Contacts of the strand formed by residues 748 - 753 (chain B) in PDB entry 1FO4
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 CYS 748 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B CYS* 3.6 30.7 - - + -
594B ASP* 3.9 17.7 - - - -
745B GLU* 4.6 2.5 - - - +
746B THR 3.5 7.3 + - - +
747B HIS* 1.3 78.6 + - - +
749B THR* 1.3 71.6 + - - +
750B ILE* 5.1 2.5 - - - -
764B VAL* 3.6 2.1 - - - +
765B SER* 3.0 34.5 + - - -
805B SER* 6.2 0.4 - - - -
808B VAL* 4.9 3.9 - - - +
824B ARG* 5.7 1.6 - - - -
825B CYS 3.4 10.5 - - - -
826B MET* 3.8 25.8 - - + -
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Residues in contact with THR 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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593B CYS* 4.2 0.2 - - - -
748B CYS* 1.3 79.6 + - - +
750B ILE* 1.3 80.7 + - - +
751B ALA 4.2 0.4 - - - +
762B LEU* 4.2 7.6 - - + -
763B PHE 3.5 5.2 - - - -
764B VAL* 3.1 18.8 - - + +
805B SER 4.7 0.9 + - - -
808B VAL* 4.3 9.5 - - - +
809B SER* 2.7 44.1 + - - -
812B VAL* 4.0 14.4 - - + +
824B ARG* 3.3 4.2 - - - +
825B CYS 3.1 31.1 + - - -
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Residues in contact with ILE 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B CYS* 3.3 37.9 - - - +
596B ILE* 3.9 19.5 - - + -
602B GLU* 3.7 17.3 - - - +
748B CYS* 5.1 1.3 - - - -
749B THR* 1.3 77.2 - - - +
751B ALA* 1.3 61.0 + - - +
752B ILE* 3.8 22.4 - - + -
761B GLU 4.1 0.5 - - - +
762B LEU* 3.2 6.1 - - - +
763B PHE* 2.8 44.9 + - + +
823B VAL 3.5 6.1 - - - +
824B ARG* 3.6 35.9 - - + +
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Residues in contact with ALA 751 (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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749B THR* 4.7 0.2 - - + -
750B ILE* 1.3 71.7 - - - +
752B ILE* 1.3 62.8 + - - +
753B PRO* 3.6 3.5 - - - +
760B MET* 4.1 7.9 - - - -
761B GLU 3.9 2.9 - - - -
762B LEU* 4.1 9.4 - - + -
812B VAL* 3.5 25.7 - - + +
813B ALA* 3.9 11.7 - - - +
816B ALA* 3.7 16.0 - - + +
822B PRO* 3.3 4.0 - - - +
823B VAL 2.9 30.4 + - - -
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Residues in contact with ILE 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 6.6 0.2 - - + -
599B TYR* 3.6 30.7 - - + +
602B GLU* 4.7 0.2 - - - +
750B ILE* 3.8 18.2 - - + -
751B ALA* 1.3 74.6 - - - +
753B PRO* 1.3 72.8 - - + +
754B LYS* 3.5 21.5 + - + +
760B MET* 3.3 6.2 - - - +
761B GLU* 2.8 46.9 + - + +
763B PHE* 3.9 21.1 - - + -
822B PRO* 3.3 28.3 - - + -
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Residues in contact with PRO 753 (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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751B ALA 3.6 3.1 - - - +
752B ILE* 1.3 87.7 - - + +
754B LYS* 1.3 62.9 + - - +
755B GLY 3.3 4.4 + - - +
759B GLU 4.1 5.4 - - - +
760B MET* 4.4 8.5 - - + -
816B ALA* 3.7 23.1 - - + +
817B TYR* 5.1 1.1 - - - -
820B GLY* 3.5 27.0 - - - +
821B HIS 3.4 27.8 - - - +
822B PRO* 3.6 10.5 - - + +
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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