Contacts of the strand formed by residues 842 - 850 (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 PHE 842 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698A ILE* 4.2 0.7 - - - -
734A LEU 4.1 0.2 - - - +
735A TYR* 3.3 9.1 - - - -
736A ILE* 2.9 53.7 + - + +
840A HIS* 3.5 17.4 + - + -
841A PRO* 1.3 82.2 - - - +
843A LEU* 1.3 59.5 - - - +
863A HIS* 3.9 26.9 - + + -
864A TYR 3.3 5.6 - - - -
865A SER* 3.4 15.5 - - - -
877A ILE* 4.7 8.5 - - + -
878A MET* 3.6 39.5 - - + -
881A ALA* 3.9 21.1 - - + -
915A GLY 4.9 0.2 - - - -
918A GLN* 3.6 32.5 - - + -
919A ALA 5.1 0.2 - - - -
922A ILE* 4.3 7.0 - - + -
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Residues in contact with LEU 843 (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* 3.8 35.8 - - + +
699A GLU* 4.6 20.4 - - + +
702A ILE* 4.9 3.4 - - + -
733A GLU* 3.6 36.6 - - + +
734A LEU 3.3 18.2 - - - +
735A TYR* 4.2 15.5 - - + -
842A PHE* 1.3 74.1 - - - +
844A ALA* 1.3 64.2 + - - +
845A ARG* 4.4 16.8 - - - +
863A HIS* 3.7 0.9 - - - +
864A TYR* 2.9 40.1 + - + +
1295A ARG* 4.3 1.3 - - - +
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Residues in contact with ALA 844 (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 3.9 0.2 - - - +
733A GLU* 3.2 7.0 - - - +
734A LEU* 2.8 44.1 + - + +
843A LEU* 1.3 76.3 - - - +
845A ARG* 1.3 62.2 + - - +
846A TYR* 4.0 2.7 + - + -
861A VAL* 4.3 6.5 - - + -
862A ASP 3.4 8.5 - - - +
863A HIS* 4.7 1.8 - - + -
864A TYR* 5.2 0.2 - - - -
922A ILE* 3.4 44.9 - - + -
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Residues in contact with ARG 845 (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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699A GLU* 5.4 6.1 - - - +
702A ILE* 3.8 35.0 - - - +
732A GLY 3.5 7.9 - - - +
733A GLU* 3.4 28.2 + - + +
843A LEU* 4.4 10.7 - - + +
844A ALA* 1.3 76.2 - - - +
846A TYR* 1.3 59.4 + - - +
860A GLU 3.9 0.5 - - - +
861A VAL* 3.4 2.2 - - - +
862A ASP* 2.9 47.5 + - + +
864A TYR* 4.2 21.7 + - - -
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Residues in contact with TYR 846 (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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730A VAL* 4.5 6.5 - - + -
731A SER* 3.3 8.2 + - - -
732A GLY* 3.0 68.7 + - - +
733A GLU 3.6 12.3 + - - -
734A LEU* 4.3 4.9 - - + -
844A ALA 4.2 6.5 - - - -
845A ARG* 1.3 77.0 - - - +
847A LYS* 1.3 69.0 + - - +
848A VAL* 4.9 0.9 - - + -
859A LEU* 5.0 0.2 - - + -
860A GLU 3.1 10.5 - - - +
861A VAL* 4.0 18.2 - - + -
922A ILE* 5.0 7.6 - - + -
925A ASN* 3.3 20.1 + - - -
926A TRP* 3.8 29.6 - + + -
929A GLU* 2.6 38.8 + - - -
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Residues in contact with LYS 847 (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* 3.5 46.3 - - + +
729A VAL* 4.2 15.5 - - + -
730A VAL 3.2 7.0 - - - -
731A SER* 3.5 17.5 - - - +
846A TYR* 1.3 78.7 - - - +
848A VAL* 1.3 60.9 + - - +
859A LEU* 3.4 3.5 - - - +
860A GLU* 2.8 50.9 + - + +
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Residues in contact with VAL 848 (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* 3.8 4.3 - - - -
729A VAL* 3.3 4.2 - - - -
730A VAL* 2.9 43.3 + - + +
846A TYR* 5.0 1.3 - - + -
847A LYS* 1.3 75.6 - - - +
849A GLY* 1.3 70.3 + - - +
850A PHE* 3.4 19.6 - - + -
856A ILE* 3.9 18.6 - - + -
858A ALA 3.3 10.3 - - - +
859A LEU* 3.8 17.0 - - + -
926A TRP* 4.2 27.1 - - + +
929A GLU* 6.3 0.2 - - + -
930A VAL* 4.1 10.8 - - + -
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Residues in contact with GLY 849 (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* 3.5 14.8 - - - -
726A ALA* 3.7 15.0 - - - -
728A ASN 3.5 9.2 - - - -
729A VAL* 4.3 0.2 - - - -
848A VAL* 1.3 72.3 - - - +
850A PHE* 1.3 57.5 + - - +
856A ILE* 3.6 4.0 - - - +
857A VAL 2.7 29.9 + - - -
858A ALA 2.6 21.3 + - - +
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Residues in contact with PHE 850 (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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726A ALA* 3.7 1.2 - - - +
727A ASP 2.9 5.1 + - - -
728A ASN* 2.9 57.0 + - + -
730A VAL* 3.8 21.8 - - + -
848A VAL* 3.4 23.3 - - + -
849A GLY* 1.3 74.8 - - - +
851A MET* 1.3 77.9 + - - +
855A THR 3.0 22.2 - - - +
856A ILE* 4.0 4.3 - - + -
857A VAL* 4.1 2.7 - - - +
930A VAL* 3.5 43.5 - - + -
933A THR* 3.8 22.7 - - + -
934A CYS* 3.7 17.5 - - - -
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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