Contacts of the strand formed by residues 728 - 736 (chain A) 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 ASN 728 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726A ALA* 3.5 2.8 - - - +
727A ASP* 1.3 80.7 - - - +
729A VAL* 1.3 74.4 + - - +
730A VAL* 5.6 0.4 - - + -
849A GLY* 3.5 0.7 - - - -
850A PHE* 2.9 61.0 + - + +
852A LYS* 3.9 35.6 - - - +
933A THR* 4.4 12.8 - - + +
934A CYS* 4.6 3.6 - - - +
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Residues in contact with VAL 729 (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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723A PHE* 3.9 26.0 - - + +
726A ALA* 4.4 8.3 - - + +
727A ASP 5.5 0.2 - - - -
728A ASN* 1.3 86.2 - - - +
730A VAL* 1.3 70.5 + - - +
731A SER* 4.9 2.9 - - - +
847A LYS* 4.2 31.9 - - + -
848A VAL 3.3 7.0 - - - +
849A GLY* 4.3 2.2 - - - -
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Residues in contact with VAL 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A ASN* 5.6 0.2 - - + -
729A VAL* 1.3 79.7 - - - +
731A SER* 1.3 72.8 + - - +
846A TYR* 4.1 4.4 - - + +
847A LYS* 3.2 2.9 - - - -
848A VAL* 2.9 39.6 + - + +
850A PHE* 3.8 26.2 - - + -
929A GLU* 3.8 27.6 - - + +
930A VAL* 6.2 0.2 - - + -
933A THR* 3.9 18.6 - - + +
1293A LEU* 3.9 17.9 - - + -
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Residues in contact with SER 731 (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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729A VAL* 4.3 3.7 - - - +
730A VAL* 1.3 81.4 - - - +
732A GLY* 1.3 59.7 + - - +
846A TYR* 3.3 12.2 + - - -
847A LYS* 3.5 27.5 - - - +
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Residues in contact with GLY 732 (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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731A SER* 1.3 78.4 - - - +
733A GLU* 1.3 60.0 + - - +
845A ARG* 3.5 5.0 - - - +
846A TYR* 3.0 51.2 + - - +
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Residues in contact with GLU 733 (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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732A GLY* 1.3 74.1 - - - +
734A LEU* 1.3 64.6 + - - +
843A LEU* 3.6 23.0 - - + +
844A ALA 3.2 8.3 - - - +
845A ARG* 3.4 34.8 + - + +
846A TYR* 3.6 5.4 + - - -
1295A ARG* 2.9 56.9 + - - +
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Residues in contact with LEU 734 (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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733A GLU* 1.3 77.8 - - - +
735A TYR* 1.3 62.5 + - - +
736A ILE* 5.5 1.2 - - - +
842A PHE 4.1 0.2 - - - +
843A LEU* 3.3 3.8 - - - +
844A ALA* 2.8 39.3 + - + +
846A TYR* 4.3 6.5 - - + -
921A PHE* 3.4 32.1 - - + -
922A ILE* 3.8 17.7 - - + +
925A ASN* 3.4 47.6 - - + +
1295A ARG* 3.8 6.7 - - + +
1296A LEU 3.4 27.1 - - - +
1297A ASP* 3.5 12.8 - - - +
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Residues in contact with TYR 735 (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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698A ILE* 4.4 12.6 - - + -
699A GLU* 5.8 4.5 - - - -
734A LEU* 1.3 76.0 - - - +
736A ILE* 1.3 69.9 + - - +
737A GLY* 3.6 21.6 - - - -
841A PRO* 3.5 25.0 - - + +
842A PHE 3.3 17.5 - - - -
843A LEU* 4.2 14.1 - - + -
921A PHE* 4.2 2.1 - - - -
1295A ARG* 3.7 14.8 - - - +
1297A ASP* 3.0 22.2 + - + +
1298A SER* 3.0 28.2 + - - +
1304A LYS* 6.5 0.4 - - - -
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Residues in contact with ILE 736 (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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734A LEU* 5.4 0.9 - - + +
735A TYR* 1.3 81.6 - - - +
737A GLY* 1.3 73.4 + - - +
841A PRO* 3.3 3.8 - - - +
842A PHE* 2.9 40.8 + - + +
918A GLN* 3.2 55.6 - - + +
921A PHE* 3.4 24.0 - - + -
922A ILE* 4.1 7.9 - - + -
1205A LEU* 5.0 8.1 - - + -
1206A PHE* 4.6 9.9 - - + -
1298A SER* 3.6 24.7 - - - +
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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