with LEU 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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726B MET* 3.2 56.9 + - + +
727B GLY* 5.6 1.6 - - - -
728B THR* 4.8 14.0 - - + +
743B ARG* 1.3 93.8 - - - +
745B GLN* 1.3 61.2 + - - +
746B THR* 4.2 9.2 - - - +
747B GLY* 5.0 7.4 - - - +
766B PRO 5.8 1.1 - - - +
767B ASN 4.7 11.9 - - - +
768B GLY* 6.1 1.1 - - - -
769B PHE* 5.1 5.2 - - + -
799B GLY* 3.5 29.2 - - - +
800B TYR 3.2 25.4 - - - +
801B GLY* 4.3 3.4 - - - -
1035B ARG* 4.5 11.9 - - + -
1J MET* 5.4 3.3 - - - +
60J PHE* 5.5 2.1 - - - -
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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