Contacts of the strand formed by residues 893 - 902 (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 893 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716A LYS 3.3 4.5 - - - -
717A GLY* 3.5 4.3 - - - -
718A ASP* 2.7 48.9 + - - +
719A LEU* 3.9 9.0 - - - +
721A LYS* 4.5 8.3 + - - +
722A GLY* 3.5 14.6 - - - +
725A GLU* 4.5 4.8 + - - -
857A VAL* 2.8 28.0 + - - +
858A ALA* 3.1 7.7 - - + -
859A LEU 3.0 20.6 + - - -
891A ILE* 3.5 3.9 - - - +
892A PRO* 1.3 87.4 - - - +
894A ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 894 (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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714A ILE* 4.7 1.6 - - + +
715A GLU* 3.4 5.1 - - - +
716A LYS* 2.9 44.0 + - + +
719A LEU* 3.9 4.9 - - - +
859A LEU* 3.2 15.3 - - + +
885A MET* 3.7 41.3 - - + -
886A ASP* 4.9 2.9 - - + -
891A ILE* 3.7 44.2 - - + +
893A ASN* 1.3 75.5 - - - +
895A ARG* 1.3 65.6 + - - +
954A HIS* 3.7 31.6 - - + -
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Residues in contact with ARG 895 (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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711A GLU* 4.9 3.2 + - - -
713A LYS* 3.5 29.6 - - + +
714A ILE 3.6 4.3 - - - +
715A GLU* 3.2 41.2 + - + -
719A LEU* 3.2 27.3 - - + +
859A LEU 2.9 8.3 + - - +
860A GLU* 3.2 18.4 + - + +
861A VAL 2.8 25.1 + - - +
862A ASP* 3.7 23.2 + - - -
885A MET* 4.0 4.4 - - - +
894A ILE* 1.3 74.1 - - - +
896A GLY* 1.3 60.1 + - - +
897A THR* 3.7 11.0 - - + +
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Residues in contact with GLY 896 (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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713A LYS* 3.3 4.2 - - - +
714A ILE 3.0 33.1 + - - +
861A VAL 3.0 8.7 - - - -
863A HIS* 4.7 0.2 - - - -
882A LEU* 3.6 9.4 - - - +
885A MET* 3.6 25.0 - - - -
894A ILE* 4.9 0.2 - - - +
895A ARG* 1.3 76.2 - - - +
897A THR* 1.3 63.4 + - - +
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Residues in contact with THR 897 (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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711A GLU* 3.6 29.2 + - - +
712A LEU 3.0 9.2 - - - -
713A LYS* 4.0 7.9 - - + -
861A VAL 2.8 5.9 + - - -
862A ASP* 2.6 35.1 + - - +
863A HIS* 2.7 37.2 + - - -
864A TYR* 5.9 0.3 - - - -
882A LEU* 4.1 3.8 - - - -
895A ARG* 3.7 28.7 - - - +
896A GLY* 1.3 80.2 - - - +
898A GLY* 1.3 55.4 + - - +
899A ARG* 6.0 0.7 - - - +
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Residues in contact with GLY 898 (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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710A SER 4.4 1.0 - - - +
711A GLU* 3.5 6.6 - - - +
712A LEU* 2.8 41.9 + - - +
863A HIS 3.3 6.3 - - - -
878A MET* 3.8 27.1 - - - -
882A LEU* 4.9 0.7 - - - -
897A THR* 1.3 76.5 - - - +
899A ARG* 1.3 64.8 + - - +
900A LEU* 5.4 0.4 - - - -
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Residues in contact with ARG 899 (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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705A ASN* 4.6 4.8 + - - -
707A PHE* 3.7 44.5 - - + +
708A TYR 4.7 0.4 + - - -
709A GLY 2.6 31.1 + - - -
710A SER* 3.4 12.7 - - - +
711A GLU* 3.9 29.7 + - + +
863A HIS 3.0 5.7 + - - -
864A TYR* 3.5 34.7 - - + +
865A SER* 3.1 27.0 + - - -
878A MET* 3.6 2.4 - - - +
897A THR* 6.0 0.4 - - - +
898A GLY* 1.3 80.4 - - - +
900A LEU* 1.3 66.0 + - - +
901A CYS 3.7 0.6 + - - -
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Residues in contact with LEU 900 (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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707A PHE* 3.1 9.6 - - - +
708A TYR* 3.0 60.5 + - + +
710A SER 5.8 2.2 + - - +
712A LEU* 5.2 2.5 - - + -
865A SER* 3.8 14.4 - - - +
867A ALA* 4.6 4.9 - - + -
871A ARG* 5.9 2.9 - - + -
874A SER* 3.5 26.2 - - - +
875A HIS* 3.7 41.5 - - + +
878A MET* 3.6 23.1 - - + -
898A GLY 5.8 0.2 - - - +
899A ARG* 1.3 77.6 - - - +
901A CYS* 1.3 61.0 + - - +
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Residues in contact with CYS 901 (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* 3.5 34.3 - - - -
701A ALA* 3.6 23.6 - - + -
702A ILE* 4.8 0.2 - - - -
706A SER 3.6 4.3 - - - -
707A PHE* 4.1 15.7 - - - -
708A TYR* 4.5 0.2 - - - -
864A TYR* 4.2 12.1 - - - -
865A SER 2.7 23.6 + - - +
866A ASN* 4.2 4.5 - - - -
867A ALA* 2.9 31.1 + - - +
868A GLY 3.7 0.3 + - - -
899A ARG 4.6 0.2 - - - -
900A LEU* 1.3 71.7 - - - +
902A LYS* 1.3 61.7 + - - +
903A THR* 3.5 8.7 + - + +
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Residues in contact with LYS 902 (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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695A ILE* 4.0 3.8 - - - +
706A SER* 2.7 50.0 + - - +
707A PHE 4.1 10.5 - - - +
708A TYR* 3.5 48.9 - - + +
869A ASN* 5.6 0.7 - - - +
900A LEU 3.5 2.6 + - - -
901A CYS* 1.3 70.0 - - - +
903A THR* 1.3 67.8 + - - +
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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