Contacts of the strand formed by residues 743 - 746 (chain D) in PDB entry 1O23
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 743 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659D PRO* 3.8 0.7 - - - +
660D MET* 3.0 49.1 + - + +
661D ASN* 4.4 2.4 + - + -
664D ASN* 4.8 0.2 + - - -
678D ALA* 3.1 10.3 - - + +
684D PHE* 3.7 43.2 - - + -
739D ALA 3.6 11.0 - - - +
740D VAL* 3.0 35.7 + - + +
741D ILE 3.2 2.8 - - - +
742D GLY* 1.3 78.3 - - - +
744D CYS* 1.3 63.0 + - - +
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Residues in contact with CYS 744 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657D LEU* 4.3 17.9 - - + -
658D ILE 3.2 13.9 - - - +
659D PRO* 3.8 16.6 - - - -
660D MET* 3.6 6.5 - - - -
664D ASN* 4.2 8.5 - - - -
666D TYR* 5.1 4.0 - - - -
675D ILE* 4.9 0.9 - - - -
676D SER* 3.7 26.9 - - - -
678D ALA 2.9 8.0 + - - +
679D MET* 3.3 5.0 - - - -
680D ASP 2.9 25.1 + - - -
684D PHE* 3.7 4.9 - - - -
695D VAL* 5.8 0.4 - - - -
742D GLY 3.6 10.8 - - - -
743D LYS* 1.3 81.3 - - - +
745D ARG* 1.3 59.6 + - - +
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Residues in contact with ARG 745 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D ILE* 2.8 46.8 + - + -
550D GLU* 3.9 11.9 - - - +
551D PHE* 3.7 36.1 - - + +
552D ASN* 6.1 0.2 - - - +
656D ASP 3.5 1.0 - - - +
657D LEU* 3.4 5.9 - - - +
658D ILE* 2.9 34.2 + - - +
660D MET* 3.6 29.1 - - + -
679D MET* 5.8 0.2 - - - -
680D ASP* 3.3 23.6 + - + +
684D PHE* 5.4 0.4 - - + -
744D CYS* 1.3 73.9 - - - +
746D MET* 1.3 61.6 + - - +
747D ILE 4.0 0.2 - - - -
748D ARG* 6.0 2.2 - - - +
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Residues in contact with MET 746 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551D PHE* 4.5 3.5 - - - -
656D ASP* 3.1 28.3 - - - +
657D LEU* 4.1 9.6 - - + -
679D MET* 3.1 36.6 - - + -
680D ASP* 3.0 19.4 + - - +
681D LYS* 3.9 23.8 - - + -
745D ARG* 1.3 75.1 + - - +
747D ILE* 1.3 69.9 + - - +
748D ARG* 3.0 11.2 + - - +
749D HIS* 3.5 8.3 - - - -
808D MN 2.7 24.2 - - - +
810D UPG 3.2 32.1 - - - +
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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